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Calcium in PDB 4lm8: Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc

Protein crystallography data

The structure of Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc, PDB code: 4lm8 was solved by 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) 45.80 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.120, 90.440, 154.340, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 20.3

Other elements in 4lm8:

The structure of Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc 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 (pdb code 4lm8). 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, PDB code: 4lm8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4lm8

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Calcium binding site 1 out of 5 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca811

b:8.9
occ:1.00
 O A:ILE53 2.3 9.3 1.0
OE2 A:GLU165 2.4 10.5 1.0
O A:HOH970 2.4 8.9 1.0
OD1 A:ASP52 2.4 10.7 1.0
O A:HOH939 2.4 10.6 1.0
O A:HOH1451 2.4 9.5 1.0
OE1 A:GLU165 2.5 10.1 1.0
CD A:GLU165 2.8 9.2 1.0
C A:ILE53 3.4 8.8 1.0
CG A:ASP52 3.5 10.4 1.0
OD2 A:ASP52 3.9 9.2 1.0
N A:ILE53 4.0 6.9 1.0
O A:HOH1036 4.2 16.2 1.0
CA A:ILE53 4.2 5.7 1.0
CG A:GLU165 4.3 10.3 1.0
N A:THR54 4.3 10.7 1.0
CA A:THR54 4.4 10.5 1.0
O A:HOH1039 4.6 11.4 1.0
CZ A:PHE167 4.6 9.6 1.0
CB A:ILE53 4.7 7.7 1.0
O A:HOH1295 4.8 29.8 1.0
CE1 A:PHE167 4.8 8.6 1.0
C A:ASP52 4.8 9.8 1.0
CB A:ASP52 4.8 10.6 1.0
O A:HOH986 4.9 11.8 1.0
O A:HOH985 4.9 8.9 1.0

Calcium binding site 2 out of 5 in 4lm8

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Calcium binding site 2 out of 5 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca812

b:22.1
occ:1.00
 OD1 A:ASN231 2.3 12.4 1.0
O A:ASN231 2.4 9.5 1.0
O A:HOH1032 2.4 12.1 1.0
O A:ASN234 2.4 9.5 1.0
O A:LYS237 2.5 14.0 1.0
C A:ASN231 3.3 12.1 1.0
CG A:ASN231 3.5 9.9 1.0
C A:ASN234 3.6 10.9 1.0
C A:LYS237 3.6 17.0 1.0
CA A:ASN231 3.6 10.2 1.0
CG A:LYS237 3.6 14.9 1.0
N A:LYS237 3.8 13.6 1.0
CG A:PRO246 3.9 16.6 1.0
CB A:ASN231 4.1 7.6 1.0
CA A:LYS237 4.1 15.9 1.0
CD A:PRO246 4.3 15.1 1.0
OD1 A:ASN234 4.3 12.3 1.0
CA A:ASN234 4.3 10.6 1.0
N A:ASN234 4.4 9.9 1.0
N A:VAL232 4.5 8.4 1.0
CB A:LYS237 4.5 17.1 1.0
CB A:ASN234 4.5 15.4 1.0
ND2 A:ASN231 4.5 12.9 1.0
N A:ALA235 4.5 13.4 1.0
N A:ASN236 4.6 14.5 1.0
O A:SER284 4.6 12.9 1.0
N A:ALA238 4.7 12.1 1.0
CA A:ALA235 4.7 17.3 1.0
CE A:LYS237 4.8 15.3 1.0
CD A:LYS237 4.8 12.9 1.0
C A:ALA235 4.8 18.7 1.0
O A:HIS230 4.8 8.7 1.0
C A:ALA238 4.8 13.9 1.0
O A:ALA238 4.8 12.7 1.0
N A:ASN231 4.9 8.7 1.0
CG A:ASN234 4.9 10.8 1.0
CA A:ALA238 4.9 13.5 1.0
CA A:VAL232 5.0 10.6 1.0
C A:ASN236 5.0 16.5 1.0

Calcium binding site 3 out of 5 in 4lm8

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Calcium binding site 3 out of 5 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca813

b:15.4
occ:1.00
 O A:HOH1490 2.3 27.0 1.0
O A:HOH1063 2.3 18.2 1.0
O A:HOH1087 2.4 18.2 1.0
OD1 A:ASP472 2.4 17.2 1.0
O A:GLN520 2.4 13.8 1.0
O A:HOH965 2.4 18.9 1.0
O A:HOH995 2.5 27.2 1.0
OD2 A:ASP472 3.0 21.1 1.0
CG A:ASP472 3.1 16.6 1.0
C A:GLN520 3.5 19.9 1.0
O A:LEU473 4.2 14.0 1.0
CA A:GLN520 4.3 16.5 1.0
O A:HOH1236 4.4 39.7 1.0
N A:LEU521 4.5 11.6 1.0
O A:HOH1437 4.5 34.9 1.0
N A:THR337 4.5 19.2 1.0
CB A:GLN520 4.6 16.9 1.0
O A:HOH1732 4.6 49.0 1.0
CB A:ASP472 4.6 17.7 1.0
CA A:LEU521 4.6 14.9 1.0
O A:HOH1100 4.7 24.8 1.0
O A:HOH1626 4.7 38.0 1.0
O A:ILE335 4.8 17.9 1.0
N A:LEU473 4.8 13.1 1.0
O A:HOH1220 4.8 24.7 1.0
CA A:GLU336 4.8 17.1 1.0
O A:THR337 4.9 18.9 1.0

Calcium binding site 4 out of 5 in 4lm8

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Calcium binding site 4 out of 5 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca814

b:38.4
occ:1.00
 O A:HOH1323 2.3 31.7 1.0
O A:HOH1282 2.4 26.9 1.0
O A:GLN651 2.4 22.1 1.0
O A:HOH1836 2.5 38.5 1.0
O A:HOH1272 3.2 44.0 1.0
C A:GLN651 3.6 14.8 1.0
O A:HOH1079 4.2 39.0 1.0
CB A:GLN651 4.3 16.1 1.0
O A:HOH1008 4.4 18.8 1.0
CA A:GLN651 4.5 13.4 1.0
N A:SER652 4.6 14.1 1.0
CA A:SER652 4.7 15.9 1.0

Calcium binding site 5 out of 5 in 4lm8

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Calcium binding site 5 out of 5 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Mtrc


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca815

b:14.2
occ:1.00
 O A:HOH1453 2.3 18.9 1.0
O A:HOH1452 2.3 18.6 1.0
O A:GLU162 2.3 11.4 1.0
O A:HOH1040 2.4 15.0 1.0
OE1 A:GLU202 2.4 22.1 1.0
OE2 A:GLU202 2.4 13.1 1.0
O A:HOH1410 2.5 23.2 1.0
CD A:GLU202 2.7 14.6 1.0
C A:GLU162 3.6 10.0 1.0
O A:HOH1502 4.0 29.1 1.0
N A:GLU162 4.1 12.4 1.0
O A:HOH1059 4.2 15.8 1.0
CG A:GLU202 4.3 9.2 1.0
CA A:GLU162 4.4 11.8 1.0
NE2 A:HIS183 4.4 17.6 1.0
O A:HOH1264 4.5 28.3 1.0
N A:MET163 4.5 8.9 1.0
CE1 A:HIS183 4.5 21.3 1.0
CA A:MET163 4.6 7.4 1.0
O A:HOH1611 4.6 35.1 1.0
O A:HOH1783 4.6 37.2 1.0
O A:HOH1249 4.7 24.0 1.0
CB A:MET163 4.7 9.1 1.0
O A:HOH1338 4.7 28.6 1.0
CB A:GLU162 4.8 12.7 1.0
O A:HOH1237 4.8 26.9 1.0
O A:HOH1052 4.9 13.2 1.0
CD2 A:HIS183 4.9 20.0 1.0

Reference:

M.J.Edwards, D.J.Richardson, T.A.Clarke. Insights Into Electron Transfer at the Microbe-Mineral Interface: the X-Ray Crystal Structures of Shewanella Oneidensis Mtrc and Omca To Be Published.
Page generated: Tue Jul 8 23:54:05 2025

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