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Calcium in PDB 8qc9: Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc (A293BOC-Lys)

Protein crystallography data

The structure of Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc (A293BOC-Lys), PDB code: 8qc9 was solved by B.W.Nash, C.J.Lockwood, M.J.Edwards, K.Whiting, 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) 58.63 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.078, 90.021, 154.522, 90, 90, 90
R / Rfree (%) 17.3 / 21.4

Other elements in 8qc9:

The structure of Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc (A293BOC-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 (A293BOC-Lys) (pdb code 8qc9). 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 (A293BOC-Lys), PDB code: 8qc9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 8qc9

Go back to Calcium Binding Sites List in 8qc9
Calcium binding site 1 out of 5 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc (A293BOC-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 (A293BOC-Lys) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca711

b:18.7
occ:1.00
 O A:ILE53 2.3 16.1 1.0
O A:HOH1267 2.4 14.0 1.0
OE2 A:GLU165 2.4 19.5 1.0
OD1 A:ASP52 2.4 15.7 1.0
O A:HOH1306 2.4 16.2 1.0
O A:HOH878 2.4 15.6 1.0
OE1 A:GLU165 2.5 16.1 1.0
CD A:GLU165 2.8 18.6 1.0
C A:ILE53 3.4 19.1 1.0
CG A:ASP52 3.4 21.2 1.0
OD2 A:ASP52 3.8 19.9 1.0
N A:ILE53 4.1 17.0 1.0
O A:HOH1224 4.3 19.2 1.0
CA A:ILE53 4.3 14.4 1.0
N A:THR54 4.3 18.4 1.0
CG A:GLU165 4.3 19.2 1.0
CA A:THR54 4.4 17.6 1.0
O A:HOH977 4.6 17.0 1.0
CZ A:PHE167 4.7 16.1 1.0
CB A:ILE53 4.7 15.7 1.0
CB A:ASP52 4.8 16.2 1.0
C A:ASP52 4.8 20.6 1.0
O A:HOH927 4.9 16.6 1.0
CE2 A:PHE167 4.9 15.1 1.0
O A:HOH1399 4.9 30.5 1.0
O A:HOH1497 5.0 17.6 1.0
O A:HOH1302 5.0 27.9 1.0

Calcium binding site 2 out of 5 in 8qc9

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Calcium binding site 2 out of 5 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc (A293BOC-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 (A293BOC-Lys) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca712

b:25.9
occ:1.00
 O A:HOH1165 2.2 34.9 1.0
OD1 A:ASP472 2.4 20.3 1.0
O A:GLN520 2.4 25.4 1.0
O A:HOH895 2.5 21.6 1.0
O A:HOH1387 2.5 25.3 1.0
O A:HOH949 2.6 19.5 1.0
O A:HOH1235 2.6 33.0 1.0
O A:HOH801 2.8 36.7 1.0
OD2 A:ASP472 3.0 22.4 1.0
CG A:ASP472 3.0 22.3 1.0
C A:GLN520 3.5 22.6 1.0
O A:LEU473 4.2 20.9 1.0
CA A:GLN520 4.3 22.5 1.0
N A:LEU521 4.4 23.2 1.0
O A:HOH1396 4.4 36.5 1.0
O A:HOH1433 4.5 36.2 1.0
N A:THR337 4.5 25.6 1.0
CB A:ASP472 4.5 17.4 1.0
CA A:LEU521 4.6 23.1 1.0
CB A:GLN520 4.6 20.5 1.0
O A:HOH1524 4.6 22.9 1.0
O A:HOH963 4.6 38.4 1.0
O A:HOH985 4.6 30.2 1.0
O A:ILE335 4.6 26.5 1.0
CA A:GLU336 4.8 24.2 1.0
O A:THR337 4.8 22.5 1.0
N A:LEU473 4.8 15.8 1.0
O A:HOH1584 4.8 41.2 1.0

Calcium binding site 3 out of 5 in 8qc9

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Calcium binding site 3 out of 5 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc (A293BOC-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 (A293BOC-Lys) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca713

b:30.6
occ:1.00
 O A:GLU162 2.3 17.2 1.0
O A:ACT723 2.4 35.6 1.0
OE1 A:GLU202 2.4 24.3 1.0
O A:HOH1123 2.5 24.6 1.0
OE2 A:GLU202 2.5 28.8 1.0
O A:HOH1208 2.6 25.5 1.0
O A:HOH1209 2.7 25.1 1.0
CD A:GLU202 2.8 24.7 1.0
C A:ACT723 3.2 31.4 1.0
C A:GLU162 3.5 19.3 1.0
OXT A:ACT723 3.5 33.3 1.0
N A:GLU162 4.1 19.0 1.0
O A:HOH820 4.2 22.4 1.0
CG A:GLU202 4.3 20.7 1.0
CA A:GLU162 4.3 20.2 1.0
O A:HOH1192 4.4 29.7 1.0
N A:MET163 4.4 16.4 1.0
CA A:MET163 4.5 17.3 1.0
NE2 A:HIS183 4.5 24.9 1.0
CB A:MET163 4.5 20.4 1.0
CH3 A:ACT723 4.6 23.9 1.0
CE1 A:HIS183 4.7 26.8 1.0
CB A:GLU162 4.7 17.6 1.0
O A:HOH1237 4.8 28.4 1.0
O A:HOH1147 4.9 24.8 1.0
CD2 A:HIS183 4.9 24.5 1.0

Calcium binding site 4 out of 5 in 8qc9

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Calcium binding site 4 out of 5 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc (A293BOC-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 (A293BOC-Lys) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca714

b:33.7
occ:1.00
 O A:ASN234 2.3 17.9 1.0
O A:ASN231 2.3 19.3 1.0
O A:HOH954 2.4 16.4 1.0
OD1 A:ASN231 2.4 18.9 1.0
O A:LYS237 2.6 22.3 1.0
C A:ASN231 3.2 18.7 1.0
C A:ASN234 3.5 18.7 1.0
CA A:ASN231 3.5 16.4 1.0
CG A:ASN231 3.5 21.1 1.0
C A:LYS237 3.6 22.4 1.0
CG A:LYS237 3.8 23.0 1.0
N A:LYS237 3.8 21.9 1.0
CG A:PRO246 3.9 22.9 1.0
CB A:ASN231 4.1 16.2 1.0
CA A:LYS237 4.2 25.0 1.0
OD1 A:ASN234 4.3 20.0 1.0
CA A:ASN234 4.3 17.5 1.0
CD A:PRO246 4.3 24.8 1.0
N A:ASN234 4.3 18.4 1.0
CB A:ASN234 4.4 16.6 1.0
N A:VAL232 4.4 16.2 1.0
N A:ASN236 4.4 22.3 1.0
N A:ALA235 4.5 21.3 1.0
CB A:LYS237 4.6 18.5 1.0
O A:SER284 4.6 20.1 1.0
ND2 A:ASN231 4.6 17.2 1.0
N A:ALA238 4.7 23.9 1.0
CA A:ALA235 4.7 22.1 1.0
C A:ALA235 4.8 24.3 1.0
O A:HIS230 4.8 16.2 1.0
N A:ASN231 4.8 16.1 1.0
CG A:ASN234 4.8 19.2 1.0
CE A:LYS237 4.9 18.4 1.0
CA A:VAL232 4.9 15.9 1.0
C A:ASN236 4.9 21.5 1.0
C A:ALA238 5.0 19.9 1.0
CD A:LYS237 5.0 24.9 1.0
CA A:ALA238 5.0 22.3 1.0

Calcium binding site 5 out of 5 in 8qc9

Go back to Calcium Binding Sites List in 8qc9
Calcium binding site 5 out of 5 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc (A293BOC-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 (A293BOC-Lys) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca715

b:45.9
occ:1.00
 O A:GLN651 2.3 26.6 1.0
O A:HOH1290 2.5 31.4 1.0
O A:HOH1025 2.6 35.0 1.0
O A:HOH1440 2.8 28.9 1.0
O A:HOH1503 2.8 41.8 1.0
C A:GLN651 3.5 26.0 1.0
CB A:GLN651 4.2 19.9 1.0
O A:HOH961 4.4 23.9 1.0
CA A:GLN651 4.4 21.2 1.0
N A:SER652 4.4 24.1 1.0
CA A:SER652 4.5 27.5 1.0
O A:HOH1118 4.5 38.8 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 09:02:44 2024

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