Calcium in PDB 7qth: Crystal Structure of the Shewanella Oneidensis MR1 Mtrc Mutant C453A
Protein crystallography data
The structure of Crystal Structure of the Shewanella Oneidensis MR1 Mtrc Mutant C453A, PDB code: 7qth
was solved by
M.J.Edwards,
T.A.Clarke,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
77.73 /
1.90
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
53.061,
89.797,
154.286,
90,
90,
90
|
R / Rfree (%)
|
15.1 /
19.6
|
Other elements in 7qth:
The structure of Crystal Structure of the Shewanella Oneidensis MR1 Mtrc Mutant C453A also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of the Shewanella Oneidensis MR1 Mtrc Mutant C453A
(pdb code 7qth). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the
Crystal Structure of the Shewanella Oneidensis MR1 Mtrc Mutant C453A, PDB code: 7qth:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
Calcium binding site 1 out
of 5 in 7qth
Go back to
Calcium Binding Sites List in 7qth
Calcium binding site 1 out
of 5 in the Crystal Structure of the Shewanella Oneidensis MR1 Mtrc Mutant C453A
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 the Shewanella Oneidensis MR1 Mtrc Mutant C453A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca811
b:10.5
occ:1.00
|
O
|
A:ILE53
|
2.2
|
11.5
|
1.0
|
OE2
|
A:GLU165
|
2.3
|
10.3
|
1.0
|
O
|
A:HOH1211
|
2.4
|
9.8
|
1.0
|
O
|
A:HOH1510
|
2.4
|
10.1
|
1.0
|
OD1
|
A:ASP52
|
2.4
|
12.3
|
1.0
|
OE1
|
A:GLU165
|
2.4
|
11.6
|
1.0
|
O
|
A:HOH1501
|
2.4
|
11.9
|
1.0
|
CD
|
A:GLU165
|
2.7
|
10.0
|
1.0
|
C
|
A:ILE53
|
3.4
|
11.3
|
1.0
|
CG
|
A:ASP52
|
3.4
|
13.0
|
1.0
|
OD2
|
A:ASP52
|
3.9
|
12.1
|
1.0
|
N
|
A:ILE53
|
4.1
|
11.1
|
1.0
|
O
|
A:HOH1333
|
4.1
|
18.6
|
1.0
|
CA
|
A:ILE53
|
4.2
|
10.5
|
1.0
|
CG
|
A:GLU165
|
4.2
|
9.5
|
1.0
|
N
|
A:THR54
|
4.3
|
11.1
|
1.0
|
CA
|
A:THR54
|
4.4
|
11.7
|
1.0
|
CZ
|
A:PHE167
|
4.7
|
11.9
|
1.0
|
O
|
A:HOH1195
|
4.7
|
15.7
|
1.0
|
CB
|
A:ILE53
|
4.7
|
10.1
|
1.0
|
CB
|
A:ASP52
|
4.7
|
13.2
|
1.0
|
O
|
A:HOH1551
|
4.8
|
29.9
|
1.0
|
C
|
A:ASP52
|
4.8
|
12.1
|
1.0
|
O
|
A:HOH1123
|
4.8
|
20.6
|
1.0
|
CE1
|
A:PHE167
|
4.9
|
11.9
|
1.0
|
O
|
A:HOH1654
|
4.9
|
12.0
|
1.0
|
CA
|
A:ASP52
|
5.0
|
12.2
|
1.0
|
|
Calcium binding site 2 out
of 5 in 7qth
Go back to
Calcium Binding Sites List in 7qth
Calcium binding site 2 out
of 5 in the Crystal Structure of the Shewanella Oneidensis MR1 Mtrc Mutant C453A
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 the Shewanella Oneidensis MR1 Mtrc Mutant C453A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca812
b:9.6
occ:0.50
|
O
|
A:ASN231
|
2.3
|
10.1
|
1.0
|
OD1
|
A:ASN231
|
2.3
|
12.2
|
1.0
|
O
|
A:ASN234
|
2.3
|
12.1
|
1.0
|
O
|
A:HOH1204
|
2.4
|
11.8
|
1.0
|
O
|
A:LYS237
|
2.4
|
13.9
|
1.0
|
C
|
A:ASN231
|
3.2
|
10.3
|
1.0
|
CG
|
A:ASN231
|
3.4
|
11.6
|
1.0
|
CA
|
A:ASN231
|
3.5
|
10.2
|
1.0
|
C
|
A:LYS237
|
3.5
|
15.1
|
1.0
|
C
|
A:ASN234
|
3.5
|
11.5
|
1.0
|
CG
|
A:LYS237
|
3.8
|
15.8
|
1.0
|
N
|
A:LYS237
|
3.8
|
14.7
|
1.0
|
CG
|
A:PRO246
|
3.9
|
16.6
|
1.0
|
CB
|
A:ASN231
|
4.1
|
10.7
|
1.0
|
CA
|
A:LYS237
|
4.1
|
15.4
|
1.0
|
CD
|
A:PRO246
|
4.2
|
16.6
|
1.0
|
CA
|
A:ASN234
|
4.3
|
11.5
|
1.0
|
OD1
|
A:ASN234
|
4.3
|
11.6
|
1.0
|
N
|
A:ASN234
|
4.3
|
11.2
|
1.0
|
CB
|
A:ASN234
|
4.4
|
11.4
|
1.0
|
N
|
A:VAL232
|
4.4
|
9.7
|
1.0
|
CB
|
A:LYS237
|
4.5
|
15.6
|
1.0
|
ND2
|
A:ASN231
|
4.5
|
11.3
|
1.0
|
N
|
A:ALA235
|
4.5
|
12.9
|
1.0
|
N
|
A:ASN236
|
4.5
|
13.9
|
1.0
|
N
|
A:ALA238
|
4.6
|
14.5
|
1.0
|
O
|
A:SER284
|
4.6
|
11.7
|
1.0
|
CA
|
A:ALA235
|
4.8
|
14.3
|
1.0
|
N
|
A:ASN231
|
4.8
|
9.9
|
1.0
|
C
|
A:ALA235
|
4.8
|
14.6
|
1.0
|
O
|
A:HIS230
|
4.8
|
10.2
|
1.0
|
CG
|
A:ASN234
|
4.9
|
10.7
|
1.0
|
CA
|
A:VAL232
|
4.9
|
10.6
|
1.0
|
C
|
A:ALA238
|
4.9
|
15.2
|
1.0
|
C
|
A:ASN236
|
4.9
|
15.6
|
1.0
|
O
|
A:ALA238
|
5.0
|
15.6
|
1.0
|
CA
|
A:ALA238
|
5.0
|
15.5
|
1.0
|
CE
|
A:LYS237
|
5.0
|
14.7
|
1.0
|
CD
|
A:LYS237
|
5.0
|
15.9
|
1.0
|
|
Calcium binding site 3 out
of 5 in 7qth
Go back to
Calcium Binding Sites List in 7qth
Calcium binding site 3 out
of 5 in the Crystal Structure of the Shewanella Oneidensis MR1 Mtrc Mutant C453A
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 the Shewanella Oneidensis MR1 Mtrc Mutant C453A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca813
b:15.3
occ:1.00
|
OD1
|
A:ASP472
|
2.3
|
14.0
|
1.0
|
O
|
A:GLN520
|
2.4
|
14.1
|
1.0
|
O
|
A:HOH1289
|
2.4
|
17.5
|
1.0
|
O
|
A:HOH1607
|
2.4
|
13.7
|
1.0
|
O
|
A:HOH1323
|
2.4
|
21.2
|
1.0
|
O
|
A:HOH1179
|
2.5
|
15.7
|
1.0
|
O
|
A:HOH1474
|
2.6
|
25.6
|
1.0
|
OD2
|
A:ASP472
|
3.0
|
16.3
|
1.0
|
CG
|
A:ASP472
|
3.0
|
14.8
|
1.0
|
C
|
A:GLN520
|
3.5
|
15.3
|
1.0
|
O
|
A:LEU473
|
4.2
|
13.8
|
1.0
|
CA
|
A:GLN520
|
4.2
|
16.0
|
1.0
|
O
|
A:HOH1647
|
4.3
|
36.8
|
1.0
|
O
|
A:HOH1585
|
4.3
|
39.0
|
1.0
|
N
|
A:LEU521
|
4.4
|
15.0
|
1.0
|
CB
|
A:ASP472
|
4.5
|
15.0
|
1.0
|
O
|
A:HOH1687
|
4.5
|
16.3
|
1.0
|
CB
|
A:GLN520
|
4.5
|
16.0
|
1.0
|
O
|
A:HOH1169
|
4.5
|
24.6
|
1.0
|
CA
|
A:LEU521
|
4.6
|
16.3
|
1.0
|
N
|
A:THR337
|
4.6
|
16.8
|
1.0
|
O
|
A:HOH1736
|
4.6
|
41.3
|
1.0
|
O
|
A:HOH1350
|
4.6
|
25.6
|
1.0
|
O
|
A:ILE335
|
4.8
|
16.9
|
1.0
|
N
|
A:LEU473
|
4.8
|
13.0
|
1.0
|
O
|
A:THR337
|
4.9
|
13.9
|
1.0
|
CA
|
A:GLU336
|
4.9
|
17.1
|
1.0
|
|
Calcium binding site 4 out
of 5 in 7qth
Go back to
Calcium Binding Sites List in 7qth
Calcium binding site 4 out
of 5 in the Crystal Structure of the Shewanella Oneidensis MR1 Mtrc Mutant C453A
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 the Shewanella Oneidensis MR1 Mtrc Mutant C453A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca814
b:10.8
occ:0.50
|
O
|
A:HOH1415
|
2.1
|
27.5
|
1.0
|
O
|
A:HOH1296
|
2.3
|
30.6
|
1.0
|
O
|
A:ACT825
|
2.3
|
33.1
|
1.0
|
O
|
A:GLU162
|
2.3
|
10.8
|
1.0
|
OE1
|
A:GLU202
|
2.4
|
15.3
|
1.0
|
OE2
|
A:GLU202
|
2.4
|
20.1
|
1.0
|
O
|
A:HOH1048
|
2.4
|
21.9
|
1.0
|
CD
|
A:GLU202
|
2.7
|
16.4
|
1.0
|
C
|
A:ACT825
|
3.4
|
35.8
|
1.0
|
C
|
A:GLU162
|
3.5
|
12.3
|
1.0
|
CH3
|
A:ACT825
|
3.9
|
34.4
|
1.0
|
N
|
A:GLU162
|
4.1
|
12.6
|
1.0
|
O
|
A:HOH951
|
4.1
|
16.6
|
1.0
|
CG
|
A:GLU202
|
4.2
|
14.9
|
1.0
|
CA
|
A:GLU162
|
4.3
|
12.3
|
1.0
|
NE2
|
A:HIS183
|
4.5
|
18.2
|
1.0
|
N
|
A:MET163
|
4.5
|
12.2
|
1.0
|
O
|
A:HOH1325
|
4.5
|
38.1
|
1.0
|
OXT
|
A:ACT825
|
4.5
|
36.5
|
1.0
|
CE1
|
A:HIS183
|
4.5
|
20.3
|
1.0
|
CA
|
A:MET163
|
4.6
|
12.6
|
1.0
|
CB
|
A:MET163
|
4.7
|
14.3
|
1.0
|
O
|
A:HOH1294
|
4.7
|
34.4
|
1.0
|
CB
|
A:GLU162
|
4.8
|
12.6
|
1.0
|
O
|
A:HOH1506
|
4.8
|
11.4
|
1.0
|
CD2
|
A:HIS183
|
4.9
|
18.6
|
1.0
|
O
|
A:HOH1107
|
5.0
|
28.9
|
1.0
|
ND1
|
A:HIS183
|
5.0
|
18.9
|
1.0
|
|
Calcium binding site 5 out
of 5 in 7qth
Go back to
Calcium Binding Sites List in 7qth
Calcium binding site 5 out
of 5 in the Crystal Structure of the Shewanella Oneidensis MR1 Mtrc Mutant C453A
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 the Shewanella Oneidensis MR1 Mtrc Mutant C453A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca815
b:31.8
occ:1.00
|
O
|
A:GLN651
|
2.3
|
15.9
|
1.0
|
O
|
A:HOH1387
|
2.4
|
32.4
|
1.0
|
O
|
A:HOH1606
|
2.5
|
24.3
|
1.0
|
O
|
A:HOH1175
|
2.5
|
23.4
|
1.0
|
O
|
A:HOH1724
|
2.6
|
28.0
|
1.0
|
O
|
A:HOH1610
|
2.7
|
25.2
|
1.0
|
C
|
A:GLN651
|
3.5
|
16.8
|
1.0
|
CB
|
A:GLN651
|
4.4
|
17.1
|
1.0
|
N
|
A:SER652
|
4.4
|
15.8
|
1.0
|
O
|
A:HOH1274
|
4.4
|
14.9
|
1.0
|
CA
|
A:GLN651
|
4.5
|
15.3
|
1.0
|
CA
|
A:SER652
|
4.5
|
16.7
|
1.0
|
O
|
A:HOH1242
|
4.6
|
32.6
|
1.0
|
O
|
A:HOH1653
|
4.6
|
39.0
|
1.0
|
O
|
A:HOH1730
|
4.8
|
44.3
|
1.0
|
|
Reference:
M.Norman,
M.J.Edwards,
T.A.Clarke.
An Oxygen Sensitive Switch Prevents Peroxide Formation From Extracellular Flavocytochromes in Shewanella Oneidensis To Be Published.
Page generated: Fri Jul 19 03:32:05 2024
|