Calcium in PDB 3rkh: Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Nitrite (Full Occupancy)

The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Nitrite (Full Occupancy), PDB code: 3rkh was solved by A.A.Trofimov, K.M.Polyakov, T.V.Tikhonova, A.V.Tikhonov, P.V.Dorovatovskii, V.O.Popov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	100.00 / 1.83
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	192.800, 192.800, 192.800, 90.00, 90.00, 90.00
R / Rfree (%)	14.1 / 16.2

The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Nitrite (Full Occupancy) 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 A Complex with Nitrite (Full Occupancy) (pdb code 3rkh). 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 A Complex with Nitrite (Full Occupancy), PDB code: 3rkh:
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 A Complex with Nitrite (Full Occupancy)


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 Nitrite (Full Occupancy) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2 b:19.0 occ:1.00 O A:LYS358 2.3 16.9 1.0 OE1 A:GLN360 2.3 20.1 1.0 O A:TYR303 2.3 17.6 1.0 OE2 A:GLU302 2.4 18.7 1.0 OE1 A:GLU302 2.4 17.8 1.0 O A:HOH955 2.4 18.2 1.0 O A:HOH954 2.6 20.1 1.0 CD A:GLU302 2.7 19.0 1.0 CD A:GLN360 3.4 20.4 1.0 C A:LYS358 3.5 16.5 1.0 C A:TYR303 3.5 17.4 1.0 N A:TYR303 3.9 15.8 1.0 NE2 A:GLN360 4.0 23.8 1.0 CA A:LEU359 4.1 15.7 1.0 OH A:TYR335 4.2 18.2 1.0 N A:GLN360 4.2 16.0 1.0 N A:LEU359 4.2 16.1 1.0 CG A:GLU302 4.2 17.5 1.0 CA A:TYR303 4.3 17.1 1.0 OD1 A:ASP346 4.3 19.1 1.0 OD1 A:ASN304 4.4 18.5 1.0 C A:LEU359 4.4 16.4 1.0 N A:ASN304 4.5 17.2 1.0 OD2 A:ASP346 4.5 18.4 1.0 CA A:LYS358 4.5 16.6 1.0 CE1 A:PHE328 4.6 17.8 1.0 CB A:LYS358 4.6 16.4 1.0 CG A:GLN360 4.6 19.8 1.0 CA A:ASN304 4.8 17.9 1.0 CB A:GLN360 4.8 17.8 1.0 CG A:ASP346 4.8 16.1 1.0 N A:LYS358 4.8 16.3 1.0 C A:GLU302 4.9 16.4 1.0 CG A:LYS358 4.9 15.7 1.0

Calcium binding site 2 out of 2 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Nitrite (Full Occupancy)


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 Nitrite (Full Occupancy) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2 b:18.2 occ:1.00 O B:LYS358 2.3 16.4 1.0 O B:TYR303 2.3 16.5 1.0 OE1 B:GLN360 2.3 18.9 1.0 OE2 B:GLU302 2.4 18.0 1.0 O B:HOH972 2.4 15.5 1.0 OE1 B:GLU302 2.5 16.6 1.0 O B:HOH971 2.5 16.8 1.0 CD B:GLU302 2.8 16.4 1.0 CD B:GLN360 3.4 21.2 1.0 C B:LYS358 3.5 16.3 1.0 C B:TYR303 3.5 16.5 1.0 N B:TYR303 3.9 14.8 1.0 NE2 B:GLN360 3.9 24.7 1.0 CA B:LEU359 4.1 14.4 1.0 N B:GLN360 4.2 15.3 1.0 OH B:TYR335 4.3 18.0 1.0 N B:LEU359 4.3 14.8 1.0 CG B:GLU302 4.3 14.7 1.0 OD1 B:ASN304 4.3 20.2 1.0 OD1 B:ASP346 4.4 18.0 1.0 CA B:TYR303 4.4 15.4 1.0 C B:LEU359 4.4 15.4 1.0 OD2 B:ASP346 4.5 18.1 1.0 N B:ASN304 4.5 15.7 1.0 CE1 B:PHE328 4.5 16.9 1.0 CA B:LYS358 4.5 16.8 1.0 CB B:LYS358 4.6 16.3 1.0 CG B:GLN360 4.7 19.0 1.0 CA B:ASN304 4.7 17.1 1.0 CB B:GLN360 4.7 18.0 1.0 CG B:ASP346 4.7 15.9 1.0 N B:LYS358 4.8 16.3 1.0 CG B:LYS358 4.9 15.5 1.0 C B:GLU302 4.9 15.3 1.0

A.A.Trofimov, K.M.Polyakov, T.V.Tikhonova, A.V.Tikhonov, T.N.Safonova, K.M.Boyko, P.V.Dorovatovskii, V.O.Popov. Covalent Modifications of the Catalytic Tyrosine in Octahaem Cytochrome C Nitrite Reductase and Their Effect on the Enzyme Activity. Acta Crystallogr.,Sect.D V. 68 144 2012.
ISSN: ISSN 0907-4449
PubMed: 22281743
DOI: 10.1107/S0907444911052632