Cobalt in PDB 3sxq: Structure of A Hexameric Multiheme C Nitrite Reductase From the Extremophile Bacterium Thiolkalivibrio Paradoxus

The structure of Structure of A Hexameric Multiheme C Nitrite Reductase From the Extremophile Bacterium Thiolkalivibrio Paradoxus, PDB code: 3sxq was solved by K.M.Polyakov, A.A.Trofimov, T.V.Tikhonova, A.V.Tikhonov, K.M.Boyko, V.O.Popov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.90 / 1.90
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	193.640, 193.640, 193.640, 90.00, 90.00, 90.00
R / Rfree (%)	13.8 / 16.2

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

Iron	(Fe)	16 atoms
Chlorine	(Cl)	2 atoms
Calcium	(Ca)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Cobalt atom in the Structure of A Hexameric Multiheme C Nitrite Reductase From the Extremophile Bacterium Thiolkalivibrio Paradoxus (pdb code 3sxq). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Structure of A Hexameric Multiheme C Nitrite Reductase From the Extremophile Bacterium Thiolkalivibrio Paradoxus, PDB code: 3sxq:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Structure of A Hexameric Multiheme C Nitrite Reductase From the Extremophile Bacterium Thiolkalivibrio Paradoxus


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of A Hexameric Multiheme C Nitrite Reductase From the Extremophile Bacterium Thiolkalivibrio Paradoxus within 5.0Å range: probe atom residue distance (Å) B Occ A:Co527 b:9.9 occ:0.10 O A:HOH769 2.0 13.1 1.0 O A:HOH548 2.2 11.0 1.0 O2D A:HEC1004 2.5 11.9 1.0 O A:HOH568 2.5 12.8 1.0 NE2 A:HIS113 2.6 10.8 1.0 O1D A:HEC1004 2.9 12.4 1.0 O A:HOH623 2.9 14.4 1.0 CGD A:HEC1004 3.1 14.6 1.0 CE1 A:HIS113 3.4 9.5 1.0 O A:HOH746 3.5 16.2 1.0 O A:HOH630 3.6 20.5 1.0 CD2 A:HIS113 3.6 7.2 1.0 NZ A:LYS90 3.6 17.2 1.0 O2A A:HEC1004 4.2 9.7 1.0 O A:HOH690 4.4 12.4 1.0 O A:ALA114 4.4 9.1 1.0 CD2 A:HIS361 4.5 11.2 1.0 CBD A:HEC1004 4.6 6.0 1.0 ND1 A:HIS113 4.6 14.3 1.0 O A:ALA484 4.6 11.0 1.0 CD A:LYS90 4.7 13.3 1.0 CG A:HIS113 4.7 11.6 1.0 CE A:LYS90 4.8 13.4 1.0 CBA A:HEC1004 4.9 6.3 1.0 CGA A:HEC1004 5.0 12.2 1.0 OD1 A:ASN486 5.0 15.6 1.0 ND2 A:ASN486 5.0 11.5 1.0

Cobalt binding site 2 out of 4 in the Structure of A Hexameric Multiheme C Nitrite Reductase From the Extremophile Bacterium Thiolkalivibrio Paradoxus


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of A Hexameric Multiheme C Nitrite Reductase From the Extremophile Bacterium Thiolkalivibrio Paradoxus within 5.0Å range: probe atom residue distance (Å) B Occ A:Co528 b:11.4 occ:0.70 OE1 A:GLU88 1.9 17.2 1.0 ND1 A:HIS85 1.9 18.1 1.0 O A:HOH1073 2.1 17.3 1.0 O A:HOH1074 2.1 20.8 1.0 O A:HOH1072 2.2 24.5 1.0 O A:HOH1075 2.2 20.5 1.0 CE1 A:HIS85 2.8 22.6 1.0 CD A:GLU88 2.9 18.8 1.0 CG A:HIS85 3.1 15.8 1.0 OE2 A:GLU88 3.3 16.1 1.0 CB A:HIS85 3.6 12.3 1.0 OE1 A:GLU115 3.9 14.0 1.0 NE2 A:HIS85 4.0 20.8 1.0 OE2 A:GLU115 4.0 12.6 1.0 CD2 A:HIS85 4.1 14.7 1.0 CG A:GLU88 4.3 9.8 1.0 CD A:GLU115 4.4 20.4 1.0 O A:ARG94 4.6 13.1 1.0 O A:HOH664 4.6 15.5 1.0 O A:HOH603 4.8 32.8 1.0 CB A:GLU88 4.9 8.1 1.0

Cobalt binding site 3 out of 4 in the Structure of A Hexameric Multiheme C Nitrite Reductase From the Extremophile Bacterium Thiolkalivibrio Paradoxus


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of A Hexameric Multiheme C Nitrite Reductase From the Extremophile Bacterium Thiolkalivibrio Paradoxus within 5.0Å range: probe atom residue distance (Å) B Occ B:Co527 b:10.7 occ:0.10 O B:HOH773 2.0 11.8 1.0 O B:HOH572 2.1 11.3 1.0 NE2 B:HIS113 2.4 14.6 1.0 O B:HOH590 2.6 14.6 1.0 O2D B:HEC1004 2.7 13.9 1.0 O B:HOH645 3.0 13.4 1.0 O1D B:HEC1004 3.1 12.4 1.0 CE1 B:HIS113 3.2 7.8 1.0 CGD B:HEC1004 3.3 13.0 1.0 CD2 B:HIS113 3.4 6.7 1.0 O B:HOH755 3.5 17.5 1.0 NZ B:LYS90 3.5 15.0 1.0 O B:HOH660 3.6 19.2 1.0 O B:HOH725 4.3 13.6 1.0 O2A B:HEC1004 4.3 10.3 1.0 ND1 B:HIS113 4.4 13.9 1.0 O B:ALA114 4.4 9.6 1.0 CG B:HIS113 4.5 7.3 1.0 CD B:LYS90 4.5 11.5 1.0 CD2 B:HIS361 4.6 7.5 1.0 CE B:LYS90 4.6 10.8 1.0 O B:ALA484 4.7 9.8 1.0 CBD B:HEC1004 4.8 6.8 1.0

Cobalt binding site 4 out of 4 in the Structure of A Hexameric Multiheme C Nitrite Reductase From the Extremophile Bacterium Thiolkalivibrio Paradoxus


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structure of A Hexameric Multiheme C Nitrite Reductase From the Extremophile Bacterium Thiolkalivibrio Paradoxus within 5.0Å range: probe atom residue distance (Å) B Occ B:Co528 b:12.8 occ:0.70 OE1 B:GLU88 1.9 17.4 1.0 ND1 B:HIS85 2.0 23.2 1.0 O B:HOH1074 2.1 17.4 1.0 O B:HOH1075 2.1 22.9 1.0 O B:HOH1076 2.1 20.4 1.0 O B:HOH1073 2.2 23.7 1.0 CE1 B:HIS85 2.8 25.5 1.0 CD B:GLU88 2.9 18.6 1.0 CG B:HIS85 3.1 18.8 1.0 OE2 B:GLU88 3.3 14.9 1.0 CB B:HIS85 3.6 12.6 1.0 OE1 B:GLU115 3.9 15.8 1.0 NE2 B:HIS85 4.0 22.1 1.0 OE2 B:GLU115 4.0 13.1 1.0 CD2 B:HIS85 4.1 17.6 1.0 CG B:GLU88 4.3 10.8 1.0 CD B:GLU115 4.3 22.1 1.0 O B:ARG94 4.6 14.4 1.0 O B:HOH703 4.7 15.8 1.0 CB B:GLU88 4.9 11.8 1.0

T.Tikhonova, A.Tikhonov, A.Trofimov, K.Polyakov, K.Boyko, E.Cherkashin, T.Rakitina, D.Sorokin, V.Popov. Comparative Structural and Functional Analysis of Two Octaheme Nitrite Reductases From Closely Related Thioalkalivibrio Species. Febs J. V. 279 4052 2012.
ISSN: ISSN 1742-464X
PubMed: 22935005
DOI: 10.1111/J.1742-4658.2012.08811.X