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Calcium in PDB 8qbq: Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc (A430BOC-Lys)

Protein crystallography data

The structure of Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc (A430BOC-Lys), PDB code: 8qbq was solved by B.W.Nash, C.J.Lockwood, K.Whiting, J.N.Butt, T.A.Clarke, M.J.Edwards, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.80 / 1.81
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.904, 89.609, 154.031, 90, 90, 90
R / Rfree (%) 15.5 / 18.7

Other elements in 8qbq:

The structure of Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc (A430BOC-Lys) also contains other interesting chemical elements:

Iron (Fe) 10 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc (A430BOC-Lys) (pdb code 8qbq). 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 Outer Membrane Decaheme Cytochrome Mtrc (A430BOC-Lys), PDB code: 8qbq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 8qbq

Go back to Calcium Binding Sites List in 8qbq
Calcium binding site 1 out of 5 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc (A430BOC-Lys)


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 Outer Membrane Decaheme Cytochrome Mtrc (A430BOC-Lys) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca715

b:12.6
occ:1.00
 O A:ILE53 2.3 12.7 1.0
O A:HOH974 2.4 12.5 1.0
OD1 A:ASP52 2.4 11.7 1.0
OE2 A:GLU165 2.4 14.2 1.0
O A:HOH1458 2.4 14.4 1.0
O A:HOH1509 2.4 14.8 1.0
OE1 A:GLU165 2.6 12.8 1.0
CD A:GLU165 2.8 14.1 1.0
C A:ILE53 3.4 14.7 1.0
CG A:ASP52 3.5 16.5 1.0
OD2 A:ASP52 3.8 14.6 1.0
N A:ILE53 4.1 11.4 1.0
O A:HOH1081 4.2 17.0 1.0
CA A:ILE53 4.3 11.1 1.0
N A:THR54 4.3 13.2 1.0
CG A:GLU165 4.3 11.6 1.0
CA A:THR54 4.4 12.2 1.0
O A:HOH1009 4.6 17.6 1.0
CZ A:PHE167 4.7 13.7 1.0
CB A:ILE53 4.7 12.4 1.0
O A:HOH1461 4.8 27.4 1.0
CB A:ASP52 4.8 13.4 1.0
C A:ASP52 4.8 13.4 1.0
CE2 A:PHE167 4.8 12.1 1.0
O A:HOH1060 4.9 15.8 1.0
O A:HOH1631 4.9 12.9 1.0

Calcium binding site 2 out of 5 in 8qbq

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Calcium binding site 2 out of 5 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc (A430BOC-Lys)


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 Outer Membrane Decaheme Cytochrome Mtrc (A430BOC-Lys) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca716

b:26.1
occ:1.00
 O A:HOH1125 2.3 13.2 1.0
OD1 A:ASN231 2.3 16.4 1.0
O A:ASN231 2.4 14.3 1.0
O A:ASN234 2.4 13.9 1.0
O A:LYS237 2.5 16.9 1.0
C A:ASN231 3.2 14.6 1.0
CG A:ASN231 3.4 16.1 1.0
C A:LYS237 3.5 21.2 1.0
C A:ASN234 3.5 16.9 1.0
CA A:ASN231 3.5 13.5 1.0
CG A:LYS237 3.7 19.0 1.0
N A:LYS237 3.8 17.0 1.0
CG A:PRO246 4.0 19.1 1.0
CB A:ASN231 4.1 13.5 1.0
CA A:LYS237 4.1 20.0 1.0
CD A:PRO246 4.3 16.7 1.0
CA A:ASN234 4.3 15.9 1.0
OD1 A:ASN234 4.3 14.9 1.0
N A:ASN234 4.3 14.0 1.0
CB A:ASN234 4.4 15.0 1.0
N A:VAL232 4.5 9.8 1.0
CB A:LYS237 4.5 16.9 1.0
N A:ASN236 4.5 17.4 1.0
ND2 A:ASN231 4.5 12.1 1.0
N A:ALA235 4.5 15.5 1.0
O A:SER284 4.6 14.8 1.0
N A:ALA238 4.6 19.0 1.0
CA A:ALA235 4.7 17.9 1.0
O A:HIS230 4.8 12.3 1.0
C A:ALA235 4.8 20.2 1.0
N A:ASN231 4.9 12.9 1.0
CE A:LYS237 4.9 18.4 1.0
C A:ALA238 4.9 17.8 1.0
CG A:ASN234 4.9 14.6 1.0
O A:ALA238 4.9 17.0 1.0
CD A:LYS237 4.9 18.2 1.0
CA A:ALA238 4.9 19.9 1.0
CA A:VAL232 4.9 12.0 1.0
C A:ASN236 4.9 19.9 1.0

Calcium binding site 3 out of 5 in 8qbq

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Calcium binding site 3 out of 5 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc (A430BOC-Lys)


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 Outer Membrane Decaheme Cytochrome Mtrc (A430BOC-Lys) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca717

b:18.3
occ:1.00
 O A:HOH1177 2.3 25.3 1.0
OD1 A:ASP472 2.4 19.1 1.0
O A:HOH1239 2.4 18.9 1.0
O A:GLN520 2.4 19.0 1.0
O A:HOH1565 2.4 18.4 1.0
O A:HOH1056 2.5 19.6 1.0
O A:HOH833 2.7 27.0 1.0
OD2 A:ASP472 3.0 20.5 1.0
CG A:ASP472 3.1 17.2 1.0
C A:GLN520 3.5 20.8 1.0
O A:HOH1508 3.8 32.4 1.0
O A:LEU473 4.1 17.7 1.0
CA A:GLN520 4.3 18.1 1.0
N A:LEU521 4.5 16.1 1.0
O A:HOH1030 4.5 26.6 1.0
CB A:GLN520 4.5 15.9 1.0
CB A:ASP472 4.5 17.5 1.0
O A:HOH1727 4.6 23.5 1.0
N A:THR337 4.6 19.8 1.0
CA A:LEU521 4.6 18.4 1.0
O A:HOH1594 4.6 36.0 1.0
O A:HOH1680 4.7 36.8 1.0
N A:LEU473 4.7 12.7 1.0
O A:HOH1024 4.8 27.6 1.0
O A:ILE335 4.8 22.3 1.0
CA A:GLU336 4.8 19.3 1.0
O A:THR337 4.8 19.1 1.0

Calcium binding site 4 out of 5 in 8qbq

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Calcium binding site 4 out of 5 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc (A430BOC-Lys)


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 Outer Membrane Decaheme Cytochrome Mtrc (A430BOC-Lys) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca718

b:39.6
occ:1.00
 O A:GLN651 2.4 19.8 1.0
O A:HOH1599 2.5 33.7 1.0
O A:HOH1218 2.5 26.1 1.0
O A:HOH1743 2.6 37.4 1.0
O A:HOH1342 2.6 33.6 1.0
O A:HOH1573 2.7 28.2 1.0
O A:HOH1620 2.7 39.5 1.0
C A:GLN651 3.6 21.8 1.0
CB A:GLN651 4.3 20.2 1.0
O A:HOH1132 4.4 18.5 1.0
CA A:GLN651 4.5 16.5 1.0
N A:SER652 4.5 18.1 1.0
O A:HOH1157 4.5 34.9 1.0
CA A:SER652 4.5 22.3 1.0

Calcium binding site 5 out of 5 in 8qbq

Go back to Calcium Binding Sites List in 8qbq
Calcium binding site 5 out of 5 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc (A430BOC-Lys)


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 Outer Membrane Decaheme Cytochrome Mtrc (A430BOC-Lys) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca719

b:25.1
occ:1.00
 O A:HOH1529 2.3 27.2 1.0
O A:GLU162 2.3 13.8 1.0
OE1 A:GLU202 2.4 22.2 1.0
O A:HOH1547 2.4 26.9 1.0
O A:HOH1558 2.5 28.4 1.0
O A:HOH1155 2.6 23.9 1.0
OE2 A:GLU202 2.6 28.1 1.0
CD A:GLU202 2.9 23.2 1.0
C A:GLU162 3.5 15.8 1.0
O A:HOH1553 3.7 29.3 1.0
O A:HOH850 4.1 18.3 1.0
N A:GLU162 4.2 14.1 1.0
CG A:GLU202 4.3 17.6 1.0
CA A:GLU162 4.4 13.4 1.0
NE2 A:HIS183 4.4 22.9 1.0
N A:MET163 4.5 14.2 1.0
CA A:MET163 4.5 12.8 1.0
O A:HOH1732 4.5 33.4 1.0
CB A:MET163 4.5 18.1 1.0
O A:HOH1314 4.6 29.0 1.0
O A:HOH1232 4.6 26.9 1.0
O A:HOH981 4.6 34.8 1.0
CE1 A:HIS183 4.6 24.9 1.0
O A:HOH1447 4.7 19.6 1.0
CB A:GLU162 4.8 12.3 1.0
CD2 A:HIS183 4.9 21.1 1.0

Reference:

C.W.J.Lockwood, B.W.Nash, S.E.Newton-Payne, J.H.Van Wonderen, K.P.S.Whiting, A.Connolly, A.L.Sutton-Cook, A.Crook, A.R.Aithal, M.J.Edwards, T.A.Clarke, A.Sachdeva, J.N.Butt. Genetic Code Expansion in Shewanella Oneidensis Mr-1 Allows Site-Specific Incorporation of Bioorthogonal Functional Groups Into A C -Type Cytochrome. Acs Synth Biol 2024.
ISSN: ESSN 2161-5063
PubMed: 39158169
DOI: 10.1021/ACSSYNBIO.4C00248
Page generated: Sat Sep 28 09:02:57 2024

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