Calcium in PDB 2ot4: Structure of A Hexameric Multiheme C Nitrite Reductase From the Extremophile Bacterium Thiolkalivibrio Nitratireducens

The structure of Structure of A Hexameric Multiheme C Nitrite Reductase From the Extremophile Bacterium Thiolkalivibrio Nitratireducens, PDB code: 2ot4 was solved by K.M.Polyakov, K.M.Boyko, A.Slutsky, T.V.Tikhonova, A.N.Antipov, R.A.Zvyagilskaya, A.N.Popov, 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)	24.04 / 1.50
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	193.917, 193.917, 193.917, 90.00, 90.00, 90.00
R / Rfree (%)	12.6 / 14.1

The structure of Structure of A Hexameric Multiheme C Nitrite Reductase From the Extremophile Bacterium Thiolkalivibrio Nitratireducens also contains other interesting chemical elements:

Iron

(Fe)

18 atoms

The binding sites of Calcium atom in the Structure of A Hexameric Multiheme C Nitrite Reductase From the Extremophile Bacterium Thiolkalivibrio Nitratireducens (pdb code 2ot4). 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 A Hexameric Multiheme C Nitrite Reductase From the Extremophile Bacterium Thiolkalivibrio Nitratireducens, PDB code: 2ot4:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of A Hexameric Multiheme C Nitrite Reductase From the Extremophile Bacterium Thiolkalivibrio Nitratireducens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of A Hexameric Multiheme C Nitrite Reductase From the Extremophile Bacterium Thiolkalivibrio Nitratireducens within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2744 b:18.5 occ:1.00 OE1 A:GLN360 2.3 19.1 0.7 O A:LYS358 2.3 16.0 1.0 O A:TYR303 2.3 15.4 1.0 OE2 A:GLU302 2.4 16.0 1.0 O A:HOH3069 2.4 20.1 1.0 O A:HOH3068 2.5 18.2 1.0 OE1 A:GLU302 2.6 15.2 1.0 CD A:GLU302 2.8 15.3 1.0 H A:TYR303 3.3 15.0 1.0 CD A:GLN360 3.4 18.4 0.7 C A:TYR303 3.5 15.1 1.0 C A:LYS358 3.5 14.7 1.0 HH A:TYR335 3.5 17.4 0.0 HA A:LEU359 3.5 14.2 1.0 HE21 A:GLN360 3.6 21.1 0.0 HG3 A:GLN360 3.6 16.5 0.3 HE1 A:PHE328 3.8 16.3 1.0 NE2 A:GLN360 3.9 21.2 0.7 HB3 A:LYS358 4.0 14.8 1.0 N A:TYR303 4.0 15.2 1.0 HA A:ASN304 4.0 16.0 1.0 H A:GLN360 4.1 14.5 1.0 OE1 A:GLN360 4.2 16.9 0.3 OH A:TYR335 4.2 17.4 1.0 CA A:LEU359 4.3 13.9 1.0 OD1 A:ASN304 4.3 21.6 1.0 HB2 A:GLN360 4.3 16.3 1.0 CG A:GLU302 4.3 14.1 1.0 N A:LEU359 4.3 14.2 1.0 H A:LYS358 4.4 14.9 1.0 HD13 A:LEU359 4.4 16.1 0.0 OD1 A:ASP346 4.4 16.1 1.0 CA A:TYR303 4.4 15.2 1.0 HG3 A:LYS358 4.4 15.2 1.0 CG A:GLN360 4.4 16.6 0.3 N A:GLN360 4.4 14.1 1.0 N A:ASN304 4.4 15.4 1.0 OD2 A:ASP346 4.5 17.8 1.0 CA A:LYS358 4.6 14.5 1.0 C A:LEU359 4.6 15.0 1.0 CE1 A:PHE328 4.6 17.2 1.0 HG3 A:GLU302 4.6 14.4 1.0 CB A:LYS358 4.6 15.1 1.0 CG A:GLN360 4.6 19.5 0.7 CA A:ASN304 4.7 16.0 1.0 CD A:GLN360 4.7 16.1 0.3 HE22 A:GLN360 4.7 21.1 0.0 HG2 A:GLU302 4.8 14.4 1.0 CG A:ASP346 4.8 16.8 1.0 HA A:GLU302 4.8 14.2 1.0 N A:LYS358 4.8 14.8 1.0 CB A:GLN360 4.8 17.1 1.0 CG A:LYS358 4.9 15.2 1.0 HE1 A:TYR335 5.0 15.8 1.0 C A:GLU302 5.0 14.4 1.0 HG3 A:GLN360 5.0 19.1 0.7 HD1 A:PHE328 5.0 16.0 1.0

Calcium binding site 2 out of 2 in the Structure of A Hexameric Multiheme C Nitrite Reductase From the Extremophile Bacterium Thiolkalivibrio Nitratireducens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of A Hexameric Multiheme C Nitrite Reductase From the Extremophile Bacterium Thiolkalivibrio Nitratireducens within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2333 b:17.8 occ:1.00 OE1 B:GLN360 2.3 15.7 0.5 O B:LYS358 2.3 14.2 1.0 O B:TYR303 2.3 12.9 1.0 OE2 B:GLU302 2.4 14.0 1.0 O B:HOH2479 2.4 18.3 1.0 O B:HOH2478 2.5 17.3 1.0 OE1 B:GLU302 2.6 13.1 1.0 CD B:GLU302 2.8 13.1 1.0 H B:TYR303 3.3 13.0 1.0 CD B:GLN360 3.4 16.3 0.5 HH B:TYR335 3.5 15.1 0.0 C B:TYR303 3.5 12.8 1.0 C B:LYS358 3.5 12.6 1.0 HA B:LEU359 3.6 12.6 1.0 HE21 B:GLN360 3.6 16.6 0.0 HG3 B:GLN360 3.7 15.6 0.5 HE2 B:PHE328 3.7 13.4 1.0 HE22 B:GLN360 3.7 18.4 0.0 NE2 B:GLN360 3.9 16.6 0.5 HB3 B:LYS358 4.0 12.7 1.0 HA B:ASN304 4.0 14.2 1.0 N B:TYR303 4.0 13.1 1.0 H B:GLN360 4.1 12.8 1.0 OD1 B:ASN304 4.2 16.7 0.6 OH B:TYR335 4.2 15.1 1.0 HB2 B:GLN360 4.3 14.4 1.0 CA B:LEU359 4.3 12.7 1.0 CG B:GLU302 4.3 12.4 1.0 NE2 B:GLN360 4.3 18.5 0.5 N B:LEU359 4.3 12.1 1.0 H B:LYS358 4.4 13.2 1.0 OD1 B:ASP346 4.4 14.6 1.0 HD13 B:LEU359 4.4 14.0 0.0 CA B:TYR303 4.4 13.2 1.0 CE2 B:PHE328 4.4 13.9 1.0 N B:GLN360 4.4 12.6 1.0 N B:ASN304 4.4 12.6 1.0 HG3 B:LYS358 4.5 13.4 1.0 OD2 B:ASP346 4.5 15.8 1.0 CG B:GLN360 4.5 15.8 0.5 CA B:LYS358 4.5 12.7 1.0 HG3 B:GLU302 4.6 12.8 1.0 C B:LEU359 4.6 13.1 1.0 CB B:LYS358 4.6 12.5 1.0 CG B:GLN360 4.6 15.7 0.5 CA B:ASN304 4.7 13.9 1.0 OD1 B:ASN304 4.7 13.3 0.4 HG2 B:GLU302 4.7 12.5 1.0 HE22 B:GLN360 4.8 16.6 0.0 CG B:ASP346 4.8 14.0 1.0 HE21 B:GLN360 4.8 18.4 0.0 HA B:GLU302 4.8 12.6 1.0 N B:LYS358 4.8 13.2 1.0 CB B:GLN360 4.8 15.4 1.0 CD B:GLN360 4.8 16.7 0.5 HD2 B:PHE328 4.9 13.1 1.0 HG3 B:GLN360 4.9 15.9 0.5 CG B:LYS358 5.0 13.2 1.0 C B:GLU302 5.0 12.9 1.0 HE1 B:TYR335 5.0 13.6 1.0

K.M.Polyakov, K.M.Boyko, T.V.Tikhonova, A.Slutsky, A.N.Antipov, R.A.Zvyagilskaya, A.N.Popov, G.P.Bourenkov, V.S.Lamzin, V.O.Popov. High-Resolution Structural Analysis of A Novel Octaheme Cytochrome C Nitrite Reductase From the Haloalkaliphilic Bacterium Thioalkalivibrio Nitratireducens. J.Mol.Biol. V. 389 846 2009.
ISSN: ISSN 0022-2836
PubMed: 19393666
DOI: 10.1016/J.JMB.2009.04.037