Atomistry » Calcium » PDB 8q2a-8qx0 » 8qbz
Atomistry »
  Calcium »
    PDB 8q2a-8qx0 »
      8qbz »

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

Go back to Calcium Binding Sites List in 8qbz
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

Go back to Calcium Binding Sites List in 8qbz
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

Go back to Calcium Binding Sites List in 8qbz
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

Go back to Calcium Binding Sites List in 8qbz
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

Go back to Calcium Binding Sites List in 8qbz
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: Thu Jul 10 06:33:02 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy