Calcium in PDB 3lgq: Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Sulfite (Modified Tyr-303)

The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Sulfite (Modified Tyr-303), PDB code: 3lgq was solved by A.A.Trofimov, K.M.Polyakov, K.M.Boyko, A.A.Filimonenkov, T.V.Tikhonova, 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)	19.80 / 1.80
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	195.690, 195.690, 195.690, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 16.8

The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Sulfite (Modified Tyr-303) 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 Sulfite (Modified Tyr-303) (pdb code 3lgq). 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 Sulfite (Modified Tyr-303), PDB code: 3lgq:
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 Sulfite (Modified Tyr-303)


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 Sulfite (Modified Tyr-303) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca527 b:23.8 occ:1.00 OE1 A:GLN360 2.3 25.4 1.0 O A:LYS358 2.3 22.7 1.0 O A:TYR303 2.3 22.9 1.0 OE2 A:GLU302 2.4 23.8 1.0 O A:HOH801 2.4 22.5 1.0 O A:HOH800 2.4 23.9 1.0 OE1 A:GLU302 2.6 23.6 1.0 CD A:GLU302 2.8 22.9 1.0 C A:TYR303 3.5 22.6 1.0 CD A:GLN360 3.5 26.6 1.0 C A:LYS358 3.5 22.0 1.0 N A:TYR303 3.9 21.5 1.0 CA A:LEU359 4.3 21.4 1.0 N A:GLN360 4.3 21.8 1.0 CG A:GLU302 4.3 21.4 1.0 OH A:TYR335 4.3 22.8 1.0 N A:LEU359 4.3 21.8 1.0 OD1 A:ASN304 4.4 26.3 1.0 CG A:GLN360 4.4 25.4 1.0 OD1 A:ASP346 4.4 25.1 1.0 CA A:TYR303 4.4 21.9 1.0 N A:ASN304 4.5 23.3 1.0 NE2 A:GLN360 4.5 26.5 1.0 C A:LEU359 4.5 22.4 1.0 OD2 A:ASP346 4.6 24.2 1.0 CA A:LYS358 4.6 21.7 1.0 CD1 A:TYR303 4.6 23.6 1.0 CE1 A:PHE328 4.6 23.9 1.0 CB A:GLN360 4.6 22.5 1.0 CE1 A:TYR303 4.7 24.1 1.0 CB A:LYS358 4.7 21.4 1.0 CA A:ASN304 4.7 23.6 1.0 O A:HOH935 4.8 45.8 1.0 N A:LYS358 4.8 21.7 1.0 CG A:ASP346 4.8 23.1 1.0 CG A:TYR303 5.0 21.8 1.0 C A:GLU302 5.0 21.8 1.0

Calcium binding site 2 out of 2 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Sulfite (Modified Tyr-303)


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 Sulfite (Modified Tyr-303) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca527 b:22.0 occ:1.00 O B:LYS358 2.3 21.0 1.0 OE1 B:GLN360 2.3 22.8 1.0 OE2 B:GLU302 2.4 21.1 1.0 O B:TYR303 2.4 21.1 1.0 O B:HOH866 2.4 21.5 1.0 O B:HOH865 2.5 23.6 1.0 OE1 B:GLU302 2.6 20.2 1.0 CD B:GLU302 2.8 20.5 1.0 C B:LYS358 3.5 20.6 1.0 CD B:GLN360 3.5 26.2 1.0 C B:TYR303 3.6 20.8 1.0 N B:TYR303 4.0 20.4 1.0 CA B:LEU359 4.2 20.1 1.0 N B:GLN360 4.3 20.6 1.0 N B:LEU359 4.3 19.6 1.0 CG B:GLU302 4.3 19.6 1.0 CG B:GLN360 4.4 23.4 1.0 OD1 B:ASN304 4.4 25.7 1.0 OH B:TYR335 4.4 21.2 1.0 OD2 B:ASP346 4.4 21.9 1.0 CA B:TYR303 4.5 20.9 1.0 NE2 B:GLN360 4.5 24.8 1.0 C B:LEU359 4.5 20.5 1.0 CB B:GLN360 4.5 21.7 1.0 N B:ASN304 4.5 20.7 1.0 CA B:LYS358 4.5 20.3 1.0 OD1 B:ASP346 4.6 22.6 1.0 CD1 B:TYR303 4.6 19.9 1.0 CE1 B:PHE328 4.6 20.0 1.0 CE1 B:TYR303 4.6 22.4 1.0 CB B:LYS358 4.6 20.8 1.0 CA B:ASN304 4.8 21.6 1.0 N B:LYS358 4.8 20.6 1.0 CG B:ASP346 4.8 21.9 1.0 O B:HOH1009 4.8 36.2 1.0 CG B:LYS358 5.0 19.9 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