Calcium in PDB 6s5p: Cfucosylated Peptide SBL2 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 1.46 Angstrom Resolution
Protein crystallography data
The structure of Cfucosylated Peptide SBL2 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 1.46 Angstrom Resolution, PDB code: 6s5p
was solved by
S.Baeriswyl,
A.Stocker,
J.-L.Reymond,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
46.37 /
1.46
|
|
Space group
|
P 21 21 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
123.099,
56.264,
70.498,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
17.7 /
19.4
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Cfucosylated Peptide SBL2 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 1.46 Angstrom Resolution
(pdb code 6s5p). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the
Cfucosylated Peptide SBL2 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 1.46 Angstrom Resolution, PDB code: 6s5p:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Calcium binding site 1 out
of 8 in 6s5p
Go back to
Calcium Binding Sites List in 6s5p
Calcium binding site 1 out
of 8 in the Cfucosylated Peptide SBL2 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 1.46 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Cfucosylated Peptide SBL2 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 1.46 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca301
b:17.5
occ:1.00
|
H2O
|
A:ZDC303
|
2.0
|
21.6
|
1.0
|
|
H3O
|
A:ZDC303
|
2.3
|
21.7
|
1.0
|
|
OD1
|
A:ASN103
|
2.3
|
15.9
|
1.0
|
|
OD1
|
A:ASP104
|
2.3
|
16.1
|
1.0
|
|
O
|
A:ASN21
|
2.4
|
16.2
|
1.0
|
|
OD2
|
A:ASP101
|
2.4
|
16.4
|
1.0
|
|
O2
|
A:ZDC303
|
2.5
|
17.9
|
1.0
|
|
O
|
B:GLY114
|
2.5
|
17.3
|
1.0
|
|
O3
|
A:ZDC303
|
2.6
|
18.1
|
1.0
|
|
OD1
|
A:ASP101
|
3.0
|
17.9
|
1.0
|
|
CG
|
A:ASP101
|
3.1
|
16.5
|
1.0
|
|
H4
|
A:ZDC303
|
3.3
|
23.4
|
1.0
|
|
HD21
|
A:ASN103
|
3.4
|
21.4
|
1.0
|
|
CG
|
A:ASN103
|
3.4
|
15.9
|
1.0
|
|
C2
|
A:ZDC303
|
3.4
|
19.8
|
1.0
|
|
C3
|
A:ZDC303
|
3.4
|
19.4
|
1.0
|
|
C
|
B:GLY114
|
3.5
|
24.0
|
1.0
|
|
HA
|
A:ASP104
|
3.5
|
19.8
|
1.0
|
|
C
|
A:ASN21
|
3.6
|
17.1
|
1.0
|
|
CG
|
A:ASP104
|
3.6
|
16.1
|
1.0
|
|
OXT
|
B:GLY114
|
3.7
|
17.8
|
1.0
|
|
CA
|
A:CA302
|
3.7
|
17.0
|
1.0
|
|
H2
|
A:ZDC303
|
3.7
|
23.8
|
1.0
|
|
HA
|
A:SER22
|
3.7
|
19.8
|
1.0
|
|
ND2
|
A:ASN103
|
3.7
|
17.8
|
1.0
|
|
HB3
|
A:ASN21
|
3.7
|
19.1
|
1.0
|
|
HB2
|
A:SER22
|
3.8
|
19.7
|
1.0
|
|
C4
|
A:ZDC303
|
3.8
|
19.5
|
1.0
|
|
HB2
|
A:ASN21
|
3.8
|
19.1
|
1.0
|
|
H
|
A:ASN103
|
4.2
|
19.0
|
1.0
|
|
CB
|
A:ASN21
|
4.2
|
16.1
|
1.0
|
|
CA
|
A:ASP104
|
4.2
|
16.4
|
1.0
|
|
N
|
A:ASP104
|
4.2
|
15.7
|
1.0
|
|
H3
|
A:ZDC303
|
4.3
|
23.3
|
1.0
|
|
CA
|
A:SER22
|
4.4
|
16.6
|
1.0
|
|
N
|
A:SER22
|
4.4
|
16.5
|
1.0
|
|
OD2
|
A:ASP104
|
4.4
|
16.3
|
1.0
|
|
H4O
|
A:ZDC303
|
4.4
|
23.1
|
1.0
|
|
CB
|
A:ASP104
|
4.4
|
15.8
|
1.0
|
|
O4
|
A:ZDC303
|
4.5
|
19.2
|
1.0
|
|
H
|
A:ASP104
|
4.5
|
18.8
|
1.0
|
|
OD2
|
A:ASP99
|
4.5
|
21.6
|
1.0
|
|
C
|
A:ASN103
|
4.5
|
15.7
|
1.0
|
|
O
|
A:HOH429
|
4.5
|
27.2
|
1.0
|
|
CB
|
A:SER22
|
4.5
|
16.6
|
1.0
|
|
CB
|
A:ASP101
|
4.5
|
17.9
|
1.0
|
|
CA
|
A:ASN21
|
4.5
|
16.1
|
1.0
|
|
HD22
|
A:ASN103
|
4.6
|
21.4
|
1.0
|
|
HB2
|
A:ASP101
|
4.7
|
21.6
|
1.0
|
|
CB
|
A:ASN103
|
4.7
|
15.8
|
1.0
|
|
HB3
|
A:ASP104
|
4.7
|
18.9
|
1.0
|
|
C1
|
A:ZDC303
|
4.7
|
19.9
|
1.0
|
|
CA
|
B:GLY114
|
4.8
|
17.5
|
1.0
|
|
O
|
A:ASN103
|
4.8
|
15.6
|
1.0
|
|
N
|
A:ASN103
|
4.9
|
15.9
|
1.0
|
|
HB3
|
A:ASP101
|
4.9
|
21.6
|
1.0
|
|
CA
|
A:ASN103
|
4.9
|
15.8
|
1.0
|
|
OD1
|
A:ASP99
|
5.0
|
18.5
|
1.0
|
|
O5
|
A:ZDC303
|
5.0
|
19.4
|
1.0
|
|
Calcium binding site 2 out
of 8 in 6s5p
Go back to
Calcium Binding Sites List in 6s5p
Calcium binding site 2 out
of 8 in the Cfucosylated Peptide SBL2 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 1.46 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Cfucosylated Peptide SBL2 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 1.46 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca302
b:17.0
occ:1.00
|
OD1
|
A:ASP99
|
2.3
|
18.5
|
1.0
|
|
OD1
|
A:ASP101
|
2.4
|
17.9
|
1.0
|
|
OD2
|
A:ASP104
|
2.4
|
16.3
|
1.0
|
|
H4O
|
A:ZDC303
|
2.4
|
23.1
|
1.0
|
|
OE1
|
A:GLU95
|
2.5
|
18.4
|
1.0
|
|
O3
|
A:ZDC303
|
2.5
|
18.1
|
1.0
|
|
OE2
|
A:GLU95
|
2.5
|
17.0
|
1.0
|
|
O4
|
A:ZDC303
|
2.6
|
19.2
|
1.0
|
|
OD1
|
A:ASP104
|
2.7
|
16.1
|
1.0
|
|
CD
|
A:GLU95
|
2.8
|
16.9
|
1.0
|
|
CG
|
A:ASP104
|
2.9
|
16.1
|
1.0
|
|
H3O
|
A:ZDC303
|
3.1
|
21.7
|
1.0
|
|
C4
|
A:ZDC303
|
3.3
|
19.5
|
1.0
|
|
H
|
A:ASP101
|
3.3
|
20.2
|
1.0
|
|
CG
|
A:ASP99
|
3.4
|
18.4
|
1.0
|
|
C3
|
A:ZDC303
|
3.4
|
19.4
|
1.0
|
|
H4
|
A:ZDC303
|
3.4
|
23.4
|
1.0
|
|
CG
|
A:ASP101
|
3.4
|
16.5
|
1.0
|
|
OD2
|
A:ASP99
|
3.7
|
21.6
|
1.0
|
|
CA
|
A:CA301
|
3.7
|
17.5
|
1.0
|
|
H
|
A:TYR102
|
3.7
|
19.9
|
1.0
|
|
H3
|
A:ZDC303
|
3.8
|
23.3
|
1.0
|
|
H
|
A:ASP96
|
3.8
|
22.4
|
1.0
|
|
HA
|
A:GLU95
|
3.8
|
19.7
|
1.0
|
|
H
|
A:ASN100
|
4.0
|
20.8
|
1.0
|
|
OD2
|
A:ASP101
|
4.0
|
16.4
|
1.0
|
|
H
|
A:GLY97
|
4.0
|
23.5
|
1.0
|
|
N
|
A:ASP101
|
4.1
|
16.9
|
1.0
|
|
O
|
A:HOH461
|
4.1
|
22.6
|
1.0
|
|
H
|
A:ASP99
|
4.2
|
21.8
|
1.0
|
|
OD1
|
A:ASP96
|
4.2
|
18.2
|
1.0
|
|
CG
|
A:GLU95
|
4.3
|
17.0
|
1.0
|
|
CB
|
A:ASP104
|
4.4
|
15.8
|
1.0
|
|
N
|
A:ASN100
|
4.4
|
17.5
|
1.0
|
|
N
|
A:TYR102
|
4.4
|
16.6
|
1.0
|
|
H
|
A:ASN103
|
4.5
|
19.0
|
1.0
|
|
N
|
A:ASP96
|
4.5
|
18.6
|
1.0
|
|
CB
|
A:ASP101
|
4.6
|
17.9
|
1.0
|
|
N
|
A:GLY97
|
4.6
|
19.6
|
1.0
|
|
H
|
A:ASP104
|
4.6
|
18.8
|
1.0
|
|
HG3
|
A:GLU95
|
4.6
|
20.3
|
1.0
|
|
CA
|
A:GLU95
|
4.7
|
16.5
|
1.0
|
|
OD1
|
A:ASN103
|
4.7
|
15.9
|
1.0
|
|
C2
|
A:ZDC303
|
4.7
|
19.8
|
1.0
|
|
CB
|
A:ASP99
|
4.7
|
19.3
|
1.0
|
|
CA
|
A:ASP101
|
4.7
|
16.7
|
1.0
|
|
HB2
|
A:ASP104
|
4.7
|
18.9
|
1.0
|
|
C5
|
A:ZDC303
|
4.8
|
20.1
|
1.0
|
|
O2
|
A:ZDC303
|
4.8
|
17.9
|
1.0
|
|
HG2
|
A:GLU95
|
4.8
|
20.3
|
1.0
|
|
HA3
|
A:GLY97
|
4.8
|
24.8
|
1.0
|
|
N
|
A:ASP99
|
4.8
|
18.1
|
1.0
|
|
H2O
|
A:ZDC303
|
4.8
|
21.6
|
1.0
|
|
HB3
|
A:ASP104
|
4.8
|
18.9
|
1.0
|
|
HA
|
A:ASN100
|
4.8
|
20.9
|
1.0
|
|
CB
|
A:GLU95
|
4.9
|
16.8
|
1.0
|
|
HB2
|
A:GLU95
|
4.9
|
20.0
|
1.0
|
|
HB3
|
A:ASP101
|
4.9
|
21.6
|
1.0
|
|
CG
|
A:ASP96
|
4.9
|
19.7
|
1.0
|
|
C
|
A:ASP99
|
5.0
|
18.7
|
1.0
|
|
HB2
|
A:SER22
|
5.0
|
19.7
|
1.0
|
|
C
|
A:ASP101
|
5.0
|
16.5
|
1.0
|
|
Calcium binding site 3 out
of 8 in 6s5p
Go back to
Calcium Binding Sites List in 6s5p
Calcium binding site 3 out
of 8 in the Cfucosylated Peptide SBL2 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 1.46 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Cfucosylated Peptide SBL2 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 1.46 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca304
b:19.4
occ:1.00
|
O
|
B:ASN21
|
2.3
|
19.2
|
1.0
|
|
O2
|
B:ZDC302
|
2.4
|
20.3
|
1.0
|
|
OD1
|
B:ASN103
|
2.4
|
17.9
|
1.0
|
|
OD2
|
B:ASP101
|
2.4
|
20.2
|
1.0
|
|
OD1
|
B:ASP104
|
2.4
|
19.2
|
1.0
|
|
O
|
A:GLY114
|
2.5
|
18.3
|
1.0
|
|
O3
|
B:ZDC302
|
2.5
|
21.4
|
1.0
|
|
H3O
|
B:ZDC302
|
2.5
|
25.7
|
1.0
|
|
H2O
|
B:ZDC302
|
2.9
|
24.4
|
1.0
|
|
CG
|
B:ASP101
|
3.1
|
22.1
|
1.0
|
|
OD1
|
B:ASP101
|
3.1
|
18.9
|
1.0
|
|
C2
|
B:ZDC302
|
3.3
|
20.7
|
1.0
|
|
H4
|
B:ZDC302
|
3.3
|
26.5
|
1.0
|
|
C3
|
B:ZDC302
|
3.3
|
20.8
|
1.0
|
|
HD21
|
B:ASN103
|
3.3
|
21.8
|
1.0
|
|
CG
|
B:ASN103
|
3.4
|
17.7
|
1.0
|
|
C
|
A:GLY114
|
3.4
|
22.9
|
1.0
|
|
HA
|
B:ASP104
|
3.5
|
20.9
|
1.0
|
|
C
|
B:ASN21
|
3.5
|
18.0
|
1.0
|
|
H2
|
B:ZDC302
|
3.6
|
24.8
|
1.0
|
|
OXT
|
A:GLY114
|
3.6
|
24.3
|
1.0
|
|
CG
|
B:ASP104
|
3.6
|
22.6
|
1.0
|
|
HB3
|
B:ASN21
|
3.7
|
23.4
|
1.0
|
|
CA
|
B:CA301
|
3.7
|
20.4
|
1.0
|
|
ND2
|
B:ASN103
|
3.7
|
18.2
|
1.0
|
|
C4
|
B:ZDC302
|
3.8
|
22.0
|
1.0
|
|
HA
|
B:SER22
|
3.8
|
21.8
|
1.0
|
|
HB2
|
B:SER22
|
3.9
|
22.9
|
1.0
|
|
HB2
|
B:ASN21
|
3.9
|
23.4
|
1.0
|
|
CB
|
B:ASN21
|
4.2
|
19.4
|
1.0
|
|
H3
|
B:ZDC302
|
4.2
|
25.0
|
1.0
|
|
CA
|
B:ASP104
|
4.2
|
17.4
|
1.0
|
|
H
|
B:ASN103
|
4.2
|
20.8
|
1.0
|
|
N
|
B:ASP104
|
4.2
|
18.8
|
1.0
|
|
CA
|
B:SER22
|
4.4
|
18.2
|
1.0
|
|
N
|
B:SER22
|
4.4
|
18.3
|
1.0
|
|
O4
|
B:ZDC302
|
4.4
|
23.6
|
1.0
|
|
H
|
B:ASP104
|
4.4
|
22.6
|
1.0
|
|
OD2
|
B:ASP104
|
4.5
|
20.9
|
1.0
|
|
CB
|
B:ASP104
|
4.5
|
17.6
|
1.0
|
|
CA
|
B:ASN21
|
4.5
|
16.3
|
1.0
|
|
OD2
|
B:ASP99
|
4.5
|
22.4
|
1.0
|
|
C
|
B:ASN103
|
4.5
|
16.9
|
1.0
|
|
CB
|
B:ASP101
|
4.6
|
20.1
|
1.0
|
|
O
|
B:HOH438
|
4.6
|
29.9
|
1.0
|
|
CB
|
B:SER22
|
4.6
|
19.1
|
1.0
|
|
HD22
|
B:ASN103
|
4.6
|
21.8
|
1.0
|
|
C1
|
B:ZDC302
|
4.6
|
22.2
|
1.0
|
|
HB2
|
B:ASP101
|
4.7
|
24.2
|
1.0
|
|
CB
|
B:ASN103
|
4.8
|
17.1
|
1.0
|
|
CA
|
A:GLY114
|
4.8
|
21.1
|
1.0
|
|
HB3
|
B:ASP104
|
4.8
|
21.1
|
1.0
|
|
O
|
B:ASN103
|
4.9
|
18.3
|
1.0
|
|
O5
|
B:ZDC302
|
4.9
|
22.1
|
1.0
|
|
N
|
B:ASN103
|
5.0
|
17.3
|
1.0
|
|
HB3
|
B:ASP101
|
5.0
|
24.2
|
1.0
|
|
Calcium binding site 4 out
of 8 in 6s5p
Go back to
Calcium Binding Sites List in 6s5p
Calcium binding site 4 out
of 8 in the Cfucosylated Peptide SBL2 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 1.46 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Cfucosylated Peptide SBL2 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 1.46 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca301
b:20.4
occ:1.00
|
OD1
|
B:ASP99
|
2.4
|
20.5
|
1.0
|
|
OD1
|
B:ASP101
|
2.4
|
18.9
|
1.0
|
|
OE2
|
B:GLU95
|
2.4
|
21.4
|
1.0
|
|
O3
|
B:ZDC302
|
2.4
|
21.4
|
1.0
|
|
OD2
|
B:ASP104
|
2.5
|
20.9
|
1.0
|
|
OE1
|
B:GLU95
|
2.5
|
20.9
|
1.0
|
|
O4
|
B:ZDC302
|
2.5
|
23.6
|
1.0
|
|
OD1
|
B:ASP104
|
2.6
|
19.2
|
1.0
|
|
CD
|
B:GLU95
|
2.8
|
19.7
|
1.0
|
|
CG
|
B:ASP104
|
2.9
|
22.6
|
1.0
|
|
H3O
|
B:ZDC302
|
3.0
|
25.7
|
1.0
|
|
H4O
|
B:ZDC302
|
3.1
|
28.4
|
1.0
|
|
C4
|
B:ZDC302
|
3.3
|
22.0
|
1.0
|
|
H
|
B:ASP101
|
3.3
|
24.1
|
1.0
|
|
C3
|
B:ZDC302
|
3.3
|
20.8
|
1.0
|
|
CG
|
B:ASP99
|
3.4
|
30.6
|
1.0
|
|
H4
|
B:ZDC302
|
3.4
|
26.5
|
1.0
|
|
CG
|
B:ASP101
|
3.4
|
22.1
|
1.0
|
|
OD2
|
B:ASP99
|
3.7
|
22.4
|
1.0
|
|
H3
|
B:ZDC302
|
3.7
|
25.0
|
1.0
|
|
CA
|
A:CA304
|
3.7
|
19.4
|
1.0
|
|
H
|
B:ASP96
|
3.8
|
23.9
|
1.0
|
|
H
|
B:TYR102
|
3.8
|
21.5
|
1.0
|
|
HA
|
B:GLU95
|
3.9
|
21.7
|
1.0
|
|
OD2
|
B:ASP101
|
3.9
|
20.2
|
1.0
|
|
H
|
B:ASN100
|
4.0
|
30.1
|
1.0
|
|
H
|
B:GLY97
|
4.0
|
28.9
|
1.0
|
|
N
|
B:ASP101
|
4.1
|
20.0
|
1.0
|
|
OD1
|
B:ASP96
|
4.2
|
25.5
|
1.0
|
|
O
|
B:HOH455
|
4.2
|
26.3
|
1.0
|
|
H
|
B:ASP99
|
4.2
|
32.5
|
1.0
|
|
CG
|
B:GLU95
|
4.3
|
19.6
|
1.0
|
|
CB
|
B:ASP104
|
4.4
|
17.6
|
1.0
|
|
N
|
B:ASN100
|
4.4
|
25.1
|
1.0
|
|
N
|
B:TYR102
|
4.5
|
18.0
|
1.0
|
|
N
|
B:ASP96
|
4.5
|
19.9
|
1.0
|
|
H
|
B:ASN103
|
4.5
|
20.8
|
1.0
|
|
H
|
B:ASP104
|
4.6
|
22.6
|
1.0
|
|
N
|
B:GLY97
|
4.6
|
24.1
|
1.0
|
|
CB
|
B:ASP101
|
4.6
|
20.1
|
1.0
|
|
HG3
|
B:GLU95
|
4.6
|
23.5
|
1.0
|
|
C2
|
B:ZDC302
|
4.6
|
20.7
|
1.0
|
|
OD1
|
B:ASN103
|
4.7
|
17.9
|
1.0
|
|
CA
|
B:GLU95
|
4.7
|
18.2
|
1.0
|
|
HA3
|
B:GLY97
|
4.7
|
29.6
|
1.0
|
|
C5
|
B:ZDC302
|
4.7
|
23.9
|
1.0
|
|
CA
|
B:ASP101
|
4.7
|
19.9
|
1.0
|
|
CB
|
B:ASP99
|
4.7
|
26.2
|
1.0
|
|
HB2
|
B:ASP104
|
4.8
|
21.1
|
1.0
|
|
O2
|
B:ZDC302
|
4.8
|
20.3
|
1.0
|
|
HG2
|
B:GLU95
|
4.8
|
23.5
|
1.0
|
|
N
|
B:ASP99
|
4.8
|
27.1
|
1.0
|
|
HB3
|
B:ASP104
|
4.9
|
21.1
|
1.0
|
|
HA
|
B:ASN100
|
4.9
|
29.6
|
1.0
|
|
HB3
|
B:ASP101
|
4.9
|
24.2
|
1.0
|
|
CB
|
B:GLU95
|
4.9
|
18.6
|
1.0
|
|
CG
|
B:ASP96
|
4.9
|
22.5
|
1.0
|
|
HB2
|
B:GLU95
|
5.0
|
22.2
|
1.0
|
|
C
|
B:ASP99
|
5.0
|
21.6
|
1.0
|
|
Calcium binding site 5 out
of 8 in 6s5p
Go back to
Calcium Binding Sites List in 6s5p
Calcium binding site 5 out
of 8 in the Cfucosylated Peptide SBL2 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 1.46 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Cfucosylated Peptide SBL2 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 1.46 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca301
b:18.5
occ:1.00
|
OD1
|
C:ASP101
|
2.4
|
17.8
|
1.0
|
|
OD1
|
C:ASP99
|
2.4
|
20.1
|
1.0
|
|
OE2
|
C:GLU95
|
2.4
|
19.3
|
1.0
|
|
OD2
|
C:ASP104
|
2.4
|
17.6
|
1.0
|
|
OE1
|
C:GLU95
|
2.4
|
18.8
|
1.0
|
|
O3
|
C:ZDC303
|
2.4
|
19.9
|
1.0
|
|
O4
|
C:ZDC303
|
2.5
|
19.1
|
1.0
|
|
OD1
|
C:ASP104
|
2.7
|
16.8
|
1.0
|
|
CD
|
C:GLU95
|
2.7
|
18.4
|
1.0
|
|
CG
|
C:ASP104
|
2.9
|
19.0
|
1.0
|
|
H3O
|
C:ZDC303
|
3.0
|
24.0
|
1.0
|
|
H4O
|
C:ZDC303
|
3.1
|
23.0
|
1.0
|
|
H
|
C:ASP101
|
3.3
|
23.3
|
1.0
|
|
C4
|
C:ZDC303
|
3.4
|
19.0
|
1.0
|
|
C3
|
C:ZDC303
|
3.4
|
18.6
|
1.0
|
|
CG
|
C:ASP99
|
3.4
|
21.2
|
1.0
|
|
CG
|
C:ASP101
|
3.4
|
20.6
|
1.0
|
|
H4
|
C:ZDC303
|
3.5
|
22.8
|
1.0
|
|
H3
|
C:ZDC303
|
3.7
|
22.3
|
1.0
|
|
OD2
|
C:ASP99
|
3.7
|
20.0
|
1.0
|
|
CA
|
C:CA302
|
3.7
|
18.4
|
1.0
|
|
H
|
C:TYR102
|
3.8
|
21.7
|
1.0
|
|
H
|
C:ASP96
|
3.8
|
21.9
|
1.0
|
|
HA
|
C:GLU95
|
3.9
|
25.9
|
1.0
|
|
H
|
C:ASN100
|
3.9
|
22.5
|
1.0
|
|
OD2
|
C:ASP101
|
4.0
|
20.2
|
1.0
|
|
H
|
C:GLY97
|
4.0
|
23.4
|
1.0
|
|
O
|
C:HOH447
|
4.1
|
25.5
|
1.0
|
|
N
|
C:ASP101
|
4.1
|
19.4
|
1.0
|
|
H
|
C:ASP99
|
4.1
|
26.9
|
1.0
|
|
OD1
|
C:ASP96
|
4.2
|
19.1
|
1.0
|
|
CG
|
C:GLU95
|
4.2
|
19.5
|
1.0
|
|
N
|
C:ASN100
|
4.4
|
18.7
|
1.0
|
|
CB
|
C:ASP104
|
4.4
|
16.0
|
1.0
|
|
N
|
C:TYR102
|
4.4
|
18.1
|
1.0
|
|
H
|
C:ASN103
|
4.5
|
22.1
|
1.0
|
|
N
|
C:ASP96
|
4.5
|
18.2
|
1.0
|
|
CB
|
C:ASP101
|
4.6
|
19.6
|
1.0
|
|
HG3
|
C:GLU95
|
4.6
|
23.4
|
1.0
|
|
N
|
C:GLY97
|
4.6
|
19.5
|
1.0
|
|
H
|
C:ASP104
|
4.6
|
18.0
|
1.0
|
|
OD1
|
C:ASN103
|
4.7
|
17.2
|
1.0
|
|
HA3
|
C:GLY97
|
4.7
|
25.1
|
1.0
|
|
CA
|
C:GLU95
|
4.7
|
21.6
|
1.0
|
|
C2
|
C:ZDC303
|
4.7
|
19.9
|
1.0
|
|
HB2
|
C:ASP104
|
4.7
|
19.2
|
1.0
|
|
HG2
|
C:GLU95
|
4.7
|
23.4
|
1.0
|
|
CA
|
C:ASP101
|
4.7
|
21.9
|
1.0
|
|
O2
|
C:ZDC303
|
4.7
|
19.8
|
1.0
|
|
CB
|
C:ASP99
|
4.8
|
20.4
|
1.0
|
|
N
|
C:ASP99
|
4.8
|
22.4
|
1.0
|
|
C5
|
C:ZDC303
|
4.8
|
21.1
|
1.0
|
|
H2O
|
C:ZDC303
|
4.8
|
23.8
|
1.0
|
|
HA
|
C:ASN100
|
4.9
|
22.1
|
1.0
|
|
HB3
|
C:ASP104
|
4.9
|
19.2
|
1.0
|
|
CB
|
C:GLU95
|
4.9
|
20.4
|
1.0
|
|
HB3
|
C:ASP101
|
4.9
|
23.5
|
1.0
|
|
HB2
|
C:GLU95
|
4.9
|
24.5
|
1.0
|
|
C
|
C:ASP99
|
5.0
|
25.2
|
1.0
|
|
CG
|
C:ASP96
|
5.0
|
17.6
|
1.0
|
|
C
|
C:ASP101
|
5.0
|
18.9
|
1.0
|
|
Calcium binding site 6 out
of 8 in 6s5p
Go back to
Calcium Binding Sites List in 6s5p
Calcium binding site 6 out
of 8 in the Cfucosylated Peptide SBL2 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 1.46 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Cfucosylated Peptide SBL2 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 1.46 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca302
b:18.4
occ:1.00
|
H2O
|
C:ZDC303
|
2.0
|
23.8
|
1.0
|
|
OD1
|
C:ASN103
|
2.3
|
17.2
|
1.0
|
|
O
|
C:ASN21
|
2.4
|
18.9
|
1.0
|
|
H3O
|
C:ZDC303
|
2.4
|
24.0
|
1.0
|
|
OD2
|
C:ASP101
|
2.4
|
20.2
|
1.0
|
|
O
|
D:GLY114
|
2.4
|
17.7
|
1.0
|
|
OD1
|
C:ASP104
|
2.4
|
16.8
|
1.0
|
|
O2
|
C:ZDC303
|
2.4
|
19.8
|
1.0
|
|
O3
|
C:ZDC303
|
2.5
|
19.9
|
1.0
|
|
OD1
|
C:ASP101
|
3.1
|
17.8
|
1.0
|
|
CG
|
C:ASP101
|
3.1
|
20.6
|
1.0
|
|
HD21
|
C:ASN103
|
3.3
|
20.9
|
1.0
|
|
CG
|
C:ASN103
|
3.3
|
16.1
|
1.0
|
|
C3
|
C:ZDC303
|
3.4
|
18.6
|
1.0
|
|
H4
|
C:ZDC303
|
3.4
|
22.8
|
1.0
|
|
C2
|
C:ZDC303
|
3.4
|
19.9
|
1.0
|
|
C
|
D:GLY114
|
3.4
|
18.0
|
1.0
|
|
C
|
C:ASN21
|
3.5
|
18.5
|
1.0
|
|
HA
|
C:ASP104
|
3.5
|
19.1
|
1.0
|
|
HB3
|
C:ASN21
|
3.6
|
22.3
|
1.0
|
|
OXT
|
D:GLY114
|
3.7
|
20.2
|
1.0
|
|
CG
|
C:ASP104
|
3.7
|
19.0
|
1.0
|
|
H2
|
C:ZDC303
|
3.7
|
23.9
|
1.0
|
|
ND2
|
C:ASN103
|
3.7
|
17.4
|
1.0
|
|
CA
|
C:CA301
|
3.7
|
18.5
|
1.0
|
|
HA
|
C:SER22
|
3.8
|
22.4
|
1.0
|
|
C4
|
C:ZDC303
|
3.8
|
19.0
|
1.0
|
|
HB2
|
C:ASN21
|
3.8
|
22.3
|
1.0
|
|
HB2
|
C:SER22
|
3.9
|
25.2
|
1.0
|
|
CB
|
C:ASN21
|
4.1
|
18.7
|
1.0
|
|
H
|
C:ASN103
|
4.2
|
22.1
|
1.0
|
|
H3
|
C:ZDC303
|
4.2
|
22.3
|
1.0
|
|
CA
|
C:ASP104
|
4.2
|
15.8
|
1.0
|
|
N
|
C:ASP104
|
4.3
|
15.1
|
1.0
|
|
CA
|
C:SER22
|
4.4
|
18.8
|
1.0
|
|
N
|
C:SER22
|
4.4
|
18.4
|
1.0
|
|
O4
|
C:ZDC303
|
4.4
|
19.1
|
1.0
|
|
C
|
C:ASN103
|
4.5
|
15.4
|
1.0
|
|
CA
|
C:ASN21
|
4.5
|
18.3
|
1.0
|
|
OD2
|
C:ASP104
|
4.5
|
17.6
|
1.0
|
|
H
|
C:ASP104
|
4.5
|
18.0
|
1.0
|
|
CB
|
C:ASP104
|
4.5
|
16.0
|
1.0
|
|
CB
|
C:ASP101
|
4.5
|
19.6
|
1.0
|
|
HD22
|
C:ASN103
|
4.5
|
20.9
|
1.0
|
|
OD2
|
C:ASP99
|
4.6
|
20.0
|
1.0
|
|
CB
|
C:SER22
|
4.6
|
21.0
|
1.0
|
|
O
|
C:HOH466
|
4.7
|
35.5
|
1.0
|
|
CB
|
C:ASN103
|
4.7
|
16.0
|
1.0
|
|
HB2
|
C:ASP101
|
4.7
|
23.5
|
1.0
|
|
C1
|
C:ZDC303
|
4.7
|
20.5
|
1.0
|
|
O
|
C:ASN103
|
4.8
|
15.1
|
1.0
|
|
CA
|
D:GLY114
|
4.8
|
19.6
|
1.0
|
|
HB3
|
C:ASP104
|
4.9
|
19.2
|
1.0
|
|
N
|
C:ASN103
|
4.9
|
18.4
|
1.0
|
|
HB3
|
C:ASP101
|
4.9
|
23.5
|
1.0
|
|
CA
|
C:ASN103
|
4.9
|
16.6
|
1.0
|
|
O5
|
C:ZDC303
|
5.0
|
20.1
|
1.0
|
|
Calcium binding site 7 out
of 8 in 6s5p
Go back to
Calcium Binding Sites List in 6s5p
Calcium binding site 7 out
of 8 in the Cfucosylated Peptide SBL2 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 1.46 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Cfucosylated Peptide SBL2 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 1.46 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca304
b:17.1
occ:1.00
|
O
|
D:ASN21
|
2.3
|
19.0
|
1.0
|
|
H3O
|
C:ZDC305
|
2.3
|
23.2
|
1.0
|
|
OD1
|
D:ASP104
|
2.3
|
15.8
|
1.0
|
|
OD1
|
D:ASN103
|
2.4
|
17.0
|
1.0
|
|
O2
|
C:ZDC305
|
2.4
|
18.7
|
1.0
|
|
OD2
|
D:ASP101
|
2.4
|
17.7
|
1.0
|
|
O
|
C:GLY114
|
2.5
|
17.3
|
1.0
|
|
O3
|
C:ZDC305
|
2.5
|
19.4
|
1.0
|
|
H2O
|
C:ZDC305
|
2.8
|
22.5
|
1.0
|
|
CG
|
D:ASP101
|
3.1
|
16.6
|
1.0
|
|
OD1
|
D:ASP101
|
3.1
|
15.2
|
1.0
|
|
H4
|
C:ZDC305
|
3.2
|
22.1
|
1.0
|
|
HD21
|
D:ASN103
|
3.3
|
18.7
|
1.0
|
|
C3
|
C:ZDC305
|
3.3
|
16.6
|
1.0
|
|
C2
|
C:ZDC305
|
3.4
|
17.4
|
1.0
|
|
CG
|
D:ASN103
|
3.4
|
15.1
|
1.0
|
|
C
|
C:GLY114
|
3.5
|
18.4
|
1.0
|
|
C
|
D:ASN21
|
3.5
|
17.4
|
1.0
|
|
HA
|
D:ASP104
|
3.5
|
20.0
|
1.0
|
|
CG
|
D:ASP104
|
3.6
|
18.2
|
1.0
|
|
HB3
|
D:ASN21
|
3.7
|
24.0
|
1.0
|
|
H2
|
C:ZDC305
|
3.7
|
20.9
|
1.0
|
|
OXT
|
C:GLY114
|
3.7
|
20.8
|
1.0
|
|
C4
|
C:ZDC305
|
3.7
|
18.4
|
1.0
|
|
ND2
|
D:ASN103
|
3.7
|
15.5
|
1.0
|
|
CA
|
D:CA201
|
3.8
|
18.5
|
1.0
|
|
HA
|
D:SER22
|
3.8
|
21.6
|
1.0
|
|
HB2
|
D:ASN21
|
3.8
|
24.0
|
1.0
|
|
HB2
|
D:SER22
|
4.0
|
21.1
|
1.0
|
|
CB
|
D:ASN21
|
4.1
|
20.0
|
1.0
|
|
H3
|
C:ZDC305
|
4.2
|
19.9
|
1.0
|
|
CA
|
D:ASP104
|
4.2
|
16.6
|
1.0
|
|
H
|
D:ASN103
|
4.2
|
19.9
|
1.0
|
|
H4O
|
C:ZDC305
|
4.3
|
23.4
|
1.0
|
|
N
|
D:ASP104
|
4.3
|
16.6
|
1.0
|
|
O4
|
C:ZDC305
|
4.3
|
19.5
|
1.0
|
|
N
|
D:SER22
|
4.4
|
17.6
|
1.0
|
|
CA
|
D:SER22
|
4.4
|
18.0
|
1.0
|
|
OD2
|
D:ASP104
|
4.4
|
16.3
|
1.0
|
|
CB
|
D:ASP104
|
4.4
|
17.5
|
1.0
|
|
CA
|
D:ASN21
|
4.5
|
17.2
|
1.0
|
|
OD2
|
D:ASP99
|
4.5
|
18.1
|
1.0
|
|
C
|
D:ASN103
|
4.5
|
15.1
|
1.0
|
|
H
|
D:ASP104
|
4.5
|
20.0
|
1.0
|
|
CB
|
D:ASP101
|
4.6
|
17.8
|
1.0
|
|
HD22
|
D:ASN103
|
4.6
|
18.7
|
1.0
|
|
CB
|
D:SER22
|
4.7
|
17.7
|
1.0
|
|
HB3
|
D:ASP104
|
4.7
|
21.1
|
1.0
|
|
C1
|
C:ZDC305
|
4.7
|
19.4
|
1.0
|
|
HB2
|
D:ASP101
|
4.7
|
21.3
|
1.0
|
|
CB
|
D:ASN103
|
4.8
|
16.1
|
1.0
|
|
CA
|
C:GLY114
|
4.8
|
19.1
|
1.0
|
|
O
|
D:ASN103
|
4.9
|
15.9
|
1.0
|
|
O5
|
C:ZDC305
|
4.9
|
17.9
|
1.0
|
|
N
|
D:ASN103
|
5.0
|
16.6
|
1.0
|
|
HB3
|
D:ASP101
|
5.0
|
21.3
|
1.0
|
|
Calcium binding site 8 out
of 8 in 6s5p
Go back to
Calcium Binding Sites List in 6s5p
Calcium binding site 8 out
of 8 in the Cfucosylated Peptide SBL2 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 1.46 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Cfucosylated Peptide SBL2 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 1.46 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca201
b:18.5
occ:1.00
|
H4O
|
C:ZDC305
|
2.3
|
23.4
|
1.0
|
|
OD1
|
D:ASP99
|
2.3
|
17.4
|
1.0
|
|
OE2
|
D:GLU95
|
2.4
|
16.8
|
1.0
|
|
OD1
|
D:ASP101
|
2.4
|
15.2
|
1.0
|
|
OD2
|
D:ASP104
|
2.4
|
16.3
|
1.0
|
|
OE1
|
D:GLU95
|
2.4
|
16.6
|
1.0
|
|
O3
|
C:ZDC305
|
2.5
|
19.4
|
1.0
|
|
O4
|
C:ZDC305
|
2.5
|
19.5
|
1.0
|
|
OD1
|
D:ASP104
|
2.7
|
15.8
|
1.0
|
|
CD
|
D:GLU95
|
2.7
|
15.3
|
1.0
|
|
CG
|
D:ASP104
|
2.9
|
18.2
|
1.0
|
|
H3O
|
C:ZDC305
|
3.1
|
23.2
|
1.0
|
|
CG
|
D:ASP99
|
3.3
|
19.9
|
1.0
|
|
C4
|
C:ZDC305
|
3.3
|
18.4
|
1.0
|
|
C3
|
C:ZDC305
|
3.4
|
16.6
|
1.0
|
|
H
|
D:ASP101
|
3.4
|
19.8
|
1.0
|
|
CG
|
D:ASP101
|
3.5
|
16.6
|
1.0
|
|
H4
|
C:ZDC305
|
3.5
|
22.1
|
1.0
|
|
OD2
|
D:ASP99
|
3.6
|
18.1
|
1.0
|
|
H3
|
C:ZDC305
|
3.7
|
19.9
|
1.0
|
|
CA
|
C:CA304
|
3.8
|
17.1
|
1.0
|
|
H
|
D:ASP96
|
3.8
|
19.8
|
1.0
|
|
H
|
D:GLY97
|
3.8
|
20.9
|
1.0
|
|
HA
|
D:GLU95
|
3.9
|
19.9
|
1.0
|
|
H
|
D:ASP99
|
3.9
|
22.5
|
1.0
|
|
H
|
D:TYR102
|
3.9
|
19.6
|
1.0
|
|
OD1
|
D:ASP96
|
4.0
|
19.8
|
1.0
|
|
OD2
|
D:ASP101
|
4.0
|
17.7
|
1.0
|
|
H
|
D:ASN100
|
4.1
|
19.8
|
1.0
|
|
N
|
D:ASP101
|
4.2
|
16.4
|
1.0
|
|
CG
|
D:GLU95
|
4.2
|
17.2
|
1.0
|
|
CB
|
D:ASP104
|
4.4
|
17.5
|
1.0
|
|
N
|
D:GLY97
|
4.4
|
17.4
|
1.0
|
|
HA3
|
D:GLY97
|
4.5
|
23.0
|
1.0
|
|
N
|
D:ASP96
|
4.5
|
16.4
|
1.0
|
|
N
|
D:ASN100
|
4.5
|
16.5
|
1.0
|
|
N
|
D:TYR102
|
4.5
|
16.4
|
1.0
|
|
H
|
D:ASN103
|
4.5
|
19.9
|
1.0
|
|
HG3
|
D:GLU95
|
4.6
|
20.7
|
1.0
|
|
CB
|
D:ASP101
|
4.6
|
17.8
|
1.0
|
|
N
|
D:ASP99
|
4.6
|
18.8
|
1.0
|
|
CA
|
D:GLU95
|
4.7
|
16.6
|
1.0
|
|
CB
|
D:ASP99
|
4.7
|
19.5
|
1.0
|
|
OD1
|
D:ASN103
|
4.7
|
17.0
|
1.0
|
|
C2
|
C:ZDC305
|
4.7
|
17.4
|
1.0
|
|
H
|
D:ASP104
|
4.7
|
20.0
|
1.0
|
|
HG2
|
D:GLU95
|
4.7
|
20.7
|
1.0
|
|
HB2
|
D:ASP104
|
4.8
|
21.1
|
1.0
|
|
O2
|
C:ZDC305
|
4.8
|
18.7
|
1.0
|
|
CA
|
D:ASP101
|
4.8
|
15.0
|
1.0
|
|
C5
|
C:ZDC305
|
4.8
|
19.0
|
1.0
|
|
HB3
|
D:ASP104
|
4.8
|
21.1
|
1.0
|
|
H
|
D:THR98
|
4.8
|
22.6
|
1.0
|
|
CA
|
D:GLY97
|
4.9
|
19.1
|
1.0
|
|
CB
|
D:GLU95
|
4.9
|
18.0
|
1.0
|
|
HB3
|
D:ASP101
|
4.9
|
21.3
|
1.0
|
|
C
|
D:ASP99
|
4.9
|
19.8
|
1.0
|
|
CA
|
D:ASP99
|
5.0
|
20.0
|
1.0
|
|
HA
|
D:ASN100
|
5.0
|
18.1
|
1.0
|
|
HB2
|
D:GLU95
|
5.0
|
21.6
|
1.0
|
|
CG
|
D:ASP96
|
5.0
|
20.3
|
1.0
|
|
Reference:
S.Baeriswyl,
B.H.Gan,
T.N.Siriwardena,
R.Visini,
M.Robadey,
S.Javor,
A.Stocker,
T.Darbre,
J.L.Reymond.
X-Ray Crystal Structures of Short Antimicrobial Peptides As Pseudomonas Aeruginosa Lectin B Complexes. Acs Chem.Biol. V. 14 758 2019.
ISSN: ESSN 1554-8937
PubMed: 30830745
DOI: 10.1021/ACSCHEMBIO.9B00047
Page generated: Tue Jul 16 14:31:42 2024
|
