Calcium in PDB 3s7w: Structure of the Tvnirb Form of Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase with An Oxidized GLN360 in A Complex with Hydroxylamine

The structure of Structure of the Tvnirb Form of Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase with An Oxidized GLN360 in A Complex with Hydroxylamine, PDB code: 3s7w was solved by A.A.Trofimov, K.M.Polyakov, 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)	19.70 / 1.79
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	194.890, 194.890, 194.890, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 17.2

The structure of Structure of the Tvnirb Form of Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase with An Oxidized GLN360 in A Complex with Hydroxylamine also contains other interesting chemical elements:

Iron

(Fe)

16 atoms

The binding sites of Calcium atom in the Structure of the Tvnirb Form of Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase with An Oxidized GLN360 in A Complex with Hydroxylamine (pdb code 3s7w). 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 Tvnirb Form of Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase with An Oxidized GLN360 in A Complex with Hydroxylamine, PDB code: 3s7w:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of the Tvnirb Form of Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase with An Oxidized GLN360 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 Tvnirb Form of Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase with An Oxidized GLN360 in A Complex with Hydroxylamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2 b:25.2 occ:1.00 OE1 A:GLN360 2.3 26.3 1.0 O A:LYS358 2.3 21.8 1.0 O A:TYR303 2.4 23.4 1.0 OE2 A:GLU302 2.4 24.6 1.0 O A:HOH816 2.4 25.7 1.0 O A:HOH815 2.5 25.5 1.0 OE1 A:GLU302 2.6 22.9 1.0 CD A:GLU302 2.8 25.6 1.0 C A:LYS358 3.5 22.6 1.0 CD A:GLN360 3.5 28.2 1.0 C A:TYR303 3.6 23.4 1.0 N A:TYR303 4.0 22.2 1.0 CA A:LEU359 4.2 22.2 1.0 N A:GLN360 4.3 22.7 1.0 OD1 A:ASN304 4.3 33.2 1.0 N A:LEU359 4.3 22.3 1.0 OH A:TYR335 4.3 23.7 1.0 CG A:GLU302 4.4 23.4 1.0 CG A:GLN360 4.4 27.7 1.0 OD1 A:ASP346 4.4 24.0 1.0 C A:LEU359 4.5 22.8 1.0 CA A:TYR303 4.5 22.9 1.0 NE2 A:GLN360 4.5 29.0 1.0 N A:ASN304 4.5 24.0 1.0 OD2 A:ASP346 4.5 25.2 1.0 CD1 A:TYR303 4.6 26.2 1.0 CE1 A:TYR303 4.6 26.2 1.0 CA A:LYS358 4.6 22.0 1.0 CB A:GLN360 4.6 25.3 1.0 CE1 A:PHE328 4.6 24.0 1.0 CB A:LYS358 4.7 22.0 1.0 CA A:ASN304 4.8 24.8 1.0 N A:LYS358 4.8 22.7 1.0 CG A:ASP346 4.8 22.7 1.0 CG A:TYR303 5.0 23.2 1.0

Calcium binding site 2 out of 4 in the Structure of the Tvnirb Form of Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase with An Oxidized GLN360 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 Tvnirb Form of Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase with An Oxidized GLN360 in A Complex with Hydroxylamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca525 b:36.0 occ:0.50 O A:HOH894 2.1 26.2 1.0 O2A A:HEC1006 2.6 22.6 1.0 O1 A:GOL3 2.6 31.3 1.0 O A:PRO116 2.6 21.5 1.0 O A:HOH595 3.0 31.6 1.0 O1A A:HEC1007 3.4 27.1 0.5 C1 A:GOL3 3.6 36.9 1.0 C A:PRO116 3.7 20.9 1.0 CGA A:HEC1006 3.7 24.0 1.0 OG A:SER84 4.0 23.0 1.0 O A:HOH634 4.1 36.4 1.0 CGA A:HEC1007 4.1 26.2 0.5 CG A:PRO116 4.1 22.2 1.0 CB A:SER84 4.2 22.4 1.0 O2 A:GOL3 4.2 36.9 1.0 C2 A:GOL3 4.2 40.0 1.0 CAA A:HEC1006 4.3 18.5 1.0 CD A:PRO116 4.4 19.8 1.0 O1A A:HEC1006 4.4 24.2 1.0 CA A:PRO116 4.5 20.2 1.0 N A:ARG117 4.5 20.8 1.0 CB A:PRO116 4.5 20.6 1.0 N A:PRO116 4.6 20.1 1.0 O2A A:HEC1007 4.6 28.6 0.5 CA A:ARG117 4.6 19.4 1.0 CBA A:HEC1006 4.6 18.8 1.0 CA A:SER84 4.7 22.7 1.0 O A:HOH719 4.7 25.4 1.0 OE1 A:GLU115 4.9 27.5 1.0

Calcium binding site 3 out of 4 in the Structure of the Tvnirb Form of Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase with An Oxidized GLN360 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 Tvnirb Form of Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase with An Oxidized GLN360 in A Complex with Hydroxylamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2 b:28.1 occ:1.00 OE1 B:GLN360 2.3 29.1 1.0 O B:TYR303 2.3 24.7 1.0 O B:LYS358 2.3 24.9 1.0 OE2 B:GLU302 2.4 27.4 1.0 O B:HOH824 2.5 26.7 1.0 OE1 B:GLU302 2.5 23.3 1.0 O B:HOH823 2.5 29.6 1.0 CD B:GLU302 2.8 25.8 1.0 C B:LYS358 3.5 24.4 1.0 CD B:GLN360 3.5 31.0 1.0 C B:TYR303 3.6 25.1 1.0 N B:TYR303 4.0 24.3 1.0 CA B:LEU359 4.2 24.3 1.0 N B:GLN360 4.3 24.6 1.0 N B:LEU359 4.3 23.5 1.0 CG B:GLU302 4.3 24.8 1.0 OH B:TYR335 4.4 24.7 1.0 CG B:GLN360 4.4 29.3 1.0 OD2 B:ASP346 4.4 28.1 1.0 OD1 B:ASN304 4.4 31.9 1.0 CA B:TYR303 4.5 24.5 1.0 C B:LEU359 4.5 24.6 1.0 NE2 B:GLN360 4.5 32.2 1.0 N B:ASN304 4.5 25.3 1.0 OD1 B:ASP346 4.5 26.5 1.0 CB B:GLN360 4.6 26.3 1.0 CD1 B:TYR303 4.6 25.9 1.0 CA B:LYS358 4.6 24.2 1.0 CE1 B:PHE328 4.6 26.0 1.0 CE1 B:TYR303 4.6 26.3 1.0 CB B:LYS358 4.7 24.6 1.0 CA B:ASN304 4.8 26.5 1.0 CG B:ASP346 4.8 25.6 1.0 N B:LYS358 4.8 24.2 1.0 CG B:LYS358 5.0 26.3 1.0 CG B:TYR303 5.0 25.1 1.0

Calcium binding site 4 out of 4 in the Structure of the Tvnirb Form of Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase with An Oxidized GLN360 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 Tvnirb Form of Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase with An Oxidized GLN360 in A Complex with Hydroxylamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca526 b:38.0 occ:0.50 O B:HOH902 2.1 28.2 1.0 O1A B:HEC1007 2.6 25.1 0.5 O3 B:GOL3 2.6 32.7 1.0 O1A B:HEC1006 2.6 21.3 1.0 O B:PRO116 2.7 22.5 1.0 O B:HOH610 3.0 31.6 1.0 O2A B:HEC1007 3.3 24.3 0.5 CGA B:HEC1007 3.3 22.1 0.5 C3 B:GOL3 3.6 37.8 1.0 C B:PRO116 3.8 22.3 1.0 CGA B:HEC1006 3.8 23.6 1.0 OG B:SER84 4.0 24.7 1.0 O B:HOH642 4.0 40.1 1.0 CB B:SER84 4.0 23.8 1.0 CG B:PRO116 4.1 23.8 1.0 O2 B:GOL3 4.2 35.3 1.0 CAA B:HEC1006 4.4 22.1 1.0 CD B:PRO116 4.4 22.6 1.0 O2A B:HEC1006 4.4 24.1 1.0 C2 B:GOL3 4.5 37.7 1.0 N B:PRO116 4.5 22.2 1.0 CA B:PRO116 4.6 22.4 1.0 CB B:PRO116 4.6 22.3 1.0 N B:ARG117 4.6 21.4 1.0 CA B:SER84 4.6 23.2 1.0 CA B:ARG117 4.7 21.0 1.0 CBA B:HEC1006 4.7 20.7 1.0 O B:HOH727 4.8 25.6 1.0 O B:HOH1034 4.8 53.5 1.0 CBA B:HEC1007 4.8 22.8 0.5 OE1 B:GLU115 4.9 28.2 1.0

A.A.Trofimov, K.M.Polyakov, T.V.Tikhonova, V.O.Popov. Structure of the Tvnirb Form of Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase with An Oxidized GLN360 in A Complex with Hydroxylamine To Be Published.