Calcium in PDB 3fo3: Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Dithionite (Sulfite Complex)

The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Dithionite (Sulfite Complex), PDB code: 3fo3 was solved by A.A.Trofimov, 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)	12.00 / 1.40
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	193.790, 193.790, 193.790, 90.00, 90.00, 90.00
R / Rfree (%)	12.6 / 13.9

The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Dithionite (Sulfite Complex) also contains other interesting chemical elements:

Iron	(Fe)	16 atoms
Sodium	(Na)	5 atoms

The binding sites of Calcium atom in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Dithionite (Sulfite Complex) (pdb code 3fo3). 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 Reduced By Sodium Dithionite (Sulfite Complex), PDB code: 3fo3:
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 Reduced By Sodium Dithionite (Sulfite Complex)


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 Reduced By Sodium Dithionite (Sulfite Complex) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca527 b:13.9 occ:1.00 O A:LYS358 2.3 14.2 1.0 OE1 A:GLN360 2.3 15.1 1.0 O A:TYR303 2.3 13.3 1.0 OE2 A:GLU302 2.4 14.0 1.0 O A:HOH955 2.4 15.4 1.0 O A:HOH954 2.5 15.1 1.0 OE1 A:GLU302 2.5 13.8 1.0 CD A:GLU302 2.8 13.2 1.0 H A:TYR303 3.3 13.3 1.0 HA A:LEU359 3.4 12.9 1.0 CD A:GLN360 3.5 15.2 1.0 C A:LYS358 3.5 13.7 1.0 C A:TYR303 3.5 13.4 1.0 HE1 A:PHE328 3.9 15.3 1.0 N A:TYR303 4.0 13.2 1.0 NE2 A:GLN360 4.0 16.3 1.0 HB3 A:LYS358 4.0 13.9 1.0 H A:GLN360 4.0 12.7 1.0 HA A:ASN304 4.1 14.4 1.0 CA A:LEU359 4.1 12.7 1.0 N A:LEU359 4.3 13.1 1.0 HB2 A:GLN360 4.3 13.2 1.0 CG A:GLU302 4.3 13.3 1.0 OH A:TYR335 4.3 15.2 1.0 N A:GLN360 4.3 12.7 1.0 CA A:TYR303 4.4 13.2 1.0 OD1 A:ASN304 4.4 17.7 1.0 H A:LYS358 4.4 14.0 1.0 OD1 A:ASP346 4.4 15.1 1.0 HG3 A:LYS358 4.4 14.2 1.0 C A:LEU359 4.4 12.4 1.0 N A:ASN304 4.5 14.3 1.0 OD2 A:ASP346 4.5 16.4 1.0 CA A:LYS358 4.6 13.5 1.0 HG3 A:GLU302 4.6 13.3 1.0 CB A:LYS358 4.6 14.4 1.0 CE1 A:PHE328 4.7 15.4 1.0 CG A:GLN360 4.7 13.8 1.0 HA A:GLU302 4.7 13.2 1.0 CA A:ASN304 4.7 14.1 1.0 HG2 A:GLU302 4.8 13.4 1.0 CG A:ASP346 4.8 15.1 1.0 N A:LYS358 4.9 14.1 1.0 CB A:GLN360 4.9 13.8 1.0 C A:GLU302 5.0 13.5 1.0 CG A:LYS358 5.0 13.9 1.0

Calcium binding site 2 out of 4 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Dithionite (Sulfite Complex)


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 Reduced By Sodium Dithionite (Sulfite Complex) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca528 b:18.7 occ:0.50 O A:HOH733 2.3 18.2 1.0 O A:PRO116 2.3 12.7 1.0 O A:HOH1146 2.4 14.5 1.0 O2A A:HEC1006 2.4 14.1 1.0 O A:HOH726 2.8 20.7 1.0 O2A A:HEC1007 2.8 14.0 0.5 HG2 A:PRO116 3.0 12.0 1.0 HB3 A:SER84 3.3 12.1 1.0 C A:PRO116 3.4 11.3 1.0 HA A:ARG117 3.5 11.0 1.0 CGA A:HEC1006 3.5 12.9 1.0 CGA A:HEC1007 3.6 13.3 0.5 O1A A:HEC1007 3.7 14.1 0.5 O1A A:HEC1007 3.7 14.4 0.5 CG A:PRO116 3.8 12.0 1.0 HD2 A:PRO116 3.9 11.8 1.0 OG A:SER84 3.9 13.1 1.0 HB3 A:GLU115 3.9 12.4 1.0 HAA2 A:HEC1006 4.0 11.8 1.0 HAA1 A:HEC1006 4.0 12.0 1.0 CB A:SER84 4.0 12.3 1.0 CGA A:HEC1007 4.1 13.2 0.5 NA A:NA544 4.2 23.2 0.5 O A:HOH852 4.2 32.4 1.0 HA A:SER84 4.2 12.1 1.0 CD A:PRO116 4.3 12.1 1.0 O A:HOH860 4.3 16.0 1.0 N A:ARG117 4.3 11.0 1.0 O1A A:HEC1006 4.3 13.9 1.0 O2A A:HEC1007 4.3 15.0 0.5 CA A:PRO116 4.3 11.2 1.0 CA A:ARG117 4.3 10.9 1.0 HB2 A:PRO116 4.3 11.5 1.0 O A:HOH749 4.3 24.5 1.0 CAA A:HEC1006 4.3 11.9 1.0 N A:PRO116 4.3 11.9 1.0 CB A:PRO116 4.4 11.6 1.0 HG3 A:PRO116 4.5 11.8 1.0 CBA A:HEC1006 4.5 12.2 1.0 CA A:SER84 4.6 12.0 1.0 OE1 A:GLU115 4.7 19.9 1.0 CB A:GLU115 4.8 12.4 1.0 HB2 A:SER84 4.8 12.4 1.0 HB2 A:GLU115 4.9 12.4 1.0 C A:GLU115 4.9 11.4 1.0 O A:HOH850 4.9 13.7 1.0

Calcium binding site 3 out of 4 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Dithionite (Sulfite Complex)


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 Reduced By Sodium Dithionite (Sulfite Complex) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca527 b:13.3 occ:1.00 O B:LYS358 2.3 13.5 1.0 OE1 B:GLN360 2.3 14.6 1.0 O B:TYR303 2.4 13.5 1.0 OE2 B:GLU302 2.4 13.9 1.0 O B:HOH961 2.4 14.5 1.0 O B:HOH960 2.5 14.9 1.0 OE1 B:GLU302 2.5 13.2 1.0 CD B:GLU302 2.8 13.2 1.0 H B:TYR303 3.3 12.8 1.0 HA B:LEU359 3.4 12.6 1.0 CD B:GLN360 3.4 14.0 1.0 C B:LYS358 3.5 12.7 1.0 C B:TYR303 3.5 13.5 1.0 HE2 B:PHE328 3.9 13.8 1.0 N B:TYR303 4.0 12.8 1.0 H B:GLN360 4.0 12.5 1.0 HB3 B:LYS358 4.0 13.1 1.0 NE2 B:GLN360 4.0 15.9 1.0 HA B:ASN304 4.1 14.2 1.0 CA B:LEU359 4.2 12.4 1.0 N B:LEU359 4.3 12.7 1.0 HB2 B:GLN360 4.3 12.6 1.0 OH B:TYR335 4.3 14.5 1.0 N B:GLN360 4.3 12.5 1.0 CG B:GLU302 4.3 13.2 1.0 H B:LYS358 4.4 12.9 1.0 OD1 B:ASN304 4.4 18.0 1.0 CA B:TYR303 4.4 13.2 1.0 HG3 B:LYS358 4.4 13.9 1.0 OD1 B:ASP346 4.4 14.5 1.0 C B:LEU359 4.4 12.6 1.0 OD2 B:ASP346 4.5 14.9 1.0 N B:ASN304 4.5 13.2 1.0 CA B:LYS358 4.6 12.5 1.0 HG3 B:GLU302 4.6 13.1 1.0 CB B:LYS358 4.6 13.8 1.0 CE2 B:PHE328 4.6 14.0 1.0 CG B:GLN360 4.7 13.1 1.0 CA B:ASN304 4.7 14.0 1.0 HA B:GLU302 4.8 12.6 1.0 HG2 B:GLU302 4.8 13.2 1.0 CG B:ASP346 4.8 14.5 1.0 N B:LYS358 4.8 13.1 1.0 CB B:GLN360 4.9 12.8 1.0 CG B:LYS358 4.9 13.4 1.0 C B:GLU302 5.0 12.5 1.0

Calcium binding site 4 out of 4 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Dithionite (Sulfite Complex)


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 Reduced By Sodium Dithionite (Sulfite Complex) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca528 b:18.2 occ:0.50 O B:HOH656 2.3 17.8 1.0 O B:PRO116 2.3 12.3 1.0 O B:HOH1152 2.4 14.3 1.0 O1A B:HEC1006 2.4 13.3 1.0 O B:HOH649 2.7 21.1 1.0 O2A B:HEC1007 2.8 13.1 0.5 HG2 B:PRO116 2.9 11.9 1.0 HB3 B:SER84 3.2 12.3 1.0 C B:PRO116 3.4 10.9 1.0 HA B:ARG117 3.5 11.1 1.0 CGA B:HEC1006 3.6 12.4 1.0 CGA B:HEC1007 3.6 12.7 0.5 O1A B:HEC1007 3.7 14.4 0.5 O1A B:HEC1007 3.7 14.3 0.5 CG B:PRO116 3.8 11.8 1.0 HD2 B:PRO116 3.9 11.3 1.0 OG B:SER84 3.9 12.8 1.0 HB3 B:GLU115 3.9 11.9 1.0 HAA2 B:HEC1006 4.0 11.8 1.0 CB B:SER84 4.0 12.3 1.0 HAA1 B:HEC1006 4.0 11.7 1.0 CGA B:HEC1007 4.1 11.6 0.5 NA B:NA548 4.1 24.8 0.5 HA B:SER84 4.2 12.0 1.0 O B:HOH866 4.2 15.7 1.0 O B:HOH858 4.2 30.6 1.0 CD B:PRO116 4.3 11.6 1.0 O B:HOH672 4.3 25.4 1.0 N B:ARG117 4.3 10.9 1.0 O2A B:HEC1006 4.3 13.8 1.0 HB2 B:PRO116 4.3 11.4 1.0 O2A B:HEC1007 4.3 13.3 0.5 CA B:ARG117 4.3 11.1 1.0 CA B:PRO116 4.3 11.0 1.0 CAA B:HEC1006 4.3 11.7 1.0 N B:PRO116 4.3 11.1 1.0 CB B:PRO116 4.4 11.8 1.0 HG3 B:PRO116 4.5 11.6 1.0 CBA B:HEC1006 4.6 12.4 1.0 CA B:SER84 4.6 11.9 1.0 OE1 B:GLU115 4.7 19.1 1.0 HB2 B:SER84 4.7 12.2 1.0 CB B:GLU115 4.8 11.8 1.0 HB2 B:GLU115 4.8 11.8 1.0 O B:HOH856 4.9 14.2 1.0 C B:GLU115 4.9 11.3 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