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Calcium in PDB 8qbz: Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc (E344BOC-Lys)

Protein crystallography data

The structure of Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc (E344BOC-Lys), PDB code: 8qbz was solved by M.J.Edwards, C.J.Lockwood, K.Whiting, B.W.Nash, J.N.Butt, T.A.Clarke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.12 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.967, 89.664, 153.545, 90, 90, 90
R / Rfree (%) 17.4 / 21.6

Other elements in 8qbz:

The structure of Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc (E344BOC-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 (E344BOC-Lys) (pdb code 8qbz). 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 (E344BOC-Lys), PDB code: 8qbz:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 8qbz

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Calcium binding site 1 out of 5 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc (E344BOC-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 (E344BOC-Lys) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca811

b:11.4
occ:1.00
 O A:ILE53 2.3 11.7 1.0
OD1 A:ASP52 2.4 12.7 1.0
O A:HOH1566 2.4 11.3 1.0
O A:HOH1050 2.4 10.6 1.0
O A:HOH1489 2.4 13.5 1.0
OE2 A:GLU165 2.4 11.1 1.0
OE1 A:GLU165 2.5 10.6 1.0
CD A:GLU165 2.8 10.6 1.0
CG A:ASP52 3.4 13.1 1.0
C A:ILE53 3.4 12.0 1.0
OD2 A:ASP52 3.8 13.2 1.0
N A:ILE53 4.1 12.5 1.0
O A:HOH1325 4.2 16.0 1.0
CA A:ILE53 4.3 12.1 1.0
N A:THR54 4.3 11.9 1.0
CG A:GLU165 4.3 10.6 1.0
CA A:THR54 4.4 12.3 1.0
O A:HOH1064 4.6 17.4 1.0
CB A:ASP52 4.7 12.7 1.0
CB A:ILE53 4.7 12.5 1.0
C A:ASP52 4.8 12.8 1.0
CZ A:PHE167 4.8 11.1 1.0
O A:HOH1049 4.8 22.0 1.0
O A:HOH1556 4.9 23.8 1.0
O A:HOH1725 4.9 12.1 1.0
O A:HOH1652 5.0 26.5 1.0
CA A:ASP52 5.0 12.8 1.0
CE1 A:PHE167 5.0 10.9 1.0

Calcium binding site 2 out of 5 in 8qbz

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Calcium binding site 2 out of 5 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc (E344BOC-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 (E344BOC-Lys) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca812

b:10.3
occ:0.50
 O A:ASN234 2.3 10.4 1.0
O A:ASN231 2.3 10.9 1.0
O A:HOH1137 2.4 11.3 1.0
O A:LYS237 2.4 12.7 1.0
OD1 A:ASN231 2.4 10.5 1.0
C A:ASN231 3.3 10.7 1.0
C A:LYS237 3.5 14.7 1.0
C A:ASN234 3.5 11.0 1.0
CG A:ASN231 3.5 10.7 1.0
CA A:ASN231 3.6 10.5 1.0
CG A:LYS237 3.7 15.7 1.0
N A:LYS237 3.7 15.8 1.0
CG A:PRO246 3.9 19.3 1.0
CA A:LYS237 4.1 15.5 1.0
CB A:ASN231 4.1 10.7 1.0
CD A:PRO246 4.2 19.4 1.0
OD1 A:ASN234 4.2 11.2 1.0
CA A:ASN234 4.3 10.9 1.0
CB A:ASN234 4.3 10.9 1.0
N A:ASN234 4.4 10.4 1.0
CB A:LYS237 4.5 15.6 1.0
N A:ALA235 4.5 11.7 1.0
N A:VAL232 4.5 10.7 1.0
N A:ASN236 4.5 15.2 1.0
N A:ALA238 4.6 14.4 1.0
O A:SER284 4.6 13.0 1.0
ND2 A:ASN231 4.6 10.5 1.0
CA A:ALA235 4.7 13.1 1.0
CG A:ASN234 4.8 10.6 1.0
C A:ALA235 4.8 14.4 1.0
O A:ALA238 4.8 13.4 1.0
N A:ASN231 4.9 10.3 1.0
C A:ALA238 4.9 14.3 1.0
CE A:LYS237 4.9 15.9 1.0
CD A:LYS237 4.9 15.8 1.0
O A:HIS230 4.9 9.4 1.0
C A:ASN236 4.9 15.8 1.0
CA A:ALA238 5.0 14.3 1.0
CA A:VAL232 5.0 10.7 1.0

Calcium binding site 3 out of 5 in 8qbz

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Calcium binding site 3 out of 5 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc (E344BOC-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 (E344BOC-Lys) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca813

b:16.8
occ:1.00
 OD1 A:ASP472 2.4 16.1 1.0
O A:HOH1337 2.4 21.5 1.0
O A:HOH1327 2.4 20.9 1.0
O A:HOH1283 2.4 17.0 1.0
O A:HOH1654 2.4 16.9 1.0
O A:HOH1279 2.4 14.1 1.0
O A:GLN520 2.4 15.9 1.0
OD2 A:ASP472 2.6 18.5 1.0
CG A:ASP472 2.8 15.5 1.0
C A:GLN520 3.5 15.7 1.0
O A:LEU473 4.1 14.1 1.0
CA A:GLN520 4.3 15.7 1.0
O A:HOH1533 4.3 33.1 1.0
CB A:ASP472 4.3 15.1 1.0
O A:HOH1692 4.3 33.9 1.0
N A:LEU521 4.5 15.7 1.0
N A:THR337 4.6 20.8 1.0
CA A:LEU521 4.6 16.6 1.0
O A:HOH1796 4.6 18.0 1.0
CB A:GLN520 4.6 14.8 1.0
O A:HOH1293 4.7 22.3 1.0
O A:HOH1130 4.7 19.7 1.0
N A:LEU473 4.7 13.2 1.0
O A:THR337 4.8 18.6 1.0
O A:ILE335 4.8 18.2 1.0
CA A:GLU336 4.8 20.2 1.0

Calcium binding site 4 out of 5 in 8qbz

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Calcium binding site 4 out of 5 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc (E344BOC-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 (E344BOC-Lys) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca814

b:35.8
occ:1.00
 O A:HOH1357 2.4 38.8 1.0
O A:HOH1222 2.4 33.7 1.0
O A:HOH1676 2.4 33.4 1.0
O A:GLN651 2.4 20.2 1.0
O A:HOH1655 2.4 31.6 1.0
C A:GLN651 3.6 16.3 1.0
CB A:GLN651 4.3 15.1 1.0
O A:HOH961 4.3 46.3 1.0
O A:HOH1242 4.4 19.4 1.0
O A:HOH1704 4.5 39.0 1.0
CA A:GLN651 4.5 15.2 1.0
N A:SER652 4.5 16.1 1.0
CA A:SER652 4.6 16.3 1.0

Calcium binding site 5 out of 5 in 8qbz

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Calcium binding site 5 out of 5 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc (E344BOC-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 (E344BOC-Lys) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca815

b:27.1
occ:1.00
 O A:HOH1502 2.3 27.6 1.0
O A:HOH1627 2.4 25.5 1.0
O A:HOH1631 2.4 25.0 1.0
O A:HOH987 2.4 23.2 1.0
O A:GLU162 2.4 15.4 1.0
OE2 A:GLU202 2.4 21.8 1.0
OE1 A:GLU202 2.5 23.4 1.0
CD A:GLU202 2.8 19.9 1.0
C A:GLU162 3.6 14.0 1.0
O A:HOH1620 3.8 30.3 1.0
O A:HOH916 4.2 21.1 1.0
N A:GLU162 4.2 14.1 1.0
CG A:GLU202 4.3 17.5 1.0
NE2 A:HIS183 4.4 21.0 1.0
CA A:GLU162 4.5 14.4 1.0
O A:HOH1083 4.5 44.2 1.0
N A:MET163 4.6 13.0 1.0
CE1 A:HIS183 4.6 21.4 1.0
CA A:MET163 4.6 13.2 1.0
O A:HOH1185 4.6 27.9 1.0
CB A:MET163 4.6 14.6 1.0
O A:HOH1401 4.6 23.1 1.0
O A:HOH912 4.7 43.8 1.0
O A:HOH1801 4.7 36.9 1.0
CD2 A:HIS183 4.8 21.4 1.0
CB A:GLU162 4.8 14.8 1.0
O A:HOH1527 4.8 9.7 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 09:02:42 2024

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