Calcium in PDB 3gm6: Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Phosphate

The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Phosphate, PDB code: 3gm6 was solved by A.A.Trofimov, K.M.Polyakov, K.M.Boyko, A.A.Filimonenkov, P.V.Dorovatovsky, T.V.Tikhonova, V.O.Popov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.90 / 1.80
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	196.560, 196.560, 196.560, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 17.2

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

Iron

(Fe)

16 atoms

The binding sites of Calcium atom in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Phosphate (pdb code 3gm6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Phosphate, PDB code: 3gm6:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Phosphate


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 Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca527 b:15.0 occ:1.00 O A:LYS358 2.3 14.2 1.0 OE1 A:GLN360 2.3 16.3 1.0 O A:TYR303 2.3 15.0 1.0 OE2 A:GLU302 2.4 16.0 1.0 O A:HOH822 2.5 11.3 1.0 OE1 A:GLU302 2.5 13.4 1.0 O A:HOH821 2.6 13.9 1.0 CD A:GLU302 2.8 14.9 1.0 H A:TYR303 3.3 14.3 1.0 C A:LYS358 3.5 14.0 1.0 CD A:GLN360 3.5 17.6 1.0 HA A:LEU359 3.6 13.7 1.0 C A:TYR303 3.6 15.8 1.0 HE1 A:PHE328 3.8 17.2 1.0 HB3 A:LYS358 4.0 13.8 1.0 N A:TYR303 4.0 14.0 1.0 HA A:ASN304 4.1 17.4 1.0 H A:GLN360 4.2 14.6 1.0 NE2 A:GLN360 4.2 18.4 1.0 CA A:LEU359 4.3 13.5 1.0 HB2 A:GLN360 4.3 15.4 1.0 N A:LEU359 4.3 13.8 1.0 CG A:GLU302 4.3 14.5 1.0 OD1 A:ASN304 4.4 27.6 1.0 OH A:TYR335 4.4 15.3 1.0 HG3 A:LYS358 4.4 14.1 1.0 OD1 A:ASP346 4.5 15.7 1.0 CA A:TYR303 4.5 15.4 1.0 N A:GLN360 4.5 14.3 1.0 H A:LYS358 4.5 14.8 1.0 N A:ASN304 4.5 16.4 1.0 OD2 A:ASP346 4.6 17.1 1.0 C A:LEU359 4.6 14.3 1.0 CA A:LYS358 4.6 13.7 1.0 HG3 A:GLU302 4.6 14.3 1.0 CE1 A:PHE328 4.6 17.6 1.0 CB A:LYS358 4.7 14.1 1.0 CG A:GLN360 4.7 17.2 1.0 CA A:ASN304 4.8 17.5 1.0 HG2 A:GLU302 4.8 14.3 1.0 CD1 A:TYR303 4.8 18.4 1.0 HD1 A:TYR303 4.8 18.3 1.0 HA A:GLU302 4.8 12.9 1.0 CG A:ASP346 4.9 14.1 1.0 CB A:GLN360 4.9 15.2 1.0 N A:LYS358 4.9 15.0 1.0 CE1 A:TYR303 5.0 18.8 1.0 CG A:LYS358 5.0 14.0 1.0

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


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 Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca527 b:14.1 occ:1.00 O B:LYS358 2.3 14.4 1.0 OE1 B:GLN360 2.3 15.4 1.0 O B:TYR303 2.3 13.8 1.0 OE2 B:GLU302 2.4 15.6 1.0 O B:HOH875 2.4 10.5 1.0 O B:HOH874 2.5 15.6 1.0 OE1 B:GLU302 2.6 12.7 1.0 CD B:GLU302 2.8 12.6 1.0 H B:TYR303 3.3 12.4 1.0 C B:LYS358 3.5 14.3 1.0 CD B:GLN360 3.5 17.2 1.0 HA B:LEU359 3.6 13.7 1.0 C B:TYR303 3.6 14.3 1.0 HE2 B:PHE328 3.8 15.3 1.0 HA B:ASN304 4.0 15.3 1.0 HB3 B:LYS358 4.0 13.9 1.0 N B:TYR303 4.1 12.5 1.0 H B:GLN360 4.1 13.8 1.0 NE2 B:GLN360 4.2 17.0 1.0 OD1 B:ASN304 4.3 17.4 0.5 CA B:LEU359 4.3 13.8 1.0 HB2 B:GLN360 4.3 14.1 1.0 N B:LEU359 4.3 13.7 1.0 CG B:GLU302 4.3 12.1 1.0 OH B:TYR335 4.4 12.8 1.0 OD1 B:ASP346 4.4 13.2 1.0 H B:LYS358 4.4 14.3 1.0 N B:GLN360 4.5 13.8 1.0 HG3 B:LYS358 4.5 14.0 1.0 CA B:TYR303 4.5 13.0 1.0 OD2 B:ASP346 4.5 14.7 1.0 N B:ASN304 4.5 14.4 1.0 CA B:LYS358 4.6 13.7 1.0 CE2 B:PHE328 4.6 15.4 1.0 C B:LEU359 4.6 13.9 1.0 HG3 B:GLU302 4.6 12.2 1.0 CB B:LYS358 4.7 14.7 1.0 OD1 B:ASN304 4.7 13.7 0.5 CG B:GLN360 4.7 15.3 1.0 CA B:ASN304 4.7 15.2 1.0 HG2 B:GLU302 4.8 12.2 1.0 CD1 B:TYR303 4.8 16.0 1.0 CG B:ASP346 4.8 15.1 1.0 HA B:GLU302 4.8 11.4 1.0 HD1 B:TYR303 4.9 15.6 1.0 N B:LYS358 4.9 14.3 1.0 CB B:GLN360 4.9 14.3 1.0 CG B:LYS358 5.0 13.3 1.0 HG3 B:GLN360 5.0 15.5 1.0

A.A.Trofimov, K.M.Polyakov, K.M.Boiko, A.A.Filimonenkov, P.V.Dorovatovskii, T.V.Tikhonova, V.O.Popov, M.V.Koval'chuk. Structure of Octaheme Cytochrome C Nitrite Reductase From Thioalkalivibrio Nitratireducens in A Complex with Phosphate Crystallography Reports V. 55 58 2010.
ISSN: ISSN 1063-7745
DOI: 10.1134/S1063774510010104