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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:

Iron (Fe) 11 atoms

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

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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

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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

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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

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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: Thu Jul 10 00:37:23 2025

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