Calcium in PDB 3mmo: Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide

The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide, PDB code: 3mmo was solved by A.A.Trofimov, K.M.Polyakov, K.M.Boyko, T.V.Tikhonova, V.S.Lamzin, G.P.Bourenkov, V.O.Popov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	11.98 / 1.55
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	194.560, 194.560, 194.560, 90.00, 90.00, 90.00
R / Rfree (%)	14.8 / 16.2

The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide also contains other interesting chemical elements:

Iron	(Fe)	16 atoms
Sodium	(Na)	6 atoms

The binding sites of Calcium atom in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide (pdb code 3mmo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide, PDB code: 3mmo:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca527 b:14.9 occ:1.00 OE1 A:GLN360 2.3 16.4 1.0 O A:LYS358 2.3 15.3 1.0 O A:TYR303 2.4 14.7 1.0 O A:HOH812 2.4 15.3 1.0 OE2 A:GLU302 2.4 15.4 1.0 OE1 A:GLU302 2.5 14.6 1.0 O A:HOH811 2.6 16.1 1.0 CD A:GLU302 2.8 16.5 1.0 H A:TYR303 3.3 15.3 1.0 CD A:GLN360 3.4 15.8 1.0 HA A:LEU359 3.4 14.3 1.0 C A:LYS358 3.5 14.5 1.0 C A:TYR303 3.5 15.4 1.0 HE1 A:PHE328 3.9 17.0 1.0 NE2 A:GLN360 4.0 17.8 1.0 N A:TYR303 4.0 15.4 1.0 H A:GLN360 4.0 13.8 1.0 HB3 A:LYS358 4.1 14.8 1.0 HA A:ASN304 4.1 16.0 1.0 CA A:LEU359 4.2 14.1 1.0 HB2 A:GLN360 4.3 14.2 1.0 N A:LEU359 4.3 14.2 1.0 OD1 A:ASN304 4.3 18.8 1.0 OH A:TYR335 4.3 17.1 1.0 CG A:GLU302 4.3 14.9 1.0 N A:GLN360 4.3 13.7 1.0 CA A:TYR303 4.4 15.4 1.0 H A:LYS358 4.4 15.5 1.0 OD1 A:ASP346 4.5 15.8 1.0 C A:LEU359 4.5 14.3 1.0 HG3 A:LYS358 4.5 14.8 1.0 OD2 A:ASP346 4.5 18.3 1.0 N A:ASN304 4.5 15.0 1.0 CA A:LYS358 4.6 14.8 1.0 CE1 A:PHE328 4.6 17.2 1.0 HG3 A:GLU302 4.6 15.3 1.0 CB A:LYS358 4.7 15.0 1.0 CG A:GLN360 4.7 15.4 1.0 HA A:GLU302 4.7 14.8 1.0 CA A:ASN304 4.8 16.0 1.0 HG2 A:GLU302 4.8 15.3 1.0 CG A:ASP346 4.8 16.9 1.0 CB A:GLN360 4.9 14.8 1.0 N A:LYS358 4.9 15.4 1.0 C A:GLU302 4.9 15.1 1.0 HD1 A:PHE328 5.0 16.1 1.0

Calcium binding site 2 out of 4 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca528 b:16.6 occ:0.50 O A:HOH885 2.3 20.5 1.0 O A:HOH587 2.4 22.7 1.0 O2A A:HEC1006 2.5 13.4 1.0 O A:PRO116 2.6 14.0 1.0 O A:HOH1088 2.8 23.5 1.0 HG2 A:PRO116 3.1 13.4 1.0 HB3 A:SER84 3.3 12.7 1.0 O1A A:HEC1007 3.4 10.5 0.5 C A:PRO116 3.6 13.2 1.0 CGA A:HEC1006 3.7 12.5 1.0 HA A:ARG117 3.7 12.2 1.0 HD2 A:PRO116 3.8 12.3 1.0 OG A:SER84 3.9 13.1 1.0 NA A:NA537 3.9 22.9 0.5 CB A:SER84 4.0 13.5 1.0 CG A:PRO116 4.0 14.0 1.0 HB3 A:GLU115 4.0 13.3 1.0 HAA2 A:HEC1006 4.1 12.4 1.0 CGA A:HEC1007 4.1 13.7 0.5 HAA1 A:HEC1006 4.1 12.4 1.0 O A:HOH1089 4.1 24.7 0.5 HA A:SER84 4.2 12.8 1.0 O A:HOH731 4.2 21.7 1.0 CD A:PRO116 4.3 12.4 1.0 O2A A:HEC1007 4.4 14.7 0.5 O1A A:HEC1006 4.4 13.6 1.0 HB2 A:PRO116 4.4 13.1 1.0 O A:HOH956 4.4 32.1 1.0 CAA A:HEC1006 4.5 12.5 1.0 N A:ARG117 4.5 11.9 1.0 CA A:PRO116 4.5 12.9 1.0 N A:PRO116 4.5 12.0 1.0 CA A:ARG117 4.5 12.4 1.0 CB A:PRO116 4.6 13.2 1.0 CA A:SER84 4.6 12.3 1.0 CBA A:HEC1006 4.7 13.0 1.0 HG3 A:PRO116 4.7 13.4 1.0 HB2 A:SER84 4.8 12.7 1.0 OE1 A:GLU115 4.8 23.1 1.0 O A:HOH723 4.9 14.1 1.0 CB A:GLU115 4.9 13.5 1.0 HB2 A:GLU115 5.0 13.3 1.0

Calcium binding site 3 out of 4 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca527 b:12.7 occ:1.00 OE1 B:GLN360 2.3 13.6 1.0 O B:LYS358 2.3 13.3 1.0 O B:TYR303 2.4 12.5 1.0 OE2 B:GLU302 2.4 12.8 1.0 O B:HOH891 2.4 13.5 1.0 OE1 B:GLU302 2.5 11.8 1.0 O B:HOH890 2.6 14.5 1.0 CD B:GLU302 2.9 12.4 1.0 H B:TYR303 3.3 12.8 1.0 HA B:LEU359 3.4 12.3 1.0 CD B:GLN360 3.4 13.8 1.0 C B:LYS358 3.5 12.4 1.0 C B:TYR303 3.5 12.8 1.0 NE2 B:GLN360 3.9 15.5 1.0 N B:TYR303 4.0 12.6 1.0 H B:GLN360 4.0 12.2 1.0 HB3 B:LYS358 4.1 12.3 1.0 HA B:ASN304 4.1 14.1 1.0 CA B:LEU359 4.1 12.2 1.0 N B:LEU359 4.3 12.1 1.0 HB2 B:GLN360 4.3 12.6 1.0 OH B:TYR335 4.3 14.0 1.0 OD1 B:ASN304 4.3 18.0 1.0 N B:GLN360 4.3 12.2 1.0 CG B:GLU302 4.3 13.2 1.0 CA B:TYR303 4.4 13.4 1.0 C B:LEU359 4.4 12.4 1.0 H B:LYS358 4.5 12.9 1.0 HG3 B:LYS358 4.5 12.0 1.0 OD1 B:ASP346 4.5 14.2 1.0 N B:ASN304 4.5 13.2 1.0 OD2 B:ASP346 4.5 14.5 1.0 CE1 B:PHE328 4.6 13.8 1.0 CA B:LYS358 4.6 12.6 1.0 HG3 B:GLU302 4.6 12.9 1.0 CB B:LYS358 4.7 11.8 1.0 CG B:GLN360 4.7 13.5 1.0 CA B:ASN304 4.7 14.2 1.0 HA B:GLU302 4.8 12.6 1.0 HG2 B:GLU302 4.8 12.9 1.0 CG B:ASP346 4.9 12.9 1.0 CB B:GLN360 4.9 13.2 1.0 N B:LYS358 4.9 12.6 1.0 C B:GLU302 5.0 12.8 1.0

Calcium binding site 4 out of 4 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca528 b:15.2 occ:0.50 O B:HOH962 2.3 18.2 1.0 O B:HOH714 2.4 19.9 1.0 O1A B:HEC1006 2.5 12.2 1.0 O B:PRO116 2.5 11.6 1.0 O B:HOH1166 2.7 22.3 1.0 HG2 B:PRO116 3.1 12.0 1.0 HB3 B:SER84 3.3 11.8 1.0 O1A B:HEC1007 3.4 10.3 0.5 C B:PRO116 3.6 11.8 1.0 CGA B:HEC1006 3.7 12.3 1.0 HA B:ARG117 3.7 10.9 1.0 HD2 B:PRO116 3.8 10.9 1.0 NA B:NA540 3.9 23.5 0.5 OG B:SER84 3.9 12.6 1.0 CB B:SER84 4.0 12.4 1.0 HB3 B:GLU115 4.0 11.2 1.0 CG B:PRO116 4.0 12.1 1.0 HAA2 B:HEC1006 4.0 10.9 1.0 O B:HOH1167 4.1 23.0 0.5 CGA B:HEC1007 4.1 13.2 0.5 HAA1 B:HEC1006 4.1 10.9 1.0 HA B:SER84 4.2 11.7 1.0 O B:HOH810 4.2 19.2 1.0 O B:HOH1041 4.3 18.5 0.5 CD B:PRO116 4.3 11.4 1.0 O2A B:HEC1007 4.3 13.4 0.5 O2A B:HEC1006 4.4 12.2 1.0 HB2 B:PRO116 4.4 11.6 1.0 CAA B:HEC1006 4.5 10.9 1.0 N B:PRO116 4.5 10.4 1.0 N B:ARG117 4.5 11.5 1.0 CA B:PRO116 4.5 11.1 1.0 CA B:ARG117 4.5 10.5 1.0 CB B:PRO116 4.6 12.3 1.0 CA B:SER84 4.6 11.4 1.0 CBA B:HEC1006 4.7 11.1 1.0 HG3 B:PRO116 4.7 12.0 1.0 OE1 B:GLU115 4.8 20.6 1.0 HB2 B:SER84 4.8 11.8 1.0 CB B:GLU115 4.8 11.6 1.0 O B:HOH670 4.9 21.7 0.5 HB2 B:GLU115 4.9 11.2 1.0 O B:HOH802 4.9 13.0 1.0

A.A.Trofimov, K.M.Polyakov, K.M.Boyko, T.V.Tikhonova, T.N.Safonova, A.V.Tikhonov, A.N.Popov, V.O.Popov. Structures of Complexes of Octahaem Cytochrome C Nitrite Reductase From Thioalkalivibrio Nitratireducens with Sulfite and Cyanide. Acta Crystallogr.,Sect.D V. 66 1043 2010.
ISSN: ISSN 0907-4449
PubMed: 20944237
DOI: 10.1107/S0907444910031665