Sodium 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
Cobalt	(Co)	2 atoms

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of A B12 Binding Lipoprotein From Bacteroides Thetaiotaomicron, PDB code: 7biz:
Jump to Sodium binding site number: 1; 2;

Sodium 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 Sodium with other atoms in the Na 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:Na706 b:17.1 occ:1.00 OE2 A:GLU406 2.3 18.3 1.0 O5 A:CNC701 2.3 19.7 1.0 OE2 A:GLU584 2.4 19.0 1.0 OD1 A:ASN399 2.4 19.1 1.0 OD2 A:ASP522 2.5 17.4 1.0 O A:HOH925 2.5 19.7 1.0 CG A:ASP522 3.3 17.7 1.0 CG A:ASN399 3.4 21.4 1.0 OD1 A:ASP522 3.4 19.0 1.0 CD A:GLU406 3.4 19.1 1.0 P A:CNC701 3.5 18.3 1.0 CD A:GLU584 3.6 17.9 1.0 ND2 A:ASN399 3.7 20.9 1.0 CA A:CA702 3.8 17.1 1.0 O4 A:CNC701 3.9 19.8 1.0 O A:HOH883 3.9 20.1 1.0 O A:SER582 3.9 16.9 1.0 CB A:GLU584 4.0 18.7 1.0 CG A:GLU406 4.0 16.7 1.0 N A:GLU584 4.1 16.5 1.0 O3 A:CNC701 4.2 17.8 1.0 CB A:GLU406 4.3 17.6 1.0 CG A:GLU584 4.4 19.1 1.0 OE1 A:GLU406 4.5 19.1 1.0 OE1 A:GLU584 4.5 17.4 1.0 CA A:GLU584 4.7 15.4 1.0 CB A:ASP522 4.8 17.5 1.0 OG A:SER404 4.8 19.0 1.0 CB A:ASN399 4.8 20.8 1.0 O A:ASN399 4.8 20.6 1.0 C A:THR583 4.9 17.1 1.0 C A:ASN399 4.9 18.8 1.0 O2 A:CNC701 4.9 20.0 1.0 N A:ASN399 4.9 17.2 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na706 b:21.4 occ:1.00 OE2 B:GLU406 2.2 21.1 1.0 OE1 B:GLU584 2.3 20.7 1.0 O5 B:CNC701 2.3 20.6 1.0 OD1 B:ASN399 2.4 22.6 1.0 O B:HOH870 2.5 22.7 1.0 OD2 B:ASP522 2.6 20.9 1.0 CG B:ASN399 3.4 23.1 1.0 CG B:ASP522 3.4 22.2 1.0 P B:CNC701 3.4 21.3 1.0 CD B:GLU406 3.4 21.8 1.0 CD B:GLU584 3.5 21.3 1.0 OD1 B:ASP522 3.5 21.8 1.0 ND2 B:ASN399 3.6 22.4 1.0 CA B:CA702 3.7 20.2 1.0 O4 B:CNC701 3.8 21.3 1.0 O B:HOH868 3.9 24.6 1.0 O B:SER582 3.9 18.7 1.0 CB B:GLU584 4.0 20.4 1.0 N B:GLU584 4.1 18.1 1.0 O3 B:CNC701 4.1 21.2 1.0 CG B:GLU406 4.1 20.0 1.0 CG B:GLU584 4.3 20.4 1.0 CB B:GLU406 4.3 19.4 1.0 OE1 B:GLU406 4.4 21.6 1.0 OE2 B:GLU584 4.4 19.0 1.0 CA B:GLU584 4.6 18.5 1.0 OG B:SER404 4.8 22.3 1.0 CB B:ASN399 4.8 23.2 1.0 O2 B:CNC701 4.8 22.3 1.0 O B:ASN399 4.8 23.1 1.0 C B:THR583 4.8 19.0 1.0 CB B:ASP522 4.9 20.3 1.0 C B:ASN399 4.9 23.4 1.0 N B:ASN399 4.9 21.0 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