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Calcium in PDB 4lmh: Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca

Protein crystallography data

The structure of Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca, PDB code: 4lmh was solved by M.J.Edwards, N.Baiden, T.A.Clarke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.97 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 92.640, 245.380, 135.630, 90.00, 97.89, 90.00
R / Rfree (%) 19.3 / 23

Other elements in 4lmh:

The structure of Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca also contains other interesting chemical elements:

Iron (Fe) 40 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca (pdb code 4lmh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca, PDB code: 4lmh:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4lmh

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Calcium binding site 1 out of 8 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca


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

b:30.3
occ:1.00
 OE1 A:GLU262 2.3 33.3 1.0
O2D A:HEC802 2.4 23.4 1.0
OD1 A:ASP260 2.4 22.4 1.0
O A:ILE299 2.5 20.1 1.0
O A:HOH1294 2.5 44.9 1.0
O A:HOH1295 2.5 28.4 1.0
O1D A:HEC802 2.7 31.2 1.0
CGD A:HEC802 2.8 29.1 1.0
CD A:GLU262 3.3 27.6 1.0
CG A:ASP260 3.6 22.4 1.0
C A:ILE299 3.6 23.1 1.0
OE2 A:GLU262 3.9 25.3 1.0
CA A:GLY300 3.9 23.5 1.0
O A:HOH1033 4.2 35.8 1.0
N A:GLY300 4.2 24.5 1.0
OD2 A:ASP260 4.2 21.5 1.0
CD A:PRO261 4.2 25.5 1.0
CBD A:HEC802 4.3 26.0 1.0
CG A:GLU262 4.4 27.0 1.0
CB A:GLU262 4.6 25.5 1.0
CB A:ASP260 4.6 18.7 1.0
N A:GLU262 4.7 27.1 1.0
C A:GLY300 4.7 30.9 1.0
NE2 A:GLN142 4.8 17.2 1.0
CA A:ILE299 4.8 22.9 1.0
N A:PRO261 4.9 28.0 1.0
O A:HOH979 4.9 26.2 1.0
CA A:ASP260 5.0 21.4 1.0
CAD A:HEC802 5.0 24.1 1.0
O A:HOH1223 5.0 34.5 1.0

Calcium binding site 2 out of 8 in 4lmh

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Calcium binding site 2 out of 8 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca


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

b:69.2
occ:1.00
 O A:HOH1296 2.3 49.0 1.0
O A:HOH1297 2.4 37.6 1.0
O A:HOH1234 2.4 39.8 1.0
O A:HOH1232 3.1 29.7 1.0
O A:HOH1233 3.1 39.6 1.0
O A:SER627 4.2 29.2 1.0
O2A A:HEC801 4.3 34.9 1.0
CA A:SER627 4.3 32.3 1.0
OE1 A:GLU235 4.5 66.8 1.0
O A:HOH1108 4.6 41.8 1.0
OE2 A:GLU235 4.6 72.5 1.0
C A:SER627 4.6 28.9 1.0
O A:GLN626 4.8 37.8 1.0
CB A:SER627 4.9 29.7 1.0
O A:GLU235 4.9 45.1 1.0
CD A:GLU235 5.0 67.2 1.0

Calcium binding site 3 out of 8 in 4lmh

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Calcium binding site 3 out of 8 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca


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 Omca within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca912

b:51.5
occ:1.00
 O B:HOH1420 2.3 42.9 1.0
O1D B:HEC903 2.4 44.9 1.0
OE1 B:GLU262 2.4 54.0 1.0
O B:HOH1419 2.4 47.6 1.0
OD1 B:ASP260 2.4 38.6 1.0
O B:ILE299 2.6 30.5 1.0
O2D B:HEC903 2.8 43.2 1.0
CGD B:HEC903 3.0 42.8 1.0
CD B:GLU262 3.5 50.6 1.0
CG B:ASP260 3.6 37.6 1.0
C B:ILE299 3.7 32.9 1.0
O B:HOH1333 4.0 26.9 1.0
OE2 B:GLU262 4.0 53.4 1.0
O B:HOH1388 4.1 41.5 1.0
CD B:PRO261 4.2 40.3 1.0
OD2 B:ASP260 4.3 34.8 1.0
CG B:PRO261 4.4 43.5 1.0
CB B:ILE299 4.4 34.6 1.0
CBD B:HEC903 4.4 33.9 1.0
O B:GLY300 4.5 53.6 1.0
N B:GLY300 4.5 46.0 1.0
CG B:GLU262 4.5 47.9 1.0
CA B:ILE299 4.6 37.1 1.0
CA B:GLY300 4.6 48.1 1.0
CB B:ASP260 4.7 31.1 1.0
CB B:GLU262 4.8 48.1 1.0
CG2 B:ILE299 4.8 29.8 1.0
O B:HOH1138 4.9 48.6 1.0
NE2 B:GLN142 4.9 39.2 1.0
C B:GLY300 4.9 52.3 1.0
N B:GLU262 4.9 41.4 1.0
N B:PRO261 4.9 45.2 1.0

Calcium binding site 4 out of 8 in 4lmh

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Calcium binding site 4 out of 8 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca


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 Omca within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca913

b:58.5
occ:1.00
 O B:HOH1398 2.4 32.7 1.0
O B:HOH1344 2.4 22.1 1.0
O B:HOH1343 2.4 49.8 1.0
O B:HOH1345 3.0 34.4 1.0
O B:HOH1342 3.2 36.1 1.0
O B:HOH1391 3.4 50.4 1.0
O B:HOH1348 3.8 32.1 1.0
O2A B:HEC902 4.1 25.7 1.0
O B:SER627 4.3 32.3 1.0
CA B:SER627 4.4 29.9 1.0
OE1 B:GLU235 4.7 37.5 1.0
O B:GLN626 4.7 37.5 1.0
O B:HOH1285 4.7 46.0 1.0
C B:SER627 4.7 28.9 1.0
OE2 B:GLU235 4.8 47.0 1.0
CB B:SER627 4.9 29.7 1.0
O B:SER236 5.0 27.5 1.0
O B:GLU235 5.0 29.5 1.0

Calcium binding site 5 out of 8 in 4lmh

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Calcium binding site 5 out of 8 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca


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

b:39.6
occ:1.00
 O2D C:HEC802 2.3 26.2 1.0
OE1 C:GLU262 2.3 33.0 1.0
O C:HOH1279 2.4 34.2 1.0
O C:HOH1278 2.4 47.2 1.0
OD1 C:ASP260 2.4 26.2 1.0
O C:ILE299 2.5 25.8 1.0
O1D C:HEC802 2.7 36.2 1.0
CGD C:HEC802 2.8 29.6 1.0
CD C:GLU262 3.3 29.9 1.0
CG C:ASP260 3.5 27.8 1.0
C C:ILE299 3.6 27.6 1.0
OE2 C:GLU262 3.9 24.1 1.0
CA C:GLY300 4.0 23.8 1.0
OD2 C:ASP260 4.1 22.5 1.0
CBD C:HEC802 4.3 29.3 1.0
N C:GLY300 4.3 23.9 1.0
O C:HOH1261 4.3 46.6 1.0
CG C:GLU262 4.3 24.7 1.0
CD C:PRO261 4.4 29.1 1.0
CB C:GLU262 4.5 26.6 1.0
CB C:ASP260 4.5 23.7 1.0
CG C:PRO261 4.7 30.0 1.0
NE2 C:GLN142 4.8 26.6 1.0
N C:GLU262 4.8 26.3 1.0
C C:GLY300 4.8 26.8 1.0
CA C:ILE299 4.8 26.8 1.0
CA C:ASP260 4.9 25.7 1.0
N C:PRO261 4.9 30.4 1.0
O C:HOH1220 5.0 39.9 1.0
CAD C:HEC802 5.0 32.6 1.0
O C:HOH944 5.0 37.3 1.0

Calcium binding site 6 out of 8 in 4lmh

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Calcium binding site 6 out of 8 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca812

b:57.8
occ:1.00
 O C:HOH1214 2.3 42.2 1.0
O C:HOH1213 2.4 26.4 1.0
O C:HOH1216 2.5 36.2 1.0
O C:HOH1215 3.0 27.2 1.0
OE1 C:GLU235 3.9 67.2 1.0
O C:SER627 4.0 28.4 1.0
O C:HOH1148 4.0 27.6 1.0
O C:GLU235 4.2 44.1 1.0
CA C:SER236 4.5 26.3 1.0
OE2 C:GLU235 4.5 71.5 1.0
O C:ALA238 4.5 29.7 1.0
O2A C:HEC801 4.6 30.0 1.0
O C:SER236 4.6 26.0 1.0
CD C:GLU235 4.6 68.2 1.0
CA C:SER627 4.6 29.9 1.0
C C:SER627 4.7 28.3 1.0
C C:SER236 4.8 25.0 1.0
C C:GLU235 5.0 45.2 1.0

Calcium binding site 7 out of 8 in 4lmh

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Calcium binding site 7 out of 8 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca811

b:38.7
occ:1.00
 OE1 D:GLU262 2.4 44.7 1.0
OD1 D:ASP260 2.4 33.5 1.0
O1D D:HEC802 2.5 36.4 1.0
O D:HOH1265 2.5 19.1 1.0
O D:ILE299 2.5 35.4 1.0
O2D D:HEC802 2.6 34.9 1.0
CGD D:HEC802 2.9 33.5 1.0
O D:HOH1150 3.2 45.0 1.0
CD D:GLU262 3.5 40.5 1.0
CG D:ASP260 3.5 32.2 1.0
C D:ILE299 3.6 37.4 1.0
CB D:ILE299 4.1 36.6 1.0
OE2 D:GLU262 4.1 41.5 1.0
CD D:PRO261 4.2 42.7 1.0
OD2 D:ASP260 4.2 28.8 1.0
O D:HOH984 4.2 25.1 1.0
CG D:PRO261 4.3 40.8 1.0
CA D:ILE299 4.4 38.5 1.0
CBD D:HEC802 4.4 33.0 1.0
CG2 D:ILE299 4.5 36.5 1.0
N D:GLY300 4.5 36.8 1.0
CG D:GLU262 4.6 42.8 1.0
CB D:ASP260 4.6 27.5 1.0
O D:GLY300 4.6 42.3 1.0
CB D:GLU262 4.6 40.9 1.0
O D:HOH1085 4.7 28.1 1.0
N D:GLU262 4.7 37.5 1.0
CA D:GLY300 4.7 37.0 1.0
N D:PRO261 4.8 42.3 1.0
N D:ILE299 4.8 37.6 1.0
CA D:ASP260 4.9 29.5 1.0
NE2 D:GLN142 5.0 28.5 1.0
C D:GLY300 5.0 48.9 1.0

Calcium binding site 8 out of 8 in 4lmh

Go back to Calcium Binding Sites List in 4lmh
Calcium binding site 8 out of 8 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca812

b:60.0
occ:1.00
 O D:HOH1451 2.3 35.7 1.0
O D:HOH1351 2.4 29.6 1.0
O D:HOH1352 2.4 40.2 1.0
O D:HOH1230 2.5 51.0 1.0
O D:HOH1301 3.8 33.2 1.0
OE2 D:GLU235 4.1 43.1 1.0
O D:SER627 4.2 22.3 1.0
OE1 D:GLU235 4.3 30.0 1.0
O2A D:HEC801 4.3 27.3 1.0
O D:GLU235 4.4 25.1 1.0
O D:HOH932 4.4 11.0 1.0
O D:HOH1350 4.4 40.3 1.0
CA D:SER627 4.5 24.5 1.0
O D:SER236 4.5 21.5 1.0
CD D:GLU235 4.5 39.6 1.0
O D:HOH1263 4.5 40.9 1.0
CA D:SER236 4.5 23.9 1.0
C D:SER627 4.7 23.7 1.0
O D:ALA238 4.8 32.3 1.0
C D:SER236 4.8 22.5 1.0
CB D:SER627 4.9 21.4 1.0

Reference:

M.J.Edwards, N.Baiden, T.A.Clarke, D.J.Richardson. Insights Into Electron Transfer at the Microbe-Mineral Interface: the X-Ray Crystal Structures of Shewanella Oneidensis Mtrc and Omca Febs Letters 2014.
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