Cobalt in PDB 7biz: Structure of A B12 Binding Lipoprotein From Bacteroides Thetaiotaomicron

The structure of Structure of A B12 Binding Lipoprotein From Bacteroides Thetaiotaomicron, PDB code: 7biz was solved by J.Abellon-Ruiz, B.Van Den Berg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	85.70 / 1.53
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	128.052, 128.052, 135.051, 90, 90, 120
R / Rfree (%)	16.5 / 19.2

The structure of Structure of A B12 Binding Lipoprotein From Bacteroides Thetaiotaomicron also contains other interesting chemical elements:

Calcium	(Ca)	4 atoms
Sodium	(Na)	2 atoms

The binding sites of Cobalt atom in the Structure of A B12 Binding Lipoprotein From Bacteroides Thetaiotaomicron (pdb code 7biz). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Structure of A B12 Binding Lipoprotein From Bacteroides Thetaiotaomicron, PDB code: 7biz:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Structure of A B12 Binding Lipoprotein From Bacteroides Thetaiotaomicron


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 B12 Binding Lipoprotein From Bacteroides Thetaiotaomicron within 5.0Å range: probe atom residue distance (Å) B Occ A:Co701 b:21.8 occ:1.00 CO A:CNC701 0.0 21.8 1.0 N22 A:CNC701 1.9 22.4 1.0 N23 A:CNC701 1.9 21.6 1.0 N21 A:CNC701 1.9 22.6 1.0 N24 A:CNC701 1.9 22.6 1.0 C1A A:CNC701 2.0 28.4 1.0 N3B A:CNC701 2.4 21.5 1.0 C1 A:CNC701 2.8 22.9 1.0 C11 A:CNC701 2.8 21.8 1.0 C9 A:CNC701 2.8 20.1 1.0 C4 A:CNC701 2.8 23.4 1.0 C14 A:CNC701 2.9 20.5 1.0 C16 A:CNC701 2.9 22.2 1.0 C19 A:CNC701 2.9 22.2 1.0 C6 A:CNC701 2.9 21.2 1.0 N1A A:CNC701 3.2 34.3 1.0 C10 A:CNC701 3.2 21.3 1.0 C5 A:CNC701 3.3 20.8 1.0 C15 A:CNC701 3.3 20.8 1.0 C2B A:CNC701 3.3 20.1 1.0 C20 A:CNC701 3.4 21.6 1.0 C9B A:CNC701 3.4 21.0 1.0 C4B A:CNC701 3.9 19.4 1.0 C18 A:CNC701 4.1 23.5 1.0 C3 A:CNC701 4.2 22.3 1.0 C2 A:CNC701 4.2 21.5 1.0 C8 A:CNC701 4.2 20.8 1.0 C12 A:CNC701 4.2 22.8 1.0 C17 A:CNC701 4.2 23.0 1.0 C13 A:CNC701 4.2 21.1 1.0 C7 A:CNC701 4.2 22.6 1.0 N1B A:CNC701 4.5 20.4 1.0 C8B A:CNC701 4.6 19.5 1.0 C26 A:CNC701 4.7 24.2 1.0 C37 A:CNC701 4.7 22.8 1.0 C35 A:CNC701 4.8 22.3 1.0 C53 A:CNC701 4.9 23.9 1.0 C41 A:CNC701 4.9 21.6 1.0 C54 A:CNC701 4.9 22.1 1.0 C47 A:CNC701 5.0 22.7 1.0

Cobalt binding site 2 out of 2 in the Structure of A B12 Binding Lipoprotein From Bacteroides Thetaiotaomicron


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 B12 Binding Lipoprotein From Bacteroides Thetaiotaomicron within 5.0Å range: probe atom residue distance (Å) B Occ B:Co701 b:26.5 occ:1.00 CO B:CNC701 0.0 26.5 1.0 N23 B:CNC701 1.9 26.9 1.0 N21 B:CNC701 1.9 29.0 1.0 N22 B:CNC701 1.9 27.3 1.0 N24 B:CNC701 1.9 24.7 1.0 C1A B:CNC701 2.1 32.3 1.0 N3B B:CNC701 2.4 24.8 1.0 C9 B:CNC701 2.8 23.7 1.0 C1 B:CNC701 2.8 27.8 1.0 C4 B:CNC701 2.8 25.4 1.0 C11 B:CNC701 2.8 23.9 1.0 C16 B:CNC701 2.9 26.9 1.0 C6 B:CNC701 2.9 26.8 1.0 C14 B:CNC701 2.9 24.9 1.0 C19 B:CNC701 2.9 28.4 1.0 C5 B:CNC701 3.2 26.8 1.0 N1A B:CNC701 3.2 38.5 1.0 C10 B:CNC701 3.2 22.9 1.0 C2B B:CNC701 3.3 25.8 1.0 C15 B:CNC701 3.3 26.1 1.0 C20 B:CNC701 3.3 27.1 1.0 C9B B:CNC701 3.4 26.4 1.0 C4B B:CNC701 3.9 27.9 1.0 C3 B:CNC701 4.1 25.5 1.0 C8 B:CNC701 4.1 26.2 1.0 C2 B:CNC701 4.1 28.6 1.0 C18 B:CNC701 4.2 27.1 1.0 C7 B:CNC701 4.2 25.1 1.0 C12 B:CNC701 4.2 23.6 1.0 C17 B:CNC701 4.2 27.5 1.0 C13 B:CNC701 4.2 23.3 1.0 N1B B:CNC701 4.5 23.1 1.0 C8B B:CNC701 4.6 23.2 1.0 C37 B:CNC701 4.6 28.0 1.0 C35 B:CNC701 4.7 29.5 1.0 C26 B:CNC701 4.7 29.6 1.0 C53 B:CNC701 4.8 23.6 1.0 C41 B:CNC701 4.9 25.0 1.0 C54 B:CNC701 4.9 28.6 1.0 C47 B:CNC701 5.0 24.9 1.0

E.E.Putnam, J.Abellon-Ruiz, B.J.Killinger, J.J.Rosnow, A.G.Wexler, E.Folta-Stogniew, A.T.Wright, B.Van Den Berg, A.L.Goodman. Gut Commensal Bacteroidetes Encode A Novel Class of Vitamin B 12 -Binding Proteins. Mbio V. 13 84521 2022.
ISSN: ESSN 2150-7511
PubMed: 35227073
DOI: 10.1128/MBIO.02845-21