Atomistry » Calcium » PDB 8q5n-8r1b » 8qbq
Atomistry »
  Calcium »
    PDB 8q5n-8r1b »
      8qbq »

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

Go back to Calcium Binding Sites List in 8qbq
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

Go back to Calcium Binding Sites List in 8qbq
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

Go back to Calcium Binding Sites List in 8qbq
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy