Calcium in PDB 2zo5: Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Azide

The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Azide, PDB code: 2zo5 was solved by K.M.Polyakov, K.M.Boyko, A.Slutsky, T.V.Tikhonova, A.N.Antipov, R.A.Zvyagilskaya, A.N.Popov, 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)	11.99 / 1.70
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	193.027, 193.027, 193.027, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 16.8

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

Iron	(Fe)	16 atoms
Sodium	(Na)	2 atoms

The binding sites of Calcium atom in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Azide (pdb code 2zo5). 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 A Complex with Azide, PDB code: 2zo5:
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 A Complex with Azide


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 Azide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca527 b:16.1 occ:1.00 OE1 A:GLN360 2.3 18.0 1.0 O A:LYS358 2.3 16.2 1.0 O A:TYR303 2.3 16.5 1.0 O A:HOH1238 2.4 15.5 1.0 OE2 A:GLU302 2.4 17.2 1.0 OE1 A:GLU302 2.4 15.8 1.0 O A:HOH1237 2.6 16.5 1.0 CD A:GLU302 2.8 17.3 1.0 H A:TYR303 3.2 17.1 1.0 HA A:LEU359 3.4 14.7 1.0 CD A:GLN360 3.4 19.0 1.0 C A:LYS358 3.5 15.9 1.0 C A:TYR303 3.5 17.3 1.0 HE22 A:GLN360 3.6 19.2 0.0 HH A:TYR335 3.6 17.0 0.0 HE1 A:PHE328 3.8 17.5 1.0 N A:TYR303 3.9 17.4 1.0 NE2 A:GLN360 4.0 19.2 1.0 H A:GLN360 4.0 15.1 1.0 HB3 A:LYS358 4.0 15.5 1.0 HA A:ASN304 4.1 17.9 1.0 CA A:LEU359 4.1 14.7 1.0 HB2 A:GLN360 4.2 15.9 1.0 OH A:TYR335 4.3 16.9 1.0 N A:LEU359 4.3 14.9 1.0 CG A:GLU302 4.3 16.3 1.0 OD1 A:ASN304 4.3 24.0 1.0 N A:GLN360 4.3 15.2 1.0 H A:LYS358 4.4 16.3 1.0 HD12 A:LEU359 4.4 15.8 0.0 CA A:TYR303 4.4 16.9 1.0 HG3 A:LYS358 4.4 15.6 1.0 C A:LEU359 4.4 14.6 1.0 OD1 A:ASP346 4.4 16.9 1.0 N A:ASN304 4.4 17.1 1.0 OD2 A:ASP346 4.5 17.7 1.0 CA A:LYS358 4.6 15.4 1.0 CE1 A:PHE328 4.6 17.4 1.0 HG3 A:GLU302 4.6 16.6 1.0 CB A:LYS358 4.7 15.5 1.0 CG A:GLN360 4.7 16.9 1.0 HA A:GLU302 4.7 16.0 1.0 HE21 A:GLN360 4.7 19.2 0.0 HG2 A:GLU302 4.7 16.6 1.0 CA A:ASN304 4.7 18.0 1.0 CG A:ASP346 4.8 15.5 1.0 N A:LYS358 4.8 16.6 1.0 CB A:GLN360 4.8 16.2 1.0 HD1 A:PHE328 4.9 17.0 1.0 C A:GLU302 4.9 16.8 1.0 CG A:LYS358 4.9 16.1 1.0 HE1 A:TYR335 5.0 16.2 1.0 HA A:TYR303 5.0 17.2 1.0

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


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 Azide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca528 b:19.4 occ:0.50 O A:PRO116 2.3 15.6 1.0 O A:HOH1049 2.3 21.2 1.0 O A:HOH1336 2.3 15.6 1.0 O A:HOH1396 2.5 27.2 1.0 O2A A:HEC1006 2.6 15.4 1.0 O2A A:HEC1007 3.1 19.9 0.5 HB3 A:SER84 3.2 15.1 1.0 HG2 A:PRO116 3.3 14.5 1.0 C A:PRO116 3.4 14.9 1.0 HA A:ARG117 3.5 13.3 1.0 HD2 A:PRO116 3.7 13.9 1.0 HB3 A:GLU115 3.8 14.2 1.0 O1A A:HEC1007 3.8 14.4 0.5 CGA A:HEC1006 3.8 15.4 1.0 HG A:SER84 3.9 15.1 0.0 CB A:SER84 4.0 15.2 1.0 OG A:SER84 4.0 15.1 1.0 CGA A:HEC1007 4.0 18.1 0.5 CG A:PRO116 4.1 14.9 1.0 O1A A:HEC1007 4.1 18.0 0.5 HA A:SER84 4.1 14.9 1.0 CD A:PRO116 4.2 13.6 1.0 O A:HOH1153 4.2 20.2 1.0 HAA2 A:HEC1006 4.2 14.0 1.0 N A:PRO116 4.2 13.9 1.0 HAA1 A:HEC1006 4.2 14.0 1.0 HB2 A:PRO116 4.3 14.3 1.0 CA A:PRO116 4.3 14.1 1.0 N A:ARG117 4.3 13.7 1.0 CA A:ARG117 4.3 13.3 1.0 O A:HOH1145 4.4 32.8 1.0 CB A:PRO116 4.5 14.5 1.0 O1A A:HEC1006 4.5 16.2 1.0 CGA A:HEC1007 4.5 14.4 0.5 CA A:SER84 4.5 15.1 1.0 OE1 A:GLU115 4.6 22.7 1.0 CAA A:HEC1006 4.6 14.6 1.0 CB A:GLU115 4.6 14.1 1.0 HB2 A:GLU115 4.7 14.2 1.0 O2A A:HEC1007 4.7 15.7 0.5 HB2 A:SER84 4.7 15.1 1.0 C A:GLU115 4.8 13.4 1.0 CBA A:HEC1006 4.8 14.1 1.0 HG3 A:PRO116 4.9 14.5 1.0 HB3 A:ARG117 4.9 13.3 1.0 C A:SER84 4.9 14.8 1.0

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


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 Azide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca527 b:14.5 occ:1.00 OE1 B:GLN360 2.3 16.6 1.0 O B:LYS358 2.3 14.6 1.0 O B:TYR303 2.3 13.5 1.0 OE2 B:GLU302 2.4 14.9 1.0 O B:HOH1299 2.4 14.6 1.0 O B:HOH1298 2.4 13.9 1.0 OE1 B:GLU302 2.5 13.7 1.0 CD B:GLU302 2.8 16.1 1.0 H B:TYR303 3.3 14.3 1.0 HA B:LEU359 3.4 13.1 1.0 CD B:GLN360 3.4 16.2 1.0 C B:LYS358 3.5 13.6 1.0 C B:TYR303 3.5 15.0 1.0 HH B:TYR335 3.5 14.9 0.0 HE2 B:PHE328 3.7 15.3 1.0 HE22 B:GLN360 3.8 16.0 0.0 NE2 B:GLN360 4.0 16.0 1.0 N B:TYR303 4.0 14.3 1.0 H B:GLN360 4.0 13.0 1.0 HB3 B:LYS358 4.0 13.4 1.0 HA B:ASN304 4.1 16.3 1.0 CA B:LEU359 4.1 13.0 1.0 HB2 B:GLN360 4.2 13.5 1.0 N B:LEU359 4.2 13.3 1.0 HD12 B:LEU359 4.2 14.8 0.0 CG B:GLU302 4.3 14.3 1.0 OH B:TYR335 4.3 14.8 1.0 N B:GLN360 4.3 12.9 1.0 OD1 B:ASN304 4.3 24.4 1.0 CA B:TYR303 4.4 14.8 1.0 H B:LYS358 4.4 13.9 1.0 OD1 B:ASP346 4.4 15.3 1.0 HG3 B:LYS358 4.4 13.0 1.0 N B:ASN304 4.4 15.6 1.0 C B:LEU359 4.4 13.1 1.0 CE2 B:PHE328 4.5 15.1 1.0 OD2 B:ASP346 4.5 14.2 1.0 CA B:LYS358 4.5 13.6 1.0 HG3 B:GLU302 4.6 14.6 1.0 CB B:LYS358 4.7 12.9 1.0 CG B:GLN360 4.7 14.4 1.0 CA B:ASN304 4.7 16.4 1.0 HA B:GLU302 4.7 13.2 1.0 HG2 B:GLU302 4.7 14.6 1.0 CG B:ASP346 4.8 13.6 1.0 CB B:GLN360 4.8 14.0 1.0 N B:LYS358 4.8 13.8 1.0 HE21 B:GLN360 4.9 16.0 0.0 C B:GLU302 4.9 13.9 1.0 HD2 B:PHE328 4.9 14.9 1.0 CG B:LYS358 5.0 13.1 1.0 HA B:TYR303 5.0 14.7 1.0

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


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 Azide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca528 b:19.0 occ:0.50 O B:PRO116 2.3 13.7 1.0 O B:HOH1397 2.3 15.2 1.0 O B:HOH1110 2.4 19.8 1.0 O B:HOH1456 2.5 18.3 0.5 O1A B:HEC1006 2.5 13.7 1.0 O5 B:PG41014 2.9 16.0 0.5 O2A B:HEC1007 3.1 19.4 0.5 HG2 B:PRO116 3.1 13.3 1.0 HB3 B:SER84 3.2 12.8 1.0 C B:PRO116 3.4 13.0 1.0 HA B:ARG117 3.5 12.7 1.0 C8 B:PG41014 3.6 19.2 0.5 O1A B:HEC1007 3.7 13.2 0.5 CGA B:HEC1006 3.7 14.2 1.0 C7 B:PG41014 3.8 20.9 0.5 HB3 B:GLU115 3.8 12.4 1.0 HD2 B:PRO116 3.8 12.7 1.0 CG B:PRO116 4.0 13.8 1.0 CB B:SER84 4.0 12.8 1.0 OG B:SER84 4.0 12.4 1.0 CGA B:HEC1007 4.0 17.4 0.5 HG B:SER84 4.0 12.4 0.0 O4 B:PG41014 4.0 17.8 0.5 O1A B:HEC1007 4.1 15.6 0.5 HAA1 B:HEC1006 4.1 12.1 1.0 HAA2 B:HEC1006 4.1 12.1 1.0 HA B:SER84 4.2 13.0 1.0 CD B:PRO116 4.2 13.1 1.0 N B:ARG117 4.2 13.0 1.0 N B:PRO116 4.2 12.3 1.0 O B:HOH1214 4.2 19.6 1.0 CA B:PRO116 4.3 12.2 1.0 CA B:ARG117 4.3 12.4 1.0 HB2 B:PRO116 4.3 12.5 1.0 O2A B:HEC1006 4.4 14.6 1.0 C6 B:PG41014 4.4 24.1 0.5 CGA B:HEC1007 4.4 15.8 0.5 CB B:PRO116 4.4 12.5 1.0 O B:HOH1548 4.5 24.8 0.5 CAA B:HEC1006 4.5 13.1 1.0 O B:HOH1206 4.5 35.9 1.0 CA B:SER84 4.6 12.9 1.0 OE1 B:GLU115 4.6 21.7 1.0 CB B:GLU115 4.6 12.2 1.0 HB2 B:GLU115 4.7 12.4 1.0 HG3 B:PRO116 4.7 13.3 1.0 CBA B:HEC1006 4.7 12.2 1.0 HB2 B:SER84 4.7 12.8 1.0 O2A B:HEC1007 4.7 14.5 0.5 C B:GLU115 4.8 11.4 1.0 HB3 B:ARG117 4.9 12.5 1.0 C B:SER84 5.0 13.7 1.0

K.M.Polyakov, K.M.Boyko, T.V.Tikhonova, A.Slutsky, A.N.Antipov, R.A.Zvyagilskaya, A.N.Popov, G.P.Bourenkov, V.S.Lamzin, V.O.Popov. High-Resolution Structural Analysis of A Novel Octaheme Cytochrome C Nitrite Reductase From the Haloalkaliphilic Bacterium Thioalkalivibrio Nitratireducens J.Mol.Biol. V. 389 846 2009.
ISSN: ISSN 0022-2836
PubMed: 19393666
DOI: 10.1016/J.JMB.2009.04.037