Cobalt in PDB 3ttb: Structure of the Thioalkalivibrio Paradoxus Cytochrome C Nitrite Reductase in Complex with Sulfite

The structure of Structure of the Thioalkalivibrio Paradoxus Cytochrome C Nitrite Reductase in Complex with Sulfite, PDB code: 3ttb was solved by K.M.Polyakov, A.A.Trofimov, 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)	38.99 / 2.00
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	190.990, 190.990, 190.990, 90.00, 90.00, 90.00
R / Rfree (%)	13.4 / 15.3

The structure of Structure of the Thioalkalivibrio Paradoxus Cytochrome C Nitrite Reductase in Complex with Sulfite also contains other interesting chemical elements:

Iron	(Fe)	16 atoms
Calcium	(Ca)	2 atoms

The binding sites of Cobalt atom in the Structure of the Thioalkalivibrio Paradoxus Cytochrome C Nitrite Reductase in Complex with Sulfite (pdb code 3ttb). 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 the Thioalkalivibrio Paradoxus Cytochrome C Nitrite Reductase in Complex with Sulfite, PDB code: 3ttb:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Structure of the Thioalkalivibrio Paradoxus Cytochrome C Nitrite Reductase in Complex with Sulfite


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of the Thioalkalivibrio Paradoxus Cytochrome C Nitrite Reductase in Complex with Sulfite within 5.0Å range: probe atom residue distance (Å) B Occ A:Co528 b:14.3 occ:0.50 O2D A:HEC1004 1.9 18.5 1.0 O A:HOH543 2.0 19.6 1.0 NE2 A:HIS113 2.0 17.4 1.0 O A:HOH646 2.1 28.3 1.0 O A:HOH596 2.1 16.4 1.0 O A:HOH536 2.2 18.6 1.0 CGD A:HEC1004 2.8 18.6 1.0 CE1 A:HIS113 3.0 18.3 1.0 O1D A:HEC1004 3.0 18.7 1.0 CD2 A:HIS113 3.0 17.5 1.0 NZ A:LYS90 3.8 23.2 1.0 O1 A:SO3526 3.8 22.8 1.0 O2A A:HEC1004 4.0 18.4 1.0 ND1 A:HIS113 4.1 18.2 1.0 O A:HOH608 4.1 19.7 1.0 CG A:HIS113 4.2 17.9 1.0 CBD A:HEC1004 4.3 18.3 1.0 O A:ALA114 4.4 18.5 1.0 CE2 A:PHE109 4.5 19.3 1.0 CD2 A:HIS361 4.6 17.7 1.0 CBA A:HEC1004 4.8 17.7 1.0 CGA A:HEC1004 4.8 18.0 1.0 O A:ALA484 4.8 18.4 1.0 CHA A:HEC1004 4.8 17.0 1.0 CE A:LYS90 4.8 22.9 1.0 CD A:LYS90 4.9 21.6 1.0 ND2 A:ASN486 4.9 17.9 1.0

Cobalt binding site 2 out of 4 in the Structure of the Thioalkalivibrio Paradoxus Cytochrome C Nitrite Reductase in Complex with Sulfite


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of the Thioalkalivibrio Paradoxus Cytochrome C Nitrite Reductase in Complex with Sulfite within 5.0Å range: probe atom residue distance (Å) B Occ A:Co529 b:23.8 occ:0.70 OE1 A:GLU88 1.8 22.7 1.0 ND1 A:HIS85 1.9 23.8 1.0 O A:HOH766 2.0 18.1 0.7 O A:HOH792 2.1 24.1 0.7 O A:HOH771 2.1 24.2 0.7 O A:HOH866 2.3 17.8 0.7 CD A:GLU88 2.7 21.9 1.0 CE1 A:HIS85 2.8 24.4 1.0 OE2 A:GLU88 3.0 22.9 1.0 CG A:HIS85 3.0 22.9 1.0 CB A:HIS85 3.5 21.5 1.0 OE1 A:GLU115 3.8 22.1 1.0 OE2 A:GLU115 3.9 21.8 1.0 NE2 A:HIS85 4.0 24.5 1.0 CD2 A:HIS85 4.1 23.5 1.0 CG A:GLU88 4.1 20.5 1.0 CD A:GLU115 4.2 21.4 1.0 O A:ARG94 4.5 20.5 1.0 O A:HOH808 4.6 28.1 1.0 CB A:GLU88 4.8 19.3 1.0 CA A:HIS85 5.0 20.8 1.0

Cobalt binding site 3 out of 4 in the Structure of the Thioalkalivibrio Paradoxus Cytochrome C Nitrite Reductase in Complex with Sulfite


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of the Thioalkalivibrio Paradoxus Cytochrome C Nitrite Reductase in Complex with Sulfite within 5.0Å range: probe atom residue distance (Å) B Occ B:Co528 b:19.7 occ:0.50 O B:HOH551 1.7 24.1 1.0 O2D B:HEC1004 1.9 21.6 1.0 O B:HOH652 1.9 14.5 0.5 NE2 B:HIS113 2.0 20.6 1.0 O B:HOH544 2.2 25.1 1.0 O B:HOH825 2.2 19.9 0.5 CGD B:HEC1004 2.9 20.7 1.0 CE1 B:HIS113 3.0 20.4 1.0 O B:HOH604 3.0 15.9 0.5 CD2 B:HIS113 3.1 20.3 1.0 O1D B:HEC1004 3.2 21.6 1.0 O1 B:SO3526 3.8 22.5 1.0 NZ B:LYS90 3.8 24.7 1.0 O B:HOH616 4.0 27.7 1.0 O2A B:HEC1004 4.1 19.8 1.0 ND1 B:HIS113 4.1 20.2 1.0 CG B:HIS113 4.2 20.1 1.0 O B:ALA114 4.3 19.4 1.0 CBD B:HEC1004 4.4 20.0 1.0 CD2 B:HIS361 4.6 21.4 1.0 CE2 B:PHE109 4.6 21.8 1.0 CD B:LYS90 4.7 23.3 1.0 CBA B:HEC1004 4.7 19.4 1.0 O B:ALA484 4.7 20.5 1.0 CGA B:HEC1004 4.8 19.3 1.0 CHA B:HEC1004 4.8 17.9 1.0 CE B:LYS90 4.8 23.9 1.0 OD1 B:ASN486 4.9 20.1 1.0

Cobalt binding site 4 out of 4 in the Structure of the Thioalkalivibrio Paradoxus Cytochrome C Nitrite Reductase in Complex with Sulfite


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structure of the Thioalkalivibrio Paradoxus Cytochrome C Nitrite Reductase in Complex with Sulfite within 5.0Å range: probe atom residue distance (Å) B Occ B:Co529 b:19.0 occ:0.50 O B:HOH769 1.8 29.5 1.0 OE1 B:GLU88 1.8 23.0 1.0 O B:HOH899 1.9 23.1 0.5 ND1 B:HIS85 1.9 23.0 1.0 O B:HOH794 2.1 17.1 0.5 O B:HOH774 2.1 29.9 1.0 CE1 B:HIS85 2.8 24.4 1.0 CD B:GLU88 2.9 22.6 1.0 CG B:HIS85 3.1 23.2 1.0 OE2 B:GLU88 3.4 23.7 1.0 CB B:HIS85 3.6 22.2 1.0 OE2 B:GLU115 3.8 20.6 1.0 OE1 B:GLU115 3.9 20.1 1.0 NE2 B:HIS85 4.0 24.6 1.0 CD2 B:HIS85 4.1 23.8 1.0 CD B:GLU115 4.2 20.0 1.0 CG B:GLU88 4.2 21.4 1.0 O B:ARG94 4.6 23.3 1.0 O B:HOH811 4.8 23.4 1.0 CB B:GLU88 4.8 19.7 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