Calcium in PDB 5zru: Crystal Structure of Agl-Ka Catalytic Domain
Protein crystallography data
The structure of Crystal Structure of Agl-Ka Catalytic Domain, PDB code: 5zru
was solved by
S.Yano,
K.Makabe,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
19.95 /
1.83
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.247,
126.423,
80.540,
90.00,
97.83,
90.00
|
|
R / Rfree (%)
|
14.1 /
17.1
|
Other elements in 5zru:
The structure of Crystal Structure of Agl-Ka Catalytic Domain also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Agl-Ka Catalytic Domain
(pdb code 5zru). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the
Crystal Structure of Agl-Ka Catalytic Domain, PDB code: 5zru:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 10 in 5zru
Go back to
Calcium Binding Sites List in 5zru
Calcium binding site 1 out
of 10 in the Crystal Structure of Agl-Ka Catalytic Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structure of Agl-Ka Catalytic Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca606
b:14.6
occ:1.00
|
O
|
A:VAL192
|
2.4
|
15.0
|
1.0
|
|
OD1
|
A:ASP195
|
2.4
|
17.2
|
1.0
|
|
O
|
A:GLN197
|
2.4
|
15.1
|
1.0
|
|
OD1
|
A:ASP199
|
2.5
|
15.2
|
1.0
|
|
O
|
A:HOH787
|
2.5
|
17.6
|
1.0
|
|
OD2
|
A:ASP199
|
2.5
|
13.0
|
1.0
|
|
O
|
A:HOH768
|
2.5
|
15.0
|
1.0
|
|
CG
|
A:ASP199
|
2.8
|
13.2
|
1.0
|
|
CG
|
A:ASP195
|
3.4
|
20.9
|
1.0
|
|
C
|
A:GLN197
|
3.4
|
18.9
|
1.0
|
|
C
|
A:VAL192
|
3.5
|
12.6
|
1.0
|
|
OD2
|
A:ASP195
|
3.8
|
19.2
|
1.0
|
|
N
|
A:GLN197
|
3.8
|
17.2
|
1.0
|
|
N
|
A:VAL192
|
4.0
|
14.0
|
1.0
|
|
CA
|
A:GLN197
|
4.0
|
19.9
|
1.0
|
|
CB
|
A:GLN197
|
4.2
|
20.1
|
1.0
|
|
CA
|
A:VAL192
|
4.2
|
18.3
|
1.0
|
|
CB
|
A:ASP199
|
4.3
|
10.8
|
1.0
|
|
CB
|
A:VAL192
|
4.4
|
14.7
|
1.0
|
|
N
|
A:ASP198
|
4.5
|
12.5
|
1.0
|
|
O
|
A:HOH891
|
4.5
|
24.8
|
1.0
|
|
C
|
A:ASP198
|
4.5
|
14.3
|
1.0
|
|
N
|
A:ASP199
|
4.6
|
11.4
|
1.0
|
|
N
|
A:ALA193
|
4.6
|
13.0
|
1.0
|
|
N
|
A:ASP195
|
4.6
|
17.7
|
1.0
|
|
ND1
|
A:HIS225
|
4.6
|
13.9
|
1.0
|
|
N
|
A:HIS225
|
4.6
|
9.5
|
1.0
|
|
N
|
A:GLY196
|
4.7
|
20.2
|
1.0
|
|
CB
|
A:ASP195
|
4.7
|
19.4
|
1.0
|
|
O
|
A:ASP198
|
4.8
|
15.5
|
1.0
|
|
O
|
A:THR223
|
4.8
|
11.2
|
1.0
|
|
CA
|
A:ASP199
|
4.8
|
9.5
|
1.0
|
|
C
|
A:GLY196
|
4.8
|
19.9
|
1.0
|
|
CA
|
A:ALA193
|
4.8
|
13.6
|
1.0
|
|
CA
|
A:ASP198
|
4.9
|
15.0
|
1.0
|
|
CA
|
A:PHE224
|
4.9
|
10.0
|
1.0
|
|
C
|
A:ALA193
|
4.9
|
16.0
|
1.0
|
|
N
|
A:ASN194
|
5.0
|
14.9
|
1.0
|
|
CD1
|
A:PHE224
|
5.0
|
11.4
|
1.0
|
|
Calcium binding site 2 out
of 10 in 5zru
Go back to
Calcium Binding Sites List in 5zru
Calcium binding site 2 out
of 10 in the Crystal Structure of Agl-Ka Catalytic Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structure of Agl-Ka Catalytic Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca607
b:9.8
occ:1.00
|
O
|
A:SER112
|
2.3
|
10.3
|
1.0
|
|
O
|
A:HOH932
|
2.4
|
9.4
|
1.0
|
|
O
|
A:HOH845
|
2.4
|
10.7
|
1.0
|
|
O
|
A:TRP113
|
2.4
|
10.3
|
1.0
|
|
O
|
A:HOH1032
|
2.5
|
10.1
|
1.0
|
|
O
|
A:HOH790
|
2.5
|
11.6
|
1.0
|
|
O
|
A:HOH807
|
2.6
|
11.3
|
1.0
|
|
C
|
A:SER112
|
3.4
|
10.1
|
1.0
|
|
C
|
A:TRP113
|
3.5
|
9.9
|
1.0
|
|
CB
|
A:TRP113
|
3.7
|
9.7
|
1.0
|
|
O
|
A:TYR110
|
3.8
|
10.0
|
1.0
|
|
CA
|
A:TRP113
|
3.9
|
7.7
|
1.0
|
|
O
|
A:GLY86
|
3.9
|
13.0
|
1.0
|
|
N
|
A:TRP113
|
4.0
|
7.2
|
1.0
|
|
NE2
|
A:GLN114
|
4.3
|
7.9
|
1.0
|
|
O
|
A:SER109
|
4.4
|
9.9
|
1.0
|
|
O
|
A:ARG286
|
4.4
|
11.1
|
1.0
|
|
O
|
A:ASP123
|
4.4
|
12.9
|
1.0
|
|
OD2
|
A:ASP82
|
4.4
|
11.6
|
1.0
|
|
O
|
A:TYR111
|
4.5
|
8.2
|
1.0
|
|
N
|
A:SER112
|
4.6
|
8.2
|
1.0
|
|
CA
|
A:SER112
|
4.6
|
8.7
|
1.0
|
|
C
|
A:TYR111
|
4.6
|
9.2
|
1.0
|
|
N
|
A:GLN114
|
4.7
|
9.5
|
1.0
|
|
C
|
A:TYR110
|
4.7
|
9.8
|
1.0
|
|
OD1
|
A:ASP82
|
4.8
|
11.0
|
1.0
|
|
NE
|
A:ARG286
|
4.8
|
12.9
|
1.0
|
|
CG
|
A:ASP82
|
4.9
|
12.4
|
1.0
|
|
CB
|
A:ARG286
|
4.9
|
9.1
|
1.0
|
|
C
|
A:GLY86
|
5.0
|
16.4
|
1.0
|
|
Calcium binding site 3 out
of 10 in 5zru
Go back to
Calcium Binding Sites List in 5zru
Calcium binding site 3 out
of 10 in the Crystal Structure of Agl-Ka Catalytic Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Crystal Structure of Agl-Ka Catalytic Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca608
b:21.6
occ:1.00
|
O
|
A:HOH719
|
2.1
|
15.3
|
1.0
|
|
O
|
A:HOH902
|
2.2
|
24.9
|
1.0
|
|
O
|
A:HOH1162
|
2.3
|
30.6
|
1.0
|
|
O
|
A:HOH764
|
2.3
|
32.1
|
1.0
|
|
OD1
|
A:ASP349
|
2.3
|
19.4
|
1.0
|
|
OD1
|
A:ASP372
|
2.6
|
15.9
|
1.0
|
|
OD2
|
A:ASP349
|
2.7
|
18.6
|
1.0
|
|
CG
|
A:ASP372
|
2.8
|
18.7
|
1.0
|
|
CG
|
A:ASP349
|
2.8
|
18.2
|
1.0
|
|
OD2
|
A:ASP372
|
3.2
|
31.7
|
1.0
|
|
CB
|
A:ASP372
|
3.6
|
10.8
|
1.0
|
|
O
|
A:HOH1123
|
3.9
|
21.1
|
1.0
|
|
OD2
|
A:ASP373
|
4.0
|
12.9
|
1.0
|
|
N
|
A:ASP373
|
4.2
|
10.5
|
1.0
|
|
CB
|
A:ASP349
|
4.3
|
11.4
|
1.0
|
|
O
|
A:HOH1000
|
4.3
|
23.9
|
1.0
|
|
O
|
A:HOH1266
|
4.3
|
29.9
|
1.0
|
|
ND2
|
A:ASN352
|
4.6
|
11.3
|
1.0
|
|
N
|
A:ASP349
|
4.7
|
8.7
|
1.0
|
|
CA
|
A:ASP372
|
4.8
|
9.7
|
1.0
|
|
CG
|
A:ASP373
|
4.8
|
10.6
|
1.0
|
|
CB
|
A:ASP373
|
4.8
|
9.2
|
1.0
|
|
CA
|
A:ASP349
|
4.9
|
7.5
|
1.0
|
|
C
|
A:ASP372
|
5.0
|
10.8
|
1.0
|
|
Calcium binding site 4 out
of 10 in 5zru
Go back to
Calcium Binding Sites List in 5zru
Calcium binding site 4 out
of 10 in the Crystal Structure of Agl-Ka Catalytic Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Crystal Structure of Agl-Ka Catalytic Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca609
b:21.3
occ:1.00
|
OD1
|
A:ASN552
|
2.2
|
16.7
|
1.0
|
|
NE2
|
C:HIS278
|
2.2
|
13.5
|
1.0
|
|
O
|
C:HOH709
|
2.2
|
26.7
|
1.0
|
|
O
|
C:HOH1214
|
2.8
|
21.3
|
1.0
|
|
CG
|
A:ASN552
|
3.1
|
13.3
|
1.0
|
|
CD2
|
C:HIS278
|
3.1
|
12.1
|
1.0
|
|
CE1
|
C:HIS278
|
3.1
|
12.3
|
1.0
|
|
ND2
|
A:ASN552
|
3.3
|
15.6
|
1.0
|
|
CG2
|
A:THR554
|
3.8
|
16.7
|
1.0
|
|
OD1
|
C:ASN2
|
4.0
|
18.1
|
1.0
|
|
CE1
|
C:HIS309
|
4.0
|
12.5
|
1.0
|
|
O
|
A:HOH882
|
4.1
|
19.0
|
1.0
|
|
O
|
A:HOH914
|
4.1
|
14.1
|
1.0
|
|
ND1
|
C:HIS278
|
4.2
|
11.0
|
1.0
|
|
CG
|
C:HIS278
|
4.3
|
11.3
|
1.0
|
|
CB
|
A:ASN552
|
4.5
|
10.4
|
1.0
|
|
ND1
|
C:HIS309
|
4.6
|
13.4
|
1.0
|
|
O
|
C:HOH1097
|
4.6
|
19.3
|
1.0
|
|
OD1
|
C:ASN310
|
4.7
|
11.5
|
1.0
|
|
CG
|
C:ASN310
|
4.9
|
11.6
|
1.0
|
|
O
|
A:ASN552
|
4.9
|
12.9
|
1.0
|
|
CG
|
C:ASN2
|
4.9
|
17.4
|
1.0
|
|
CA
|
A:ASN552
|
4.9
|
11.4
|
1.0
|
|
CD1
|
C:ILE177
|
5.0
|
9.4
|
1.0
|
|
Calcium binding site 5 out
of 10 in 5zru
Go back to
Calcium Binding Sites List in 5zru
Calcium binding site 5 out
of 10 in the Crystal Structure of Agl-Ka Catalytic Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of Agl-Ka Catalytic Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca610
b:23.0
occ:1.00
|
NE2
|
A:HIS278
|
2.2
|
14.3
|
1.0
|
|
O
|
A:HOH709
|
2.2
|
23.8
|
1.0
|
|
O
|
A:HOH1175
|
2.4
|
21.4
|
1.0
|
|
CD2
|
A:HIS278
|
3.1
|
11.3
|
1.0
|
|
CE1
|
A:HIS278
|
3.2
|
12.6
|
1.0
|
|
OD1
|
A:ASN2
|
4.0
|
14.1
|
1.0
|
|
CE1
|
A:HIS309
|
4.0
|
9.7
|
1.0
|
|
ND1
|
A:HIS278
|
4.3
|
9.4
|
1.0
|
|
CG
|
A:HIS278
|
4.3
|
9.6
|
1.0
|
|
O
|
A:HOH1121
|
4.6
|
14.6
|
1.0
|
|
OD1
|
A:ASN310
|
4.6
|
13.1
|
1.0
|
|
ND1
|
A:HIS309
|
4.6
|
10.8
|
1.0
|
|
CG
|
A:ASN310
|
4.8
|
10.8
|
1.0
|
|
CD1
|
A:ILE177
|
5.0
|
13.3
|
1.0
|
|
CG
|
A:ASN2
|
5.0
|
16.6
|
1.0
|
|
Calcium binding site 6 out
of 10 in 5zru
Go back to
Calcium Binding Sites List in 5zru
Calcium binding site 6 out
of 10 in the Crystal Structure of Agl-Ka Catalytic Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Crystal Structure of Agl-Ka Catalytic Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca611
b:19.6
occ:1.00
|
O
|
A:ARG50
|
2.3
|
9.3
|
1.0
|
|
OD1
|
A:ASP166
|
2.4
|
12.5
|
1.0
|
|
O
|
A:SER47
|
2.4
|
12.0
|
1.0
|
|
OG1
|
A:THR20
|
2.5
|
14.2
|
1.0
|
|
O
|
A:HOH1114
|
2.5
|
17.2
|
1.0
|
|
OG
|
A:SER47
|
2.7
|
23.2
|
1.0
|
|
OD1
|
A:ASP19
|
2.8
|
19.7
|
1.0
|
|
C
|
A:SER47
|
3.3
|
15.3
|
1.0
|
|
CB
|
A:THR20
|
3.4
|
16.6
|
1.0
|
|
C
|
A:ARG50
|
3.5
|
12.4
|
1.0
|
|
CG
|
A:ASP166
|
3.6
|
11.6
|
1.0
|
|
N
|
A:SER47
|
3.8
|
10.6
|
1.0
|
|
CB
|
A:SER47
|
3.8
|
15.8
|
1.0
|
|
CA
|
A:SER47
|
3.9
|
10.7
|
1.0
|
|
CG
|
A:ASP19
|
3.9
|
26.7
|
1.0
|
|
O
|
A:ASP166
|
4.0
|
10.6
|
1.0
|
|
OD2
|
A:ASP166
|
4.2
|
12.2
|
1.0
|
|
N
|
A:THR20
|
4.2
|
13.9
|
1.0
|
|
N
|
A:ARG50
|
4.3
|
10.9
|
1.0
|
|
CA
|
A:ARG50
|
4.3
|
11.7
|
1.0
|
|
OD2
|
A:ASP19
|
4.3
|
29.0
|
1.0
|
|
O
|
A:HOH1156
|
4.4
|
30.4
|
1.0
|
|
CB
|
A:ARG50
|
4.4
|
17.1
|
1.0
|
|
CG2
|
A:THR20
|
4.4
|
16.5
|
1.0
|
|
CB
|
A:ALA46
|
4.4
|
9.2
|
1.0
|
|
CA
|
A:THR20
|
4.5
|
12.8
|
1.0
|
|
N
|
A:TYR51
|
4.5
|
12.1
|
1.0
|
|
N
|
A:GLY48
|
4.5
|
12.5
|
1.0
|
|
C
|
A:ALA46
|
4.5
|
10.2
|
1.0
|
|
CA
|
A:TYR51
|
4.5
|
11.6
|
1.0
|
|
C
|
A:ASP166
|
4.6
|
12.1
|
1.0
|
|
CA
|
A:ASP166
|
4.6
|
8.2
|
1.0
|
|
CB
|
A:ASP166
|
4.7
|
8.2
|
1.0
|
|
O
|
A:HOH954
|
4.7
|
22.4
|
1.0
|
|
CA
|
A:GLY48
|
4.9
|
13.0
|
1.0
|
|
CB
|
A:TYR51
|
4.9
|
10.2
|
1.0
|
|
Calcium binding site 7 out
of 10 in 5zru
Go back to
Calcium Binding Sites List in 5zru
Calcium binding site 7 out
of 10 in the Crystal Structure of Agl-Ka Catalytic Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Crystal Structure of Agl-Ka Catalytic Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca606
b:14.4
occ:1.00
|
O
|
C:VAL192
|
2.3
|
13.0
|
1.0
|
|
O
|
C:HOH935
|
2.4
|
13.4
|
1.0
|
|
OD1
|
C:ASP195
|
2.4
|
14.4
|
1.0
|
|
O
|
C:GLN197
|
2.4
|
17.8
|
1.0
|
|
OD2
|
C:ASP199
|
2.5
|
12.4
|
1.0
|
|
O
|
C:HOH912
|
2.5
|
18.6
|
1.0
|
|
OD1
|
C:ASP199
|
2.6
|
13.0
|
1.0
|
|
CG
|
C:ASP199
|
2.8
|
14.0
|
1.0
|
|
CG
|
C:ASP195
|
3.5
|
20.8
|
1.0
|
|
C
|
C:GLN197
|
3.5
|
20.5
|
1.0
|
|
C
|
C:VAL192
|
3.5
|
14.0
|
1.0
|
|
N
|
C:GLN197
|
3.8
|
20.5
|
1.0
|
|
OD2
|
C:ASP195
|
3.9
|
18.9
|
1.0
|
|
CA
|
C:GLN197
|
4.0
|
19.3
|
1.0
|
|
N
|
C:VAL192
|
4.0
|
12.7
|
1.0
|
|
CB
|
C:GLN197
|
4.1
|
22.2
|
1.0
|
|
CA
|
C:VAL192
|
4.2
|
15.5
|
1.0
|
|
CB
|
C:ASP199
|
4.3
|
12.0
|
1.0
|
|
CB
|
C:VAL192
|
4.4
|
15.6
|
1.0
|
|
C
|
C:ASP198
|
4.5
|
17.1
|
1.0
|
|
N
|
C:ASP198
|
4.6
|
16.7
|
1.0
|
|
N
|
C:ASP195
|
4.6
|
18.8
|
1.0
|
|
N
|
C:ALA193
|
4.6
|
16.4
|
1.0
|
|
N
|
C:HIS225
|
4.6
|
10.4
|
1.0
|
|
N
|
C:ASP199
|
4.6
|
12.1
|
1.0
|
|
O
|
C:HOH834
|
4.6
|
24.0
|
1.0
|
|
N
|
C:GLY196
|
4.7
|
19.7
|
1.0
|
|
O
|
C:ASP198
|
4.7
|
19.6
|
1.0
|
|
ND1
|
C:HIS225
|
4.7
|
14.2
|
1.0
|
|
CB
|
C:ASP195
|
4.7
|
16.2
|
1.0
|
|
C
|
C:GLY196
|
4.7
|
21.4
|
1.0
|
|
O
|
C:THR223
|
4.8
|
13.5
|
1.0
|
|
CA
|
C:ALA193
|
4.8
|
13.8
|
1.0
|
|
CA
|
C:ASP199
|
4.9
|
11.2
|
1.0
|
|
C
|
C:ALA193
|
4.9
|
16.6
|
1.0
|
|
CA
|
C:PHE224
|
4.9
|
10.1
|
1.0
|
|
N
|
C:ASN194
|
4.9
|
13.0
|
1.0
|
|
CD2
|
C:PHE224
|
4.9
|
12.7
|
1.0
|
|
C
|
C:ASP195
|
4.9
|
21.8
|
1.0
|
|
CA
|
C:ASP198
|
4.9
|
17.2
|
1.0
|
|
CA
|
C:ASP195
|
5.0
|
22.0
|
1.0
|
|
Calcium binding site 8 out
of 10 in 5zru
Go back to
Calcium Binding Sites List in 5zru
Calcium binding site 8 out
of 10 in the Crystal Structure of Agl-Ka Catalytic Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Crystal Structure of Agl-Ka Catalytic Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca607
b:9.0
occ:1.00
|
O
|
C:SER112
|
2.3
|
8.8
|
1.0
|
|
O
|
C:HOH922
|
2.3
|
9.1
|
1.0
|
|
O
|
C:TRP113
|
2.4
|
9.8
|
1.0
|
|
O
|
C:HOH739
|
2.4
|
11.4
|
1.0
|
|
O
|
C:HOH754
|
2.4
|
10.7
|
1.0
|
|
O
|
C:HOH1062
|
2.5
|
9.1
|
1.0
|
|
O
|
C:HOH788
|
2.6
|
12.4
|
1.0
|
|
C
|
C:SER112
|
3.4
|
8.5
|
1.0
|
|
C
|
C:TRP113
|
3.4
|
8.0
|
1.0
|
|
CB
|
C:TRP113
|
3.8
|
8.6
|
1.0
|
|
CA
|
C:TRP113
|
3.9
|
8.9
|
1.0
|
|
O
|
C:TYR110
|
3.9
|
8.8
|
1.0
|
|
O
|
C:GLY86
|
4.0
|
11.0
|
1.0
|
|
N
|
C:TRP113
|
4.0
|
7.9
|
1.0
|
|
NE2
|
C:GLN114
|
4.3
|
8.2
|
1.0
|
|
O
|
C:ARG286
|
4.4
|
11.6
|
1.0
|
|
O
|
C:ASP123
|
4.4
|
12.0
|
1.0
|
|
O
|
C:TYR111
|
4.4
|
9.2
|
1.0
|
|
OD2
|
C:ASP82
|
4.4
|
12.9
|
1.0
|
|
O
|
C:SER109
|
4.4
|
10.4
|
1.0
|
|
CA
|
C:SER112
|
4.6
|
8.4
|
1.0
|
|
C
|
C:TYR111
|
4.6
|
10.5
|
1.0
|
|
N
|
C:SER112
|
4.6
|
9.0
|
1.0
|
|
N
|
C:GLN114
|
4.6
|
9.4
|
1.0
|
|
C
|
C:TYR110
|
4.8
|
10.0
|
1.0
|
|
OD1
|
C:ASP82
|
4.9
|
9.5
|
1.0
|
|
NE
|
C:ARG286
|
4.9
|
13.6
|
1.0
|
|
CG
|
C:ASP82
|
4.9
|
11.6
|
1.0
|
|
CB
|
C:ARG286
|
5.0
|
9.3
|
1.0
|
|
Calcium binding site 9 out
of 10 in 5zru
Go back to
Calcium Binding Sites List in 5zru
Calcium binding site 9 out
of 10 in the Crystal Structure of Agl-Ka Catalytic Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Crystal Structure of Agl-Ka Catalytic Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca608
b:22.9
occ:1.00
|
O
|
C:HOH706
|
2.1
|
13.7
|
1.0
|
|
O
|
C:HOH795
|
2.2
|
22.1
|
1.0
|
|
OD1
|
C:ASP349
|
2.2
|
20.4
|
1.0
|
|
O
|
C:HOH1174
|
2.3
|
31.8
|
1.0
|
|
OD1
|
C:ASP372
|
2.6
|
16.9
|
1.0
|
|
OD2
|
C:ASP349
|
2.7
|
18.0
|
1.0
|
|
CG
|
C:ASP349
|
2.8
|
14.2
|
1.0
|
|
CG
|
C:ASP372
|
2.8
|
16.3
|
1.0
|
|
OD2
|
C:ASP372
|
3.2
|
27.3
|
1.0
|
|
CB
|
C:ASP372
|
3.6
|
10.2
|
1.0
|
|
O
|
C:HOH1106
|
3.9
|
19.4
|
1.0
|
|
OD2
|
C:ASP373
|
3.9
|
10.3
|
1.0
|
|
O
|
C:HOH1263
|
4.0
|
35.0
|
1.0
|
|
O
|
C:HOH974
|
4.1
|
26.4
|
1.0
|
|
CB
|
C:ASP349
|
4.3
|
10.8
|
1.0
|
|
N
|
C:ASP373
|
4.3
|
8.9
|
1.0
|
|
ND2
|
C:ASN352
|
4.5
|
12.0
|
1.0
|
|
CG
|
C:ASP373
|
4.7
|
11.4
|
1.0
|
|
CB
|
C:ASP373
|
4.8
|
7.9
|
1.0
|
|
N
|
C:ASP349
|
4.8
|
7.9
|
1.0
|
|
CA
|
C:ASP372
|
4.8
|
10.3
|
1.0
|
|
CA
|
C:ASP349
|
4.9
|
9.2
|
1.0
|
|
CZ3
|
C:TRP321
|
4.9
|
14.1
|
1.0
|
|
C
|
C:ASP372
|
5.0
|
9.3
|
1.0
|
|
Calcium binding site 10 out
of 10 in 5zru
Go back to
Calcium Binding Sites List in 5zru
Calcium binding site 10 out
of 10 in the Crystal Structure of Agl-Ka Catalytic Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Crystal Structure of Agl-Ka Catalytic Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca609
b:17.6
occ:1.00
|
OD1
|
C:ASP166
|
2.3
|
12.7
|
1.0
|
|
O
|
C:ARG50
|
2.4
|
11.1
|
1.0
|
|
O
|
C:SER47
|
2.4
|
9.4
|
1.0
|
|
OG1
|
C:THR20
|
2.4
|
14.6
|
1.0
|
|
O
|
C:HOH1131
|
2.5
|
14.9
|
1.0
|
|
OG
|
C:SER47
|
2.6
|
16.2
|
1.0
|
|
OD1
|
C:ASP19
|
2.8
|
16.4
|
1.0
|
|
C
|
C:SER47
|
3.3
|
12.0
|
1.0
|
|
CB
|
C:THR20
|
3.5
|
15.4
|
1.0
|
|
CG
|
C:ASP166
|
3.5
|
12.1
|
1.0
|
|
C
|
C:ARG50
|
3.5
|
12.1
|
1.0
|
|
CB
|
C:SER47
|
3.7
|
13.0
|
1.0
|
|
N
|
C:SER47
|
3.8
|
8.7
|
1.0
|
|
CA
|
C:SER47
|
3.8
|
8.8
|
1.0
|
|
CG
|
C:ASP19
|
3.8
|
22.2
|
1.0
|
|
O
|
C:ASP166
|
4.1
|
11.4
|
1.0
|
|
OD2
|
C:ASP166
|
4.1
|
12.2
|
1.0
|
|
OD2
|
C:ASP19
|
4.2
|
27.4
|
1.0
|
|
N
|
C:THR20
|
4.3
|
13.1
|
1.0
|
|
N
|
C:ARG50
|
4.3
|
11.0
|
1.0
|
|
CA
|
C:ARG50
|
4.3
|
12.0
|
1.0
|
|
O
|
C:HOH1166
|
4.4
|
23.3
|
1.0
|
|
CB
|
C:ALA46
|
4.4
|
9.1
|
1.0
|
|
CB
|
C:ARG50
|
4.5
|
16.4
|
1.0
|
|
CG2
|
C:THR20
|
4.5
|
14.2
|
1.0
|
|
N
|
C:GLY48
|
4.5
|
11.3
|
1.0
|
|
N
|
C:TYR51
|
4.5
|
8.4
|
1.0
|
|
C
|
C:ALA46
|
4.5
|
8.9
|
1.0
|
|
CA
|
C:THR20
|
4.5
|
15.2
|
1.0
|
|
CA
|
C:TYR51
|
4.6
|
10.8
|
1.0
|
|
C
|
C:ASP166
|
4.6
|
10.1
|
1.0
|
|
CA
|
C:ASP166
|
4.6
|
10.0
|
1.0
|
|
CB
|
C:ASP166
|
4.7
|
9.8
|
1.0
|
|
O
|
C:HOH1075
|
4.8
|
17.3
|
1.0
|
|
CA
|
C:GLY48
|
4.9
|
12.6
|
1.0
|
|
CB
|
C:TYR51
|
5.0
|
9.8
|
1.0
|
|
Reference:
S.Yano,
K.Makabe.
Crystal Structure of Alpha-1,3-Glucanase To Be Published.
Page generated: Wed Jul 9 12:17:15 2025
|
