Calcium in PDB 3owm: Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Hydroxylamine

The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Hydroxylamine, PDB code: 3owm 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)	12.00 / 1.65
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	192.529, 192.529, 192.529, 90.00, 90.00, 90.00
R / Rfree (%)	13.9 / 15.4

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

Iron	(Fe)	16 atoms
Sodium	(Na)	1 atom

The binding sites of Calcium atom in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Hydroxylamine (pdb code 3owm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Hydroxylamine, PDB code: 3owm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Hydroxylamine


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 A Complex with Hydroxylamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2 b:14.6 occ:1.00 OE1 A:GLN360 2.3 16.8 1.0 O A:TYR303 2.3 14.0 1.0 O A:LYS358 2.3 14.5 1.0 O A:HOH882 2.3 14.7 1.0 OE2 A:GLU302 2.4 15.1 1.0 OE1 A:GLU302 2.5 14.7 1.0 O A:HOH881 2.5 16.3 1.0 CD A:GLU302 2.8 15.4 1.0 CD A:GLN360 3.4 18.1 1.0 C A:TYR303 3.5 14.8 1.0 C A:LYS358 3.5 14.3 1.0 N A:TYR303 3.9 15.0 1.0 NE2 A:GLN360 3.9 20.0 1.0 CA A:LEU359 4.1 13.3 1.0 N A:LEU359 4.3 13.6 1.0 N A:GLN360 4.3 13.2 1.0 OH A:TYR335 4.3 16.6 1.0 OD1 A:ASN304 4.3 19.1 1.0 CG A:GLU302 4.3 14.1 1.0 CA A:TYR303 4.4 14.8 1.0 OD1 A:ASP346 4.4 14.7 1.0 C A:LEU359 4.4 13.2 1.0 N A:ASN304 4.4 15.3 1.0 OD2 A:ASP346 4.5 18.1 1.0 CA A:LYS358 4.6 13.9 1.0 CE1 A:PHE328 4.6 15.7 1.0 CB A:LYS358 4.6 14.3 1.0 CG A:GLN360 4.6 16.9 1.0 CA A:ASN304 4.7 15.8 1.0 CB A:GLN360 4.8 15.3 1.0 CG A:ASP346 4.8 15.8 1.0 N A:LYS358 4.8 14.9 1.0 C A:GLU302 4.9 14.6 1.0 CG A:LYS358 4.9 14.5 1.0

Calcium binding site 2 out of 6 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Hydroxylamine


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 A Complex with Hydroxylamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3 b:25.4 occ:0.50 O A:HOH1077 2.2 19.0 1.0 O A:PRO116 2.4 14.4 1.0 O A:HOH652 2.5 28.4 1.0 O2A A:HEC1006 2.7 14.3 1.0 O A:HOH645 2.7 24.9 1.0 C A:PRO116 3.5 13.0 1.0 O1A A:HEC1007 3.5 13.2 0.5 CGA A:HEC1006 3.8 13.2 1.0 OG A:SER84 4.0 13.4 1.0 CG A:PRO116 4.0 14.4 1.0 CB A:SER84 4.0 13.2 1.0 CGA A:HEC1007 4.1 15.3 0.5 CD A:PRO116 4.1 13.1 1.0 O A:HOH668 4.1 31.3 1.0 O A:HOH779 4.2 20.6 1.0 N A:PRO116 4.3 12.6 1.0 CA A:PRO116 4.3 12.7 1.0 O2A A:HEC1007 4.3 12.0 0.5 N A:ARG117 4.4 12.4 1.0 O A:HOH771 4.4 30.1 1.0 CB A:PRO116 4.4 13.1 1.0 CA A:ARG117 4.4 11.6 1.0 O1A A:HEC1006 4.5 14.4 1.0 CAA A:HEC1006 4.5 11.7 1.0 CA A:SER84 4.6 12.6 1.0 OE1 A:GLU115 4.7 22.5 1.0 CB A:GLU115 4.7 13.1 1.0 CBA A:HEC1006 4.8 12.0 1.0 C A:GLU115 4.9 12.8 1.0

Calcium binding site 3 out of 6 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Hydroxylamine


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 A Complex with Hydroxylamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca525 b:25.8 occ:0.20 O A:HOH1082 2.4 27.0 1.0 O A:HOH1068 2.4 30.1 1.0 O A:HOH1056 3.8 28.6 1.0 OD2 A:ASP450 4.1 22.5 1.0 O A:HOH1120 4.3 38.8 1.0 O3 A:TRS524 4.3 39.0 0.1 O2 A:TRS524 4.4 39.0 0.1 O1 A:TRS524 4.4 39.0 0.1 O A:HOH943 4.6 31.7 1.0 O A:HOH976 4.7 17.3 0.6 O A:HOH1125 4.7 21.8 0.5 NZ A:LYS102 4.8 18.3 0.3 CG A:ASP450 5.0 20.1 1.0

Calcium binding site 4 out of 6 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Hydroxylamine


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 A Complex with Hydroxylamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2 b:12.6 occ:1.00 OE1 B:GLN360 2.3 14.4 1.0 O B:LYS358 2.3 13.1 1.0 O B:TYR303 2.3 12.1 1.0 OE2 B:GLU302 2.4 14.0 1.0 O B:HOH919 2.4 12.5 1.0 OE1 B:GLU302 2.5 12.1 1.0 O B:HOH918 2.5 13.7 1.0 CD B:GLU302 2.8 14.5 1.0 CD B:GLN360 3.4 16.2 1.0 C B:LYS358 3.5 12.5 1.0 C B:TYR303 3.5 12.7 1.0 N B:TYR303 3.9 12.6 1.0 NE2 B:GLN360 4.0 18.6 1.0 CA B:LEU359 4.1 11.4 1.0 N B:LEU359 4.2 11.7 1.0 OH B:TYR335 4.3 13.2 1.0 N B:GLN360 4.3 11.8 1.0 CG B:GLU302 4.3 12.4 1.0 OD1 B:ASN304 4.3 19.3 1.0 CA B:TYR303 4.4 12.9 1.0 C B:LEU359 4.4 11.9 1.0 OD1 B:ASP346 4.4 13.8 1.0 N B:ASN304 4.4 12.9 1.0 OD2 B:ASP346 4.5 14.5 1.0 CE1 B:PHE328 4.6 13.2 1.0 CA B:LYS358 4.6 12.1 1.0 CG B:GLN360 4.6 15.3 1.0 CB B:LYS358 4.6 12.0 1.0 CA B:ASN304 4.7 13.9 1.0 CB B:GLN360 4.8 14.3 1.0 CG B:ASP346 4.8 12.5 1.0 N B:LYS358 4.9 12.5 1.0 C B:GLU302 4.9 12.4 1.0 CG B:LYS358 5.0 12.2 1.0

Calcium binding site 5 out of 6 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Hydroxylamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Hydroxylamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca3 b:25.5 occ:0.50 O B:HOH1116 2.2 19.1 1.0 O B:PRO116 2.4 13.8 1.0 O B:HOH605 2.5 29.2 1.0 O1A B:HEC1006 2.6 13.0 1.0 O B:HOH598 2.8 26.3 1.0 O1A B:HEC1007 3.4 12.2 0.5 C B:PRO116 3.4 11.9 1.0 CGA B:HEC1006 3.7 12.6 1.0 CG B:PRO116 4.0 12.6 1.0 OG B:SER84 4.0 12.8 1.0 CB B:SER84 4.0 12.3 1.0 CGA B:HEC1007 4.1 14.7 0.5 O B:HOH705 4.1 31.5 1.0 O B:HOH816 4.1 18.3 1.0 CD B:PRO116 4.2 11.6 1.0 CA B:PRO116 4.3 10.8 1.0 N B:PRO116 4.3 10.2 1.0 O2A B:HEC1007 4.3 12.0 0.5 N B:ARG117 4.3 11.1 1.0 CB B:PRO116 4.4 11.5 1.0 O B:HOH808 4.4 30.2 1.0 CA B:ARG117 4.4 10.3 1.0 CAA B:HEC1006 4.4 10.9 1.0 O2A B:HEC1006 4.5 13.1 1.0 CA B:SER84 4.6 11.5 1.0 CBA B:HEC1006 4.7 10.5 1.0 CB B:GLU115 4.7 11.5 1.0 OE1 B:GLU115 4.8 22.6 1.0 C B:GLU115 4.9 10.4 1.0 O B:HOH806 5.0 12.2 1.0

Calcium binding site 6 out of 6 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Hydroxylamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Hydroxylamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca525 b:24.2 occ:0.20 O B:HOH1121 2.4 24.5 1.0 O B:HOH1107 2.5 28.4 1.0 O B:HOH1095 3.9 23.7 1.0 OD2 B:ASP450 4.0 19.5 1.0 O B:HOH1159 4.4 24.5 0.5 O3 B:TRS524 4.5 31.9 0.1 O2 B:TRS524 4.5 31.9 0.1 O1 B:TRS524 4.5 31.9 0.1 O B:HOH1164 4.5 19.0 0.5 O B:HOH980 4.7 29.9 1.0 NZ B:LYS102 4.7 18.4 0.5 O B:HOH1021 4.7 13.7 0.6 CG B:ASP450 5.0 16.5 1.0

A.A.Trofimov, K.M.Polyakov, T.V.Tikhonova, V.O.Popov. Binding of Sulfite By the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase To Be Published.