Calcium in PDB 6x6m: Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain
Protein crystallography data
The structure of Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain, PDB code: 6x6m
was solved by
S.Guo,
P.L.Davies,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
57.39 /
1.90
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
50.24,
60.868,
63.609,
66.4,
72.74,
68.35
|
|
R / Rfree (%)
|
19.6 /
21.9
|
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
16;
Binding sites:
The binding sites of Calcium atom in the Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain
(pdb code 6x6m). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the
Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain, PDB code: 6x6m:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 16 in 6x6m
Go back to
Calcium Binding Sites List in 6x6m
Calcium binding site 1 out
of 16 in the Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca601
b:40.9
occ:1.00
|
O
|
A:GLU79
|
2.2
|
42.5
|
1.0
|
|
OD1
|
A:ASP77
|
2.3
|
36.0
|
1.0
|
|
O
|
A:HOH2271
|
2.4
|
46.7
|
1.0
|
|
O
|
A:HOH2272
|
2.4
|
46.1
|
1.0
|
|
O
|
A:HOH2273
|
2.5
|
34.6
|
1.0
|
|
OD2
|
A:ASP77
|
2.6
|
39.1
|
1.0
|
|
O
|
A:HOH2165
|
2.6
|
36.3
|
1.0
|
|
CG
|
A:ASP77
|
2.8
|
27.8
|
1.0
|
|
C
|
A:GLU79
|
3.4
|
32.3
|
1.0
|
|
HA
|
A:PHE80
|
3.6
|
39.6
|
1.0
|
|
H
|
A:GLU79
|
3.8
|
41.5
|
1.0
|
|
HB3
|
A:PHE80
|
3.8
|
41.5
|
1.0
|
|
HB3
|
A:GLU79
|
4.1
|
46.1
|
1.0
|
|
O
|
A:HOH2101
|
4.2
|
41.0
|
1.0
|
|
CA
|
A:PHE80
|
4.2
|
33.0
|
1.0
|
|
CB
|
A:ASP77
|
4.3
|
26.1
|
1.0
|
|
N
|
A:PHE80
|
4.3
|
32.1
|
1.0
|
|
CA
|
A:GLU79
|
4.4
|
37.5
|
1.0
|
|
N
|
A:GLU79
|
4.4
|
34.5
|
1.0
|
|
CB
|
A:PHE80
|
4.5
|
34.6
|
1.0
|
|
O
|
A:HOH2375
|
4.6
|
54.5
|
1.0
|
|
H
|
A:ASN50
|
4.6
|
41.4
|
1.0
|
|
HB2
|
A:ASP77
|
4.7
|
31.4
|
1.0
|
|
HB3
|
A:ASP77
|
4.7
|
31.4
|
1.0
|
|
CB
|
A:GLU79
|
4.7
|
38.5
|
1.0
|
|
HA
|
A:ASP77
|
4.8
|
36.2
|
1.0
|
|
HB2
|
A:PHE80
|
4.8
|
41.5
|
1.0
|
|
O
|
A:THR48
|
4.8
|
32.7
|
1.0
|
|
O
|
A:HOH2156
|
4.8
|
37.0
|
1.0
|
|
HA
|
A:ILE49
|
4.8
|
41.5
|
1.0
|
|
HG2
|
A:GLU79
|
4.9
|
55.5
|
1.0
|
|
CA
|
A:ASP77
|
5.0
|
30.2
|
1.0
|
|
Calcium binding site 2 out
of 16 in 6x6m
Go back to
Calcium Binding Sites List in 6x6m
Calcium binding site 2 out
of 16 in the Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca602
b:35.2
occ:1.00
|
O
|
A:HOH2102
|
2.3
|
25.1
|
1.0
|
|
O
|
A:THR101
|
2.3
|
32.9
|
1.0
|
|
O
|
A:HOH2151
|
2.5
|
39.4
|
1.0
|
|
OD2
|
A:ASP17
|
2.5
|
33.3
|
1.0
|
|
O
|
A:HOH2154
|
2.5
|
29.6
|
1.0
|
|
O
|
A:HOH2208
|
2.5
|
30.4
|
1.0
|
|
OD1
|
A:ASP17
|
2.5
|
29.9
|
1.0
|
|
CG
|
A:ASP17
|
2.8
|
35.2
|
1.0
|
|
HA
|
A:ALA12
|
3.5
|
31.9
|
1.0
|
|
C
|
A:THR101
|
3.5
|
31.1
|
1.0
|
|
HG
|
A:SER100
|
3.6
|
34.1
|
1.0
|
|
H
|
A:THR101
|
3.7
|
37.3
|
1.0
|
|
HA
|
A:HIS102
|
3.8
|
37.1
|
1.0
|
|
HG12
|
A:ILE13
|
3.9
|
39.2
|
1.0
|
|
HG1
|
A:THR101
|
3.9
|
54.2
|
1.0
|
|
HB3
|
A:HIS102
|
3.9
|
30.2
|
1.0
|
|
H
|
A:ILE13
|
4.0
|
38.8
|
1.0
|
|
O
|
A:HOH2209
|
4.2
|
49.0
|
1.0
|
|
N
|
A:THR101
|
4.2
|
31.1
|
1.0
|
|
CA
|
A:CA610
|
4.2
|
73.7
|
1.0
|
|
CB
|
A:ASP17
|
4.3
|
29.0
|
1.0
|
|
O
|
A:HOH2097
|
4.3
|
34.5
|
1.0
|
|
OG
|
A:SER100
|
4.4
|
28.4
|
1.0
|
|
N
|
A:HIS102
|
4.4
|
30.0
|
1.0
|
|
CA
|
A:HIS102
|
4.4
|
30.9
|
1.0
|
|
CA
|
A:ALA12
|
4.5
|
26.6
|
1.0
|
|
CA
|
A:THR101
|
4.5
|
30.9
|
1.0
|
|
HB2
|
A:ASP17
|
4.5
|
34.8
|
1.0
|
|
OG1
|
A:THR101
|
4.5
|
45.1
|
1.0
|
|
CB
|
A:HIS102
|
4.6
|
25.2
|
1.0
|
|
O
|
A:HOH2300
|
4.7
|
50.4
|
1.0
|
|
N
|
A:ILE13
|
4.7
|
32.4
|
1.0
|
|
HB3
|
A:ASP17
|
4.7
|
34.8
|
1.0
|
|
HA
|
A:SER100
|
4.7
|
35.4
|
1.0
|
|
CG1
|
A:ILE13
|
4.8
|
32.7
|
1.0
|
|
O
|
A:ASN11
|
4.9
|
33.6
|
1.0
|
|
HA
|
A:ASP17
|
4.9
|
31.3
|
1.0
|
|
HB2
|
A:HIS102
|
5.0
|
30.2
|
1.0
|
|
Calcium binding site 3 out
of 16 in 6x6m
Go back to
Calcium Binding Sites List in 6x6m
Calcium binding site 3 out
of 16 in the Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca603
b:19.1
occ:1.00
|
OE2
|
A:GLU116
|
2.4
|
21.8
|
1.0
|
|
O
|
A:ARG161
|
2.4
|
18.0
|
1.0
|
|
OD1
|
A:ASP191
|
2.4
|
17.5
|
1.0
|
|
OD2
|
A:ASP492
|
2.4
|
25.6
|
1.0
|
|
OD1
|
A:ASP426
|
2.5
|
20.0
|
1.0
|
|
OD2
|
A:ASP426
|
2.6
|
20.7
|
1.0
|
|
OE1
|
A:GLU116
|
2.6
|
18.7
|
1.0
|
|
ND1
|
A:HIS163
|
2.6
|
20.9
|
1.0
|
|
CD
|
A:GLU116
|
2.8
|
21.9
|
1.0
|
|
CG
|
A:ASP426
|
2.9
|
22.0
|
1.0
|
|
HE1
|
A:HIS163
|
3.4
|
31.3
|
1.0
|
|
H
|
A:HIS163
|
3.4
|
21.2
|
1.0
|
|
CE1
|
A:HIS163
|
3.4
|
26.1
|
1.0
|
|
HA
|
A:ASP191
|
3.4
|
26.3
|
1.0
|
|
H
|
A:ARG161
|
3.5
|
25.2
|
1.0
|
|
CG
|
A:ASP492
|
3.5
|
25.3
|
1.0
|
|
CG
|
A:ASP191
|
3.5
|
19.4
|
1.0
|
|
C
|
A:ARG161
|
3.6
|
21.3
|
1.0
|
|
HB2
|
A:HIS163
|
3.6
|
23.3
|
1.0
|
|
H
|
A:SER192
|
3.6
|
28.6
|
1.0
|
|
CG
|
A:HIS163
|
3.8
|
20.8
|
1.0
|
|
CA
|
A:CA604
|
3.9
|
21.0
|
1.0
|
|
OD1
|
A:ASP492
|
3.9
|
20.5
|
1.0
|
|
HG13
|
A:VAL160
|
4.0
|
28.6
|
1.0
|
|
HG
|
A:SER192
|
4.0
|
31.2
|
1.0
|
|
N
|
A:HIS163
|
4.1
|
17.7
|
1.0
|
|
CB
|
A:HIS163
|
4.1
|
19.4
|
1.0
|
|
HA
|
A:ASP162
|
4.2
|
29.3
|
1.0
|
|
HB2
|
A:ARG161
|
4.2
|
27.8
|
1.0
|
|
N
|
A:ARG161
|
4.2
|
21.0
|
1.0
|
|
O
|
A:HOH2028
|
4.2
|
21.4
|
1.0
|
|
CA
|
A:ASP191
|
4.2
|
21.9
|
1.0
|
|
CB
|
A:ASP191
|
4.3
|
21.2
|
1.0
|
|
CG
|
A:GLU116
|
4.3
|
18.3
|
1.0
|
|
HB2
|
A:ASP191
|
4.3
|
25.5
|
1.0
|
|
N
|
A:SER192
|
4.4
|
23.9
|
1.0
|
|
CA
|
A:ARG161
|
4.4
|
24.3
|
1.0
|
|
CB
|
A:ASP426
|
4.4
|
28.8
|
1.0
|
|
OD2
|
A:ASP191
|
4.4
|
21.5
|
1.0
|
|
N
|
A:ASP162
|
4.6
|
21.6
|
1.0
|
|
HG2
|
A:GLU116
|
4.6
|
21.9
|
1.0
|
|
NE2
|
A:HIS163
|
4.6
|
18.9
|
1.0
|
|
CA
|
A:ASP162
|
4.7
|
24.4
|
1.0
|
|
HG12
|
A:VAL160
|
4.7
|
28.6
|
1.0
|
|
HG3
|
A:GLU116
|
4.7
|
21.9
|
1.0
|
|
CA
|
A:HIS163
|
4.8
|
20.3
|
1.0
|
|
CG1
|
A:VAL160
|
4.8
|
23.9
|
1.0
|
|
HB3
|
A:ASP492
|
4.8
|
27.0
|
1.0
|
|
HB3
|
A:ASP426
|
4.8
|
34.5
|
1.0
|
|
CB
|
A:ARG161
|
4.8
|
23.2
|
1.0
|
|
OG
|
A:SER192
|
4.8
|
26.0
|
1.0
|
|
CD2
|
A:HIS163
|
4.8
|
20.8
|
1.0
|
|
CB
|
A:ASP492
|
4.8
|
22.5
|
1.0
|
|
HB2
|
A:ASP426
|
4.8
|
34.5
|
1.0
|
|
C
|
A:ASP162
|
4.9
|
21.2
|
1.0
|
|
O
|
A:SER192
|
4.9
|
18.7
|
1.0
|
|
C
|
A:ASP191
|
4.9
|
25.2
|
1.0
|
|
HA
|
A:ASP426
|
4.9
|
27.2
|
1.0
|
|
HB3
|
A:GLU116
|
4.9
|
28.0
|
1.0
|
|
HB3
|
A:HIS163
|
5.0
|
23.3
|
1.0
|
|
Calcium binding site 4 out
of 16 in 6x6m
Go back to
Calcium Binding Sites List in 6x6m
Calcium binding site 4 out
of 16 in the Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca604
b:21.0
occ:1.00
|
OD1
|
A:ASP492
|
2.3
|
20.5
|
1.0
|
|
OD2
|
A:ASP426
|
2.3
|
20.7
|
1.0
|
|
O
|
A:SER192
|
2.3
|
18.7
|
1.0
|
|
OD1
|
A:ASP191
|
2.4
|
17.5
|
1.0
|
|
OG
|
A:SER494
|
2.5
|
22.7
|
1.0
|
|
OD2
|
A:ASP490
|
2.5
|
23.2
|
1.0
|
|
OD2
|
A:ASP191
|
2.6
|
21.5
|
1.0
|
|
CG
|
A:ASP191
|
2.8
|
19.4
|
1.0
|
|
HB2
|
A:SER494
|
3.2
|
30.8
|
1.0
|
|
CG
|
A:ASP490
|
3.2
|
23.3
|
1.0
|
|
OD1
|
A:ASP490
|
3.2
|
21.0
|
1.0
|
|
CG
|
A:ASP492
|
3.2
|
25.3
|
1.0
|
|
CB
|
A:SER494
|
3.4
|
25.7
|
1.0
|
|
CG
|
A:ASP426
|
3.5
|
22.0
|
1.0
|
|
OD2
|
A:ASP492
|
3.5
|
25.6
|
1.0
|
|
C
|
A:SER192
|
3.5
|
22.6
|
1.0
|
|
H
|
A:SER494
|
3.6
|
22.7
|
1.0
|
|
H
|
A:SER192
|
3.7
|
28.6
|
1.0
|
|
HA
|
A:ALA193
|
3.7
|
21.9
|
1.0
|
|
HB2
|
A:ASP426
|
3.8
|
34.5
|
1.0
|
|
CA
|
A:CA603
|
3.9
|
19.1
|
1.0
|
|
HB3
|
A:SER494
|
4.0
|
30.8
|
1.0
|
|
N
|
A:SER192
|
4.1
|
23.9
|
1.0
|
|
H
|
A:ASP492
|
4.1
|
24.3
|
1.0
|
|
O
|
A:HOH2280
|
4.1
|
34.5
|
1.0
|
|
CB
|
A:ASP426
|
4.2
|
28.8
|
1.0
|
|
CB
|
A:ASP191
|
4.3
|
21.2
|
1.0
|
|
OE2
|
A:GLU116
|
4.3
|
21.8
|
1.0
|
|
N
|
A:SER494
|
4.3
|
18.9
|
1.0
|
|
HG
|
A:SER192
|
4.4
|
31.2
|
1.0
|
|
OD1
|
A:ASP426
|
4.4
|
20.0
|
1.0
|
|
CA
|
A:SER192
|
4.4
|
25.0
|
1.0
|
|
N
|
A:ALA193
|
4.5
|
19.9
|
1.0
|
|
CA
|
A:SER494
|
4.5
|
22.3
|
1.0
|
|
CA
|
A:ALA193
|
4.5
|
18.3
|
1.0
|
|
HB3
|
A:ASP426
|
4.5
|
34.5
|
1.0
|
|
HB2
|
A:ALA193
|
4.6
|
22.9
|
1.0
|
|
HB3
|
A:ASP191
|
4.6
|
25.5
|
1.0
|
|
CB
|
A:ASP490
|
4.7
|
25.3
|
1.0
|
|
CB
|
A:ASP492
|
4.7
|
22.5
|
1.0
|
|
OG
|
A:SER192
|
4.7
|
26.0
|
1.0
|
|
HB2
|
A:HIS163
|
4.7
|
23.3
|
1.0
|
|
C
|
A:ASP191
|
4.8
|
25.2
|
1.0
|
|
HA
|
A:ASP191
|
4.8
|
26.3
|
1.0
|
|
HB2
|
A:ASP191
|
4.8
|
25.5
|
1.0
|
|
HB2
|
A:ASP490
|
4.8
|
30.4
|
1.0
|
|
HD3
|
A:PRO194
|
4.8
|
31.3
|
1.0
|
|
N
|
A:ASP492
|
4.9
|
20.2
|
1.0
|
|
O
|
A:HOH2210
|
4.9
|
22.5
|
0.5
|
|
CA
|
A:ASP191
|
4.9
|
21.9
|
1.0
|
|
C
|
A:ASP492
|
4.9
|
18.4
|
1.0
|
|
HA
|
A:SER494
|
5.0
|
26.8
|
1.0
|
|
HB3
|
A:ASP490
|
5.0
|
30.4
|
1.0
|
|
Calcium binding site 5 out
of 16 in 6x6m
Go back to
Calcium Binding Sites List in 6x6m
Calcium binding site 5 out
of 16 in the Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca605
b:20.0
occ:1.00
|
OD1
|
A:ASP165
|
2.3
|
22.2
|
1.0
|
|
O
|
A:VAL167
|
2.4
|
23.7
|
1.0
|
|
O
|
A:ASP162
|
2.4
|
21.3
|
1.0
|
|
O
|
A:HOH2048
|
2.4
|
19.1
|
1.0
|
|
O
|
A:HOH2072
|
2.4
|
21.9
|
1.0
|
|
OD1
|
A:ASP169
|
2.5
|
23.6
|
1.0
|
|
OD2
|
A:ASP169
|
2.7
|
24.6
|
1.0
|
|
CG
|
A:ASP169
|
2.9
|
20.4
|
1.0
|
|
CG
|
A:ASP165
|
3.3
|
25.8
|
1.0
|
|
HA
|
A:HIS163
|
3.4
|
24.4
|
1.0
|
|
H
|
A:VAL167
|
3.5
|
31.6
|
1.0
|
|
HB
|
A:VAL167
|
3.5
|
40.8
|
1.0
|
|
C
|
A:ASP162
|
3.5
|
21.2
|
1.0
|
|
C
|
A:VAL167
|
3.5
|
24.6
|
1.0
|
|
OD2
|
A:ASP165
|
3.7
|
26.1
|
1.0
|
|
H
|
A:ASP165
|
3.7
|
31.5
|
1.0
|
|
HB3
|
A:ARG161
|
4.1
|
27.8
|
1.0
|
|
N
|
A:VAL167
|
4.1
|
26.3
|
1.0
|
|
CA
|
A:HIS163
|
4.1
|
20.3
|
1.0
|
|
CA
|
A:VAL167
|
4.2
|
27.1
|
1.0
|
|
HH21
|
A:ARG161
|
4.2
|
24.3
|
1.0
|
|
HB3
|
A:ASP162
|
4.2
|
24.3
|
1.0
|
|
CB
|
A:VAL167
|
4.3
|
34.0
|
1.0
|
|
N
|
A:HIS163
|
4.3
|
17.7
|
1.0
|
|
HE
|
A:ARG161
|
4.3
|
24.8
|
1.0
|
|
O
|
A:ASP165
|
4.4
|
19.9
|
1.0
|
|
CB
|
A:ASP169
|
4.4
|
23.6
|
1.0
|
|
C
|
A:SER168
|
4.4
|
18.8
|
1.0
|
|
N
|
A:ASP165
|
4.4
|
26.2
|
1.0
|
|
O
|
A:SER168
|
4.4
|
19.3
|
1.0
|
|
H
|
A:ASP162
|
4.5
|
26.0
|
1.0
|
|
N
|
A:ASP169
|
4.5
|
18.2
|
1.0
|
|
C
|
A:HIS163
|
4.5
|
21.9
|
1.0
|
|
C
|
A:ASP165
|
4.6
|
19.1
|
1.0
|
|
CA
|
A:ASP162
|
4.6
|
24.4
|
1.0
|
|
CB
|
A:ASP165
|
4.6
|
26.5
|
1.0
|
|
HG12
|
A:VAL167
|
4.6
|
39.8
|
1.0
|
|
N
|
A:SER168
|
4.6
|
24.9
|
1.0
|
|
N
|
A:ASP162
|
4.6
|
21.6
|
1.0
|
|
O
|
A:HOH2027
|
4.7
|
47.9
|
1.0
|
|
HA
|
A:SER168
|
4.7
|
22.7
|
1.0
|
|
HA
|
A:ASP169
|
4.7
|
21.7
|
1.0
|
|
CA
|
A:ASP165
|
4.7
|
33.2
|
1.0
|
|
H
|
A:ASP169
|
4.8
|
21.8
|
1.0
|
|
NH2
|
A:ARG161
|
4.8
|
20.2
|
1.0
|
|
H
|
A:GLY164
|
4.8
|
32.8
|
1.0
|
|
HB2
|
A:ASP169
|
4.8
|
28.3
|
1.0
|
|
N
|
A:GLY164
|
4.8
|
27.3
|
1.0
|
|
CA
|
A:ASP169
|
4.8
|
18.1
|
1.0
|
|
CA
|
A:SER168
|
4.8
|
18.9
|
1.0
|
|
CB
|
A:ASP162
|
4.8
|
20.2
|
1.0
|
|
O
|
A:HOH2258
|
4.8
|
19.0
|
1.0
|
|
NE
|
A:ARG161
|
4.9
|
20.6
|
1.0
|
|
HB3
|
A:ASP169
|
4.9
|
28.3
|
1.0
|
|
HB3
|
A:ASP165
|
4.9
|
31.8
|
1.0
|
|
Calcium binding site 6 out
of 16 in 6x6m
Go back to
Calcium Binding Sites List in 6x6m
Calcium binding site 6 out
of 16 in the Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca606
b:21.4
occ:1.00
|
O
|
A:ILE412
|
2.3
|
24.0
|
1.0
|
|
O
|
A:VAL197
|
2.3
|
25.2
|
1.0
|
|
OD1
|
A:ASP421
|
2.4
|
21.1
|
1.0
|
|
O
|
A:HOH2004
|
2.4
|
27.9
|
1.0
|
|
OD1
|
A:ASP199
|
2.5
|
30.6
|
1.0
|
|
OH
|
A:TYR486
|
2.5
|
23.2
|
1.0
|
|
OD2
|
A:ASP199
|
2.5
|
25.4
|
1.0
|
|
CG
|
A:ASP199
|
2.8
|
27.7
|
1.0
|
|
H
|
A:VAL197
|
3.3
|
23.8
|
1.0
|
|
HB
|
A:ILE412
|
3.3
|
28.4
|
1.0
|
|
CG
|
A:ASP421
|
3.3
|
23.2
|
1.0
|
|
C
|
A:ILE412
|
3.5
|
20.0
|
1.0
|
|
C
|
A:VAL197
|
3.5
|
24.3
|
1.0
|
|
OD2
|
A:ASP421
|
3.6
|
19.6
|
1.0
|
|
CZ
|
A:TYR486
|
3.7
|
26.9
|
1.0
|
|
HB
|
A:VAL197
|
3.7
|
25.4
|
1.0
|
|
HE2
|
A:TYR486
|
3.7
|
31.1
|
1.0
|
|
HA
|
A:ILE412
|
3.9
|
26.5
|
1.0
|
|
N
|
A:VAL197
|
3.9
|
19.8
|
1.0
|
|
H
|
A:ASP421
|
4.0
|
26.3
|
1.0
|
|
CA
|
A:ILE412
|
4.1
|
22.1
|
1.0
|
|
CB
|
A:ILE412
|
4.1
|
23.7
|
1.0
|
|
CE2
|
A:TYR486
|
4.1
|
25.9
|
1.0
|
|
CA
|
A:VAL197
|
4.1
|
20.4
|
1.0
|
|
HD22
|
A:ASN416
|
4.2
|
30.3
|
1.0
|
|
HA
|
A:PHE413
|
4.3
|
38.4
|
1.0
|
|
CB
|
A:ASP199
|
4.3
|
28.1
|
1.0
|
|
HD13
|
A:ILE412
|
4.3
|
22.6
|
1.0
|
|
CB
|
A:VAL197
|
4.4
|
21.1
|
1.0
|
|
C
|
A:ASP198
|
4.4
|
27.4
|
1.0
|
|
HB3
|
A:ALA498
|
4.4
|
29.9
|
1.0
|
|
O
|
A:ASP198
|
4.5
|
24.4
|
1.0
|
|
O
|
A:ASP414
|
4.5
|
24.6
|
1.0
|
|
N
|
A:ASP421
|
4.6
|
21.9
|
1.0
|
|
HG22
|
A:ILE412
|
4.6
|
30.4
|
1.0
|
|
CB
|
A:ASP421
|
4.6
|
29.5
|
1.0
|
|
N
|
A:ASP198
|
4.6
|
21.8
|
1.0
|
|
N
|
A:PHE413
|
4.6
|
28.7
|
1.0
|
|
N
|
A:ASP199
|
4.6
|
23.2
|
1.0
|
|
HG12
|
A:VAL197
|
4.7
|
33.6
|
1.0
|
|
HA
|
A:ASP198
|
4.7
|
25.3
|
1.0
|
|
HB2
|
A:ASP199
|
4.7
|
33.8
|
1.0
|
|
HA
|
A:ASP199
|
4.8
|
32.0
|
1.0
|
|
HB2
|
A:ASP421
|
4.8
|
35.4
|
1.0
|
|
HB1
|
A:ALA196
|
4.8
|
21.8
|
1.0
|
|
HB3
|
A:ASP199
|
4.8
|
33.8
|
1.0
|
|
HB1
|
A:ALA498
|
4.8
|
29.9
|
1.0
|
|
CE1
|
A:TYR486
|
4.8
|
23.4
|
1.0
|
|
CA
|
A:ASP199
|
4.8
|
26.7
|
1.0
|
|
HA
|
A:ALA196
|
4.8
|
29.9
|
1.0
|
|
CA
|
A:PHE413
|
4.8
|
32.0
|
1.0
|
|
CA
|
A:ASP198
|
4.8
|
21.1
|
1.0
|
|
HA
|
A:ASP421
|
4.9
|
28.1
|
1.0
|
|
O
|
A:GLY419
|
4.9
|
29.6
|
1.0
|
|
HE1
|
A:TYR486
|
4.9
|
28.1
|
1.0
|
|
CG2
|
A:ILE412
|
4.9
|
25.4
|
1.0
|
|
O
|
A:HOH2084
|
4.9
|
25.0
|
1.0
|
|
H
|
A:ASP199
|
4.9
|
27.9
|
1.0
|
|
CA
|
A:ASP421
|
5.0
|
23.4
|
1.0
|
|
HA
|
A:ALA420
|
5.0
|
29.6
|
1.0
|
|
ND2
|
A:ASN416
|
5.0
|
25.3
|
1.0
|
|
CB
|
A:ALA498
|
5.0
|
24.9
|
1.0
|
|
Calcium binding site 7 out
of 16 in 6x6m
Go back to
Calcium Binding Sites List in 6x6m
Calcium binding site 7 out
of 16 in the Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca607
b:24.8
occ:1.00
|
OD1
|
A:ASN290
|
2.3
|
22.5
|
1.0
|
|
OXT
|
B:ASP519
|
2.4
|
23.4
|
1.0
|
|
OE2
|
A:GLU330
|
2.4
|
23.6
|
1.0
|
|
OD2
|
A:ASP342
|
2.5
|
28.0
|
1.0
|
|
O
|
B:ASP519
|
2.5
|
24.4
|
1.0
|
|
O
|
A:TYR291
|
2.5
|
25.4
|
1.0
|
|
OE1
|
A:GLU385
|
2.6
|
23.6
|
1.0
|
|
OE2
|
A:GLU385
|
2.6
|
27.9
|
1.0
|
|
C
|
B:ASP519
|
2.8
|
27.1
|
1.0
|
|
CD
|
A:GLU385
|
2.9
|
25.9
|
1.0
|
|
HG3
|
A:GLU330
|
3.1
|
23.8
|
1.0
|
|
CD
|
A:GLU330
|
3.3
|
19.5
|
1.0
|
|
HG
|
A:SER260
|
3.4
|
27.1
|
1.0
|
|
CG
|
A:ASN290
|
3.4
|
20.3
|
1.0
|
|
CG
|
A:ASP342
|
3.4
|
25.2
|
1.0
|
|
HD21
|
A:ASN290
|
3.5
|
24.5
|
1.0
|
|
HA
|
A:PRO292
|
3.5
|
34.0
|
1.0
|
|
C
|
A:TYR291
|
3.6
|
25.6
|
1.0
|
|
HD21
|
A:ASN333
|
3.7
|
33.1
|
1.0
|
|
OD1
|
A:ASP342
|
3.7
|
24.0
|
1.0
|
|
CG
|
A:GLU330
|
3.7
|
19.8
|
1.0
|
|
CA
|
A:CA608
|
3.8
|
27.5
|
1.0
|
|
ND2
|
A:ASN290
|
3.8
|
20.4
|
1.0
|
|
H
|
A:VAL293
|
4.0
|
34.1
|
1.0
|
|
OG
|
A:SER260
|
4.1
|
22.6
|
1.0
|
|
O
|
A:HOH2081
|
4.1
|
25.9
|
1.0
|
|
HG2
|
A:GLU330
|
4.1
|
23.8
|
1.0
|
|
HG23
|
A:VAL293
|
4.2
|
29.3
|
1.0
|
|
H
|
A:TYR291
|
4.2
|
26.9
|
1.0
|
|
CA
|
A:PRO292
|
4.2
|
28.3
|
1.0
|
|
N
|
A:PRO292
|
4.3
|
23.4
|
1.0
|
|
CA
|
B:ASP519
|
4.3
|
24.8
|
1.0
|
|
N
|
A:TYR291
|
4.3
|
22.4
|
1.0
|
|
OE1
|
A:GLU330
|
4.3
|
19.8
|
1.0
|
|
HA
|
A:GLU385
|
4.4
|
25.6
|
1.0
|
|
CG
|
A:GLU385
|
4.4
|
28.4
|
1.0
|
|
HA
|
A:ASN290
|
4.5
|
28.9
|
1.0
|
|
ND2
|
A:ASN333
|
4.5
|
27.6
|
1.0
|
|
CA
|
A:TYR291
|
4.6
|
22.2
|
1.0
|
|
HA
|
A:GLU330
|
4.6
|
26.6
|
1.0
|
|
N
|
A:VAL293
|
4.6
|
28.4
|
1.0
|
|
OD1
|
A:ASN333
|
4.6
|
25.1
|
1.0
|
|
HG13
|
A:VAL293
|
4.6
|
32.1
|
1.0
|
|
C
|
A:ASN290
|
4.7
|
26.9
|
1.0
|
|
CB
|
A:ASN290
|
4.7
|
24.4
|
1.0
|
|
HD22
|
A:ASN290
|
4.7
|
24.5
|
1.0
|
|
HB3
|
B:ASP519
|
4.7
|
35.2
|
1.0
|
|
CB
|
A:ASP342
|
4.7
|
22.7
|
1.0
|
|
HA
|
B:ASP519
|
4.7
|
29.8
|
1.0
|
|
HB2
|
A:ASP342
|
4.8
|
27.3
|
1.0
|
|
HB2
|
B:ASP519
|
4.8
|
35.2
|
1.0
|
|
HG2
|
A:GLU385
|
4.8
|
34.0
|
1.0
|
|
CA
|
A:ASN290
|
4.8
|
24.1
|
1.0
|
|
HG3
|
A:GLU385
|
4.9
|
34.0
|
1.0
|
|
CB
|
B:ASP519
|
4.9
|
29.3
|
1.0
|
|
C
|
A:PRO292
|
4.9
|
23.2
|
1.0
|
|
H
|
B:ASP519
|
5.0
|
32.0
|
1.0
|
|
CB
|
A:GLU330
|
5.0
|
22.9
|
1.0
|
|
Calcium binding site 8 out
of 16 in 6x6m
Go back to
Calcium Binding Sites List in 6x6m
Calcium binding site 8 out
of 16 in the Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca608
b:27.5
occ:1.00
|
OXT
|
B:ASP519
|
2.3
|
23.4
|
1.0
|
|
OD1
|
A:ASP342
|
2.3
|
24.0
|
1.0
|
|
OE2
|
A:GLU385
|
2.3
|
27.9
|
1.0
|
|
O
|
A:SER340
|
2.4
|
25.6
|
1.0
|
|
O
|
A:THR331
|
2.4
|
26.1
|
1.0
|
|
OD1
|
A:ASN333
|
2.5
|
25.1
|
1.0
|
|
OG1
|
A:THR331
|
2.8
|
26.9
|
1.0
|
|
H
|
A:THR331
|
3.0
|
35.9
|
1.0
|
|
CD
|
A:GLU385
|
3.2
|
25.9
|
1.0
|
|
C
|
A:THR331
|
3.3
|
24.6
|
1.0
|
|
HG1
|
A:THR331
|
3.4
|
32.3
|
1.0
|
|
C
|
B:ASP519
|
3.4
|
27.1
|
1.0
|
|
CG
|
A:ASP342
|
3.4
|
25.2
|
1.0
|
|
N
|
A:THR331
|
3.5
|
29.9
|
1.0
|
|
C
|
A:SER340
|
3.5
|
21.3
|
1.0
|
|
CG
|
A:ASN333
|
3.6
|
23.7
|
1.0
|
|
HA
|
B:ASP519
|
3.6
|
29.8
|
1.0
|
|
CA
|
A:THR331
|
3.7
|
29.9
|
1.0
|
|
HG2
|
A:GLU385
|
3.7
|
34.0
|
1.0
|
|
CA
|
A:CA607
|
3.8
|
24.8
|
1.0
|
|
OD2
|
A:ASP342
|
3.8
|
28.0
|
1.0
|
|
HD21
|
A:ASN290
|
3.8
|
24.5
|
1.0
|
|
HB3
|
A:SER340
|
3.9
|
34.5
|
1.0
|
|
CB
|
A:THR331
|
3.9
|
22.8
|
1.0
|
|
HA
|
A:SER340
|
3.9
|
32.4
|
1.0
|
|
CG
|
A:GLU385
|
3.9
|
28.4
|
1.0
|
|
HD21
|
A:ASN333
|
4.0
|
33.1
|
1.0
|
|
OE1
|
A:GLU385
|
4.0
|
23.6
|
1.0
|
|
HG3
|
A:GLU385
|
4.0
|
34.0
|
1.0
|
|
CA
|
B:ASP519
|
4.0
|
24.8
|
1.0
|
|
HG3
|
A:GLU330
|
4.1
|
23.8
|
1.0
|
|
O
|
A:ARG341
|
4.1
|
29.4
|
1.0
|
|
HA
|
A:ASN333
|
4.2
|
41.4
|
1.0
|
|
CA
|
A:SER340
|
4.2
|
27.0
|
1.0
|
|
C
|
A:ARG341
|
4.2
|
31.1
|
1.0
|
|
ND2
|
A:ASN333
|
4.2
|
27.6
|
1.0
|
|
O
|
B:ASP519
|
4.3
|
24.4
|
1.0
|
|
O
|
A:PRO332
|
4.3
|
34.0
|
1.0
|
|
C
|
A:PRO332
|
4.4
|
24.9
|
1.0
|
|
C
|
A:GLU330
|
4.4
|
27.4
|
1.0
|
|
HB3
|
B:ASP519
|
4.4
|
35.2
|
1.0
|
|
N
|
A:ASP342
|
4.4
|
30.1
|
1.0
|
|
HB
|
A:THR331
|
4.4
|
27.3
|
1.0
|
|
HA
|
A:GLU330
|
4.4
|
26.6
|
1.0
|
|
HA
|
A:ASP342
|
4.4
|
27.2
|
1.0
|
|
N
|
A:PRO332
|
4.5
|
31.0
|
1.0
|
|
N
|
A:ASN333
|
4.5
|
33.1
|
1.0
|
|
CB
|
A:SER340
|
4.5
|
28.8
|
1.0
|
|
N
|
A:ARG341
|
4.6
|
22.5
|
1.0
|
|
CB
|
A:ASP342
|
4.6
|
22.7
|
1.0
|
|
HA
|
A:ARG341
|
4.6
|
27.9
|
1.0
|
|
ND2
|
A:ASN290
|
4.7
|
20.4
|
1.0
|
|
HA
|
A:THR331
|
4.7
|
35.9
|
1.0
|
|
CA
|
A:ASN333
|
4.7
|
34.5
|
1.0
|
|
H
|
A:ASP342
|
4.7
|
36.1
|
1.0
|
|
CA
|
A:ASP342
|
4.7
|
22.7
|
1.0
|
|
CB
|
A:ASN333
|
4.7
|
27.8
|
1.0
|
|
CA
|
A:ARG341
|
4.7
|
23.2
|
1.0
|
|
CB
|
B:ASP519
|
4.8
|
29.3
|
1.0
|
|
HG23
|
A:THR331
|
4.8
|
27.8
|
1.0
|
|
H
|
A:ASN333
|
4.9
|
39.7
|
1.0
|
|
CA
|
A:PRO332
|
4.9
|
33.5
|
1.0
|
|
CA
|
A:GLU330
|
4.9
|
22.1
|
1.0
|
|
CG2
|
A:THR331
|
5.0
|
23.1
|
1.0
|
|
Calcium binding site 9 out
of 16 in 6x6m
Go back to
Calcium Binding Sites List in 6x6m
Calcium binding site 9 out
of 16 in the Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca609
b:27.6
occ:1.00
|
O
|
A:THR18
|
2.3
|
22.9
|
1.0
|
|
OE2
|
A:GLU23
|
2.3
|
28.8
|
1.0
|
|
O
|
A:HOH2052
|
2.4
|
22.2
|
1.0
|
|
O
|
A:HOH2076
|
2.4
|
29.1
|
1.0
|
|
OD1
|
A:ASP16
|
2.4
|
26.5
|
1.0
|
|
OE1
|
A:GLU23
|
2.5
|
27.2
|
1.0
|
|
OG1
|
A:THR14
|
2.6
|
29.0
|
1.0
|
|
CD
|
A:GLU23
|
2.7
|
23.6
|
1.0
|
|
HB
|
A:THR14
|
3.0
|
33.8
|
1.0
|
|
CB
|
A:THR14
|
3.3
|
28.1
|
1.0
|
|
CG
|
A:ASP16
|
3.3
|
29.9
|
1.0
|
|
HG21
|
A:THR14
|
3.5
|
42.4
|
1.0
|
|
H
|
A:THR18
|
3.5
|
24.2
|
1.0
|
|
OD2
|
A:ASP16
|
3.5
|
29.4
|
1.0
|
|
C
|
A:THR18
|
3.5
|
19.5
|
1.0
|
|
H
|
A:ASP16
|
3.8
|
34.4
|
1.0
|
|
HA
|
A:ILE19
|
3.9
|
26.9
|
1.0
|
|
CG2
|
A:THR14
|
3.9
|
35.4
|
1.0
|
|
H
|
A:ASP20
|
4.0
|
32.4
|
1.0
|
|
OD2
|
A:ASP20
|
4.2
|
29.6
|
1.0
|
|
N
|
A:THR18
|
4.2
|
20.1
|
1.0
|
|
CG
|
A:GLU23
|
4.2
|
23.8
|
1.0
|
|
HG23
|
A:THR14
|
4.4
|
42.4
|
1.0
|
|
CA
|
A:THR18
|
4.4
|
19.9
|
1.0
|
|
OG1
|
A:THR18
|
4.4
|
51.9
|
1.0
|
|
N
|
A:ILE19
|
4.5
|
22.4
|
1.0
|
|
H
|
A:SER15
|
4.5
|
38.5
|
1.0
|
|
O
|
A:ILE13
|
4.6
|
31.9
|
1.0
|
|
CA
|
A:ILE19
|
4.6
|
22.4
|
1.0
|
|
N
|
A:ASP16
|
4.6
|
28.7
|
1.0
|
|
HG3
|
A:GLU23
|
4.6
|
28.6
|
1.0
|
|
N
|
A:ASP20
|
4.6
|
27.0
|
1.0
|
|
O
|
A:HOH2229
|
4.6
|
41.5
|
1.0
|
|
HG2
|
A:GLU23
|
4.6
|
28.6
|
1.0
|
|
CA
|
A:THR14
|
4.7
|
32.5
|
1.0
|
|
CB
|
A:ASP16
|
4.7
|
28.5
|
1.0
|
|
HG22
|
A:THR14
|
4.7
|
42.4
|
1.0
|
|
CG
|
A:ASP20
|
4.7
|
28.9
|
1.0
|
|
HB3
|
A:ASP20
|
4.7
|
29.1
|
1.0
|
|
HD12
|
A:ILE19
|
4.7
|
30.7
|
1.0
|
|
N
|
A:SER15
|
4.8
|
32.1
|
1.0
|
|
HG23
|
A:THR18
|
4.8
|
29.2
|
1.0
|
|
H
|
A:ASP17
|
4.8
|
35.1
|
1.0
|
|
C
|
A:THR14
|
4.8
|
38.3
|
1.0
|
|
HB2
|
A:GLU23
|
4.9
|
23.0
|
1.0
|
|
HB3
|
A:ASP16
|
5.0
|
34.2
|
1.0
|
|
Calcium binding site 10 out
of 16 in 6x6m
Go back to
Calcium Binding Sites List in 6x6m
Calcium binding site 10 out
of 16 in the Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca610
b:73.7
occ:1.00
|
O
|
A:HOH2007
|
2.7
|
44.6
|
1.0
|
|
OD2
|
A:ASP17
|
2.7
|
33.3
|
1.0
|
|
O
|
A:HOH2151
|
2.7
|
39.4
|
1.0
|
|
O
|
A:HOH2300
|
3.1
|
50.4
|
1.0
|
|
HA
|
A:HIS102
|
3.8
|
37.1
|
1.0
|
|
HG1
|
A:THR101
|
3.8
|
54.2
|
1.0
|
|
CG
|
A:ASP17
|
3.8
|
35.2
|
1.0
|
|
HG
|
A:SER103
|
3.9
|
50.7
|
1.0
|
|
HB3
|
A:ASP17
|
4.0
|
34.8
|
1.0
|
|
CA
|
A:CA602
|
4.2
|
35.2
|
1.0
|
|
O
|
A:THR101
|
4.3
|
32.9
|
1.0
|
|
CB
|
A:ASP17
|
4.5
|
29.0
|
1.0
|
|
OG1
|
A:THR101
|
4.6
|
45.1
|
1.0
|
|
OG
|
A:SER103
|
4.6
|
42.3
|
1.0
|
|
CA
|
A:HIS102
|
4.7
|
30.9
|
1.0
|
|
O
|
A:ASP17
|
4.8
|
27.0
|
1.0
|
|
OD1
|
A:ASP17
|
4.8
|
29.9
|
1.0
|
|
H
|
A:SER103
|
4.8
|
36.1
|
1.0
|
|
C
|
A:THR101
|
4.9
|
31.1
|
1.0
|
|
HB2
|
A:ASP17
|
5.0
|
34.8
|
1.0
|
|
Reference:
P.L.Davies,
S.Guo.
Molecular Basis For A Bacterial Adhesins Peptide-Binding Module To Be Published.
Page generated: Tue Jul 16 17:50:57 2024
|
