Calcium in PDB 3uu9: Structure of the Free Tvnirb Form of Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase

The structure of Structure of the Free Tvnirb Form of Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase, PDB code: 3uu9 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 / 2.20
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	191.387, 191.387, 191.387, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 18.4

The structure of Structure of the Free Tvnirb Form of Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase also contains other interesting chemical elements:

Iron	(Fe)	16 atoms
Sodium	(Na)	1 atom

The binding sites of Calcium atom in the Structure of the Free Tvnirb Form of Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase (pdb code 3uu9). 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 Free Tvnirb Form of Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase, PDB code: 3uu9:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of the Free Tvnirb Form of Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase


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 Free Tvnirb Form of Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca609 b:36.2 occ:1.00 O A:LYS358 2.3 33.6 1.0 OE2 A:GLU302 2.3 36.8 1.0 O A:HOH718 2.3 32.4 1.0 O A:TYR303 2.4 33.7 1.0 OE1 A:GLN360 2.4 39.4 1.0 O A:HOH732 2.4 31.7 1.0 OE1 A:GLU302 2.5 33.4 1.0 CD A:GLU302 2.8 31.6 1.0 C A:LYS358 3.5 33.4 1.0 C A:TYR303 3.6 33.1 1.0 CD A:GLN360 3.6 41.4 1.0 N A:TYR303 3.9 32.1 1.0 N A:GLN360 4.1 34.4 1.0 CA A:LEU359 4.2 33.3 1.0 OD1 A:ASN304 4.2 39.9 1.0 OD2 A:ASP346 4.2 32.7 1.0 N A:LEU359 4.3 33.3 1.0 CG A:GLU302 4.3 31.3 1.0 OH A:TYR335 4.3 33.8 1.0 CG A:GLN360 4.3 38.2 1.0 C A:LEU359 4.4 33.9 1.0 CA A:TYR303 4.4 32.4 1.0 CA A:LYS358 4.5 32.8 1.0 CB A:GLN360 4.5 35.9 1.0 N A:ASN304 4.5 33.1 1.0 OD1 A:ASP346 4.5 36.9 1.0 CB A:LYS358 4.6 32.1 1.0 NE2 A:GLN360 4.6 42.7 1.0 CD1 A:TYR303 4.6 29.5 1.0 CE1 A:PHE328 4.6 33.5 1.0 CE1 A:TYR303 4.7 32.7 1.0 N A:LYS358 4.7 32.6 1.0 CG A:ASP346 4.7 35.2 1.0 CA A:ASN304 4.7 34.4 1.0 CG A:TYR303 4.9 31.8 1.0 CG A:LYS358 4.9 29.9 1.0 CA A:GLN360 4.9 35.2 1.0 C A:GLU302 4.9 31.7 1.0

Calcium binding site 2 out of 4 in the Structure of the Free Tvnirb Form of Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase


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 Free Tvnirb Form of Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca610 b:47.7 occ:0.50 O A:HOH711 2.2 34.1 1.0 O A:HOH761 2.6 44.3 1.0 O A:PRO116 2.6 30.1 1.0 O2A A:HEC604 2.7 31.6 0.5 O2A A:HEC603 2.7 26.5 1.0 O A:HOH822 2.8 39.4 1.0 O1A A:HEC604 3.5 28.4 0.5 C A:PRO116 3.6 30.0 1.0 CGA A:HEC604 3.6 32.1 0.5 O1A A:HEC604 3.7 31.7 0.5 O A:HOH1077 3.7 60.7 1.0 CGA A:HEC603 3.8 30.5 1.0 CG A:PRO116 3.8 31.5 1.0 O A:HOH817 4.0 40.2 1.0 OG A:SER84 4.0 33.5 1.0 CB A:SER84 4.1 31.6 1.0 CGA A:HEC604 4.1 27.5 0.5 CD A:PRO116 4.2 29.4 1.0 O A:HOH845 4.3 50.3 1.0 CAA A:HEC603 4.3 26.4 1.0 N A:PRO116 4.4 29.7 1.0 CA A:PRO116 4.4 30.2 1.0 CB A:PRO116 4.4 28.9 1.0 N A:ARG117 4.5 29.8 1.0 O2A A:HEC604 4.5 26.6 0.5 O1A A:HEC603 4.5 29.5 1.0 CA A:ARG117 4.5 29.3 1.0 OE1 A:GLU115 4.7 45.0 1.0 CBA A:HEC603 4.7 27.7 1.0 CA A:SER84 4.8 32.1 1.0 CB A:GLU115 4.8 29.2 1.0 O A:HOH1048 4.9 26.7 1.0 C A:GLU115 5.0 29.9 1.0

Calcium binding site 3 out of 4 in the Structure of the Free Tvnirb Form of Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase


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 Free Tvnirb Form of Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca609 b:34.4 occ:1.00 O B:LYS358 2.3 31.2 1.0 OE2 B:GLU302 2.3 33.9 1.0 O B:TYR303 2.3 32.1 1.0 OE1 B:GLN360 2.3 37.4 1.0 O B:HOH747 2.4 27.2 1.0 O B:HOH733 2.4 29.9 1.0 OE1 B:GLU302 2.6 32.2 1.0 CD B:GLU302 2.8 32.0 1.0 C B:LYS358 3.5 31.7 1.0 C B:TYR303 3.6 32.1 1.0 CD B:GLN360 3.6 39.0 1.0 N B:TYR303 4.0 31.4 1.0 CA B:LEU359 4.2 32.0 1.0 N B:GLN360 4.2 32.7 1.0 N B:LEU359 4.3 31.3 1.0 CG B:GLU302 4.3 29.7 1.0 CG B:GLN360 4.4 38.3 1.0 OD2 B:ASP346 4.4 31.8 1.0 C B:LEU359 4.4 32.8 1.0 OD1 B:ASP346 4.4 27.1 1.0 OD1 B:ASN304 4.4 40.4 1.0 OH B:TYR335 4.4 27.5 1.0 CA B:TYR303 4.5 31.5 1.0 N B:ASN304 4.5 32.1 1.0 CA B:LYS358 4.5 30.9 1.0 CB B:GLN360 4.5 35.0 1.0 CE1 B:PHE328 4.5 27.4 1.0 CD1 B:TYR303 4.6 30.9 1.0 CB B:LYS358 4.6 30.7 1.0 NE2 B:GLN360 4.6 40.2 1.0 CE1 B:TYR303 4.6 34.6 1.0 CG B:ASP346 4.7 30.0 1.0 N B:LYS358 4.7 29.9 1.0 CA B:ASN304 4.7 33.0 1.0 CG B:LYS358 4.9 28.6 1.0 CG B:TYR303 4.9 32.2 1.0 CA B:GLN360 5.0 34.2 1.0 C B:GLU302 5.0 31.1 1.0

Calcium binding site 4 out of 4 in the Structure of the Free Tvnirb Form of Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase


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 Free Tvnirb Form of Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca610 b:42.3 occ:0.50 O B:HOH729 2.2 30.5 1.0 O B:HOH775 2.4 43.8 1.0 O B:PRO116 2.4 30.6 1.0 O1A B:HEC603 2.6 25.5 1.0 O2A B:HEC604 2.8 32.0 0.5 O B:HOH837 2.9 42.7 1.0 C B:PRO116 3.5 29.6 1.0 CGA B:HEC604 3.7 32.0 0.5 O1A B:HEC604 3.7 30.5 0.5 O1A B:HEC604 3.8 28.8 0.5 CGA B:HEC603 3.8 28.6 1.0 CG B:PRO116 3.9 29.6 1.0 OG B:SER84 4.0 29.7 1.0 CB B:SER84 4.0 29.4 1.0 O B:HOH832 4.1 34.9 1.0 CD B:PRO116 4.1 29.1 1.0 N B:PRO116 4.3 29.5 1.0 CA B:PRO116 4.3 29.9 1.0 CGA B:HEC604 4.3 29.1 0.5 CAA B:HEC603 4.3 24.0 1.0 CB B:PRO116 4.4 28.8 1.0 N B:ARG117 4.4 29.6 1.0 CA B:ARG117 4.4 28.6 1.0 O2A B:HEC603 4.5 26.9 1.0 O2A B:HEC604 4.5 27.9 0.5 O B:HOH860 4.7 53.9 1.0 OE1 B:GLU115 4.7 42.1 1.0 CA B:SER84 4.7 29.6 1.0 CB B:GLU115 4.7 29.4 1.0 CBA B:HEC603 4.7 23.7 1.0 C B:GLU115 4.9 30.1 1.0 NA B:NA621 4.9 36.7 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