Calcium 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:

Sodium	(Na)	2 atoms
Cobalt	(Co)	2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of A B12 Binding Lipoprotein From Bacteroides Thetaiotaomicron, PDB code: 7biz:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of A B12 Binding Lipoprotein From Bacteroides Thetaiotaomicron


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 B12 Binding Lipoprotein From Bacteroides Thetaiotaomicron within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:17.1 occ:1.00 O4 A:CNC701 2.4 19.8 1.0 O A:HOH899 2.4 17.6 1.0 O A:SER582 2.4 16.9 1.0 OG A:SER582 2.5 16.6 1.0 OE2 A:GLU406 2.5 18.3 1.0 OE1 A:GLU584 2.5 17.4 1.0 OE2 A:GLU584 2.5 19.0 1.0 OE1 A:GLU406 2.6 19.1 1.0 CD A:GLU406 2.9 19.1 1.0 CD A:GLU584 2.9 17.9 1.0 C A:SER582 3.4 16.0 1.0 CB A:SER582 3.6 15.3 1.0 P A:CNC701 3.6 18.3 1.0 NA A:NA706 3.8 17.1 1.0 CA A:SER582 3.8 15.6 1.0 N A:SER582 3.8 16.1 1.0 O5 A:CNC701 3.9 19.7 1.0 O A:HOH916 4.2 18.2 1.0 CG A:GLU406 4.3 16.7 1.0 CG A:GLU584 4.4 19.1 1.0 O3 A:CNC701 4.5 17.8 1.0 O A:GLU580 4.5 17.8 1.0 O8R A:CNC701 4.5 17.8 1.0 CE2 A:PHE334 4.6 19.2 1.0 OG A:SER369 4.6 18.4 1.0 N A:THR583 4.6 16.2 1.0 OE2 A:GLU580 4.7 17.0 1.0 CB A:GLU406 4.8 17.6 1.0 O2 A:CNC701 4.8 20.0 1.0 CD2 A:PHE334 4.8 18.6 1.0 C A:THR583 4.9 17.1 1.0 N A:GLU584 4.9 16.5 1.0 C3R A:CNC701 5.0 19.6 1.0 C3P A:CNC701 5.0 20.6 1.0 C A:VAL581 5.0 17.2 1.0

Calcium binding site 2 out of 4 in the Structure of A B12 Binding Lipoprotein From Bacteroides Thetaiotaomicron


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 B12 Binding Lipoprotein From Bacteroides Thetaiotaomicron within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:17.1 occ:1.00 OD1 A:ASP424 2.3 20.7 1.0 OD1 A:ASP415 2.3 18.8 1.0 OD1 A:ASP423 2.3 18.6 1.0 OD1 A:ASN417 2.3 19.6 1.0 O A:LEU421 2.4 17.6 1.0 OD1 A:ASN419 2.4 18.1 1.0 CG A:ASP424 3.1 17.9 1.0 OD2 A:ASP424 3.3 21.1 1.0 CG A:ASN417 3.3 20.2 1.0 CG A:ASN419 3.4 19.9 1.0 CG A:ASP423 3.5 20.3 1.0 CG A:ASP415 3.5 19.4 1.0 C A:LEU421 3.5 16.6 1.0 ND2 A:ASN417 3.7 20.3 1.0 N A:LEU421 3.8 18.5 1.0 ND2 A:ASN419 3.9 18.6 1.0 N A:ASP423 4.0 16.8 1.0 OD2 A:ASP423 4.1 20.2 1.0 CA A:LEU421 4.1 16.4 1.0 N A:ASN419 4.2 19.9 1.0 CA A:ASP415 4.2 18.6 1.0 CB A:ASP415 4.3 16.7 1.0 N A:ASP424 4.4 16.2 1.0 OD2 A:ASP415 4.4 19.5 1.0 CB A:LEU421 4.4 16.8 1.0 N A:ASN417 4.5 18.9 1.0 CB A:ASP424 4.5 17.2 1.0 C A:ASP415 4.5 18.0 1.0 N A:GLY418 4.5 19.3 1.0 N A:GLY420 4.5 18.1 1.0 C A:ASP423 4.6 17.0 1.0 N A:PRO422 4.6 16.3 1.0 CB A:ASP423 4.6 17.8 1.0 CA A:ASP423 4.6 17.4 1.0 CB A:ASN419 4.6 19.0 1.0 CB A:ASN417 4.6 17.1 1.0 CA A:ASN419 4.7 19.3 1.0 C A:ASN417 4.8 21.0 1.0 N A:ILE416 4.8 17.8 1.0 CA A:ASN417 4.8 19.3 1.0 CA A:PRO422 4.8 17.7 1.0 C A:ASN419 4.8 20.3 1.0 C A:GLY420 4.9 19.0 1.0 CE2 A:PHE564 4.9 18.6 1.0 C A:PRO422 4.9 14.7 1.0 O A:ASP415 4.9 19.4 1.0 CA A:ASP424 5.0 16.2 1.0

Calcium binding site 3 out of 4 in the Structure of A B12 Binding Lipoprotein From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of A B12 Binding Lipoprotein From Bacteroides Thetaiotaomicron within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca702 b:20.2 occ:1.00 O4 B:CNC701 2.4 21.3 1.0 O B:SER582 2.4 18.7 1.0 OE2 B:GLU584 2.4 19.0 1.0 OE1 B:GLU584 2.5 20.7 1.0 O B:HOH961 2.5 20.6 1.0 OE2 B:GLU406 2.5 21.1 1.0 OG B:SER582 2.6 18.1 1.0 OE1 B:GLU406 2.6 21.6 1.0 CD B:GLU584 2.8 21.3 1.0 CD B:GLU406 2.9 21.8 1.0 C B:SER582 3.4 17.6 1.0 P B:CNC701 3.5 21.3 1.0 CB B:SER582 3.6 16.8 1.0 NA B:NA706 3.7 21.4 1.0 CA B:SER582 3.8 18.5 1.0 N B:SER582 3.8 19.0 1.0 O5 B:CNC701 3.9 20.6 1.0 O B:HOH968 4.2 21.5 1.0 CG B:GLU406 4.3 20.0 1.0 CG B:GLU584 4.3 20.4 1.0 O3 B:CNC701 4.4 21.2 1.0 O8R B:CNC701 4.5 21.9 1.0 O B:GLU580 4.5 20.2 1.0 CE2 B:PHE334 4.6 21.3 1.0 OG B:SER369 4.6 18.8 1.0 N B:THR583 4.6 18.2 1.0 CD2 B:PHE334 4.8 19.5 1.0 CB B:GLU406 4.8 19.4 1.0 O2 B:CNC701 4.8 22.3 1.0 OE2 B:GLU580 4.8 20.1 1.0 C B:THR583 4.8 19.0 1.0 C3P B:CNC701 4.9 20.6 1.0 N B:GLU584 4.9 18.1 1.0 C3R B:CNC701 5.0 21.9 1.0 C2P B:CNC701 5.0 21.5 1.0

Calcium binding site 4 out of 4 in the Structure of A B12 Binding Lipoprotein From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of A B12 Binding Lipoprotein From Bacteroides Thetaiotaomicron within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca703 b:21.4 occ:1.00 OD2 B:ASP424 2.3 25.3 1.0 OD1 B:ASP415 2.3 22.7 1.0 OD1 B:ASP423 2.3 22.8 1.0 OD1 B:ASN417 2.3 22.8 1.0 OD1 B:ASN419 2.4 23.4 1.0 O B:LEU421 2.4 21.3 1.0 CG B:ASP424 3.1 23.1 1.0 CG B:ASN417 3.3 22.9 1.0 OD1 B:ASP424 3.3 23.6 1.0 CG B:ASN419 3.4 26.2 1.0 CG B:ASP423 3.5 24.0 1.0 CG B:ASP415 3.5 23.2 1.0 C B:LEU421 3.5 24.0 1.0 ND2 B:ASN417 3.6 25.0 1.0 N B:LEU421 3.8 23.4 1.0 ND2 B:ASN419 3.9 27.6 1.0 N B:ASP423 4.0 21.7 1.0 OD2 B:ASP423 4.1 27.3 1.0 CA B:LEU421 4.1 22.5 1.0 N B:ASN419 4.1 24.1 1.0 CA B:ASP415 4.2 22.0 1.0 CB B:ASP415 4.4 22.4 1.0 OD2 B:ASP415 4.4 24.8 1.0 CB B:LEU421 4.4 22.7 1.0 N B:ASP424 4.4 20.1 1.0 N B:GLY420 4.5 24.5 1.0 CB B:ASP424 4.5 22.0 1.0 N B:ASN417 4.5 23.1 1.0 C B:ASP415 4.5 22.8 1.0 N B:GLY418 4.5 24.8 1.0 CB B:ASN419 4.6 26.7 1.0 CB B:ASP423 4.6 20.5 1.0 CA B:ASP423 4.6 21.4 1.0 CB B:ASN417 4.6 24.7 1.0 C B:ASP423 4.6 22.1 1.0 N B:PRO422 4.6 21.2 1.0 CA B:ASN419 4.7 26.1 1.0 C B:ASN419 4.8 26.0 1.0 N B:ILE416 4.8 23.6 1.0 C B:ASN417 4.8 27.1 1.0 CA B:ASN417 4.8 23.8 1.0 C B:GLY420 4.8 25.2 1.0 CA B:PRO422 4.9 21.1 1.0 CE2 B:PHE564 4.9 21.7 1.0 O B:ASP415 5.0 23.6 1.0 C B:PRO422 5.0 22.3 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