Cobalt in PDB 5m3b: Structure of Cobinamide-Bound Btuf Mutant W66L, the Periplasmic Vitamin B12 Binding Protein in E.Coli

The structure of Structure of Cobinamide-Bound Btuf Mutant W66L, the Periplasmic Vitamin B12 Binding Protein in E.Coli, PDB code: 5m3b was solved by S.A.Mireku, M.Ruetz, T.Zhou, V.M.Korkhov, B.Kraeutler, K.P.Locher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.67 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	136.280, 90.460, 50.810, 90.00, 110.74, 90.00
R / Rfree (%)	19.6 / 22.9

The binding sites of Cobalt atom in the Structure of Cobinamide-Bound Btuf Mutant W66L, the Periplasmic Vitamin B12 Binding Protein in E.Coli (pdb code 5m3b). 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 Cobinamide-Bound Btuf Mutant W66L, the Periplasmic Vitamin B12 Binding Protein in E.Coli, PDB code: 5m3b:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Structure of Cobinamide-Bound Btuf Mutant W66L, the Periplasmic Vitamin B12 Binding Protein in E.Coli


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of Cobinamide-Bound Btuf Mutant W66L, the Periplasmic Vitamin B12 Binding Protein in E.Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Co302 b:17.8 occ:1.00 CO A:CBY302 0.0 17.8 1.0 C A:CYN301 1.5 25.9 0.8 C A:CYN303 1.9 23.7 1.0 N24 A:CBY302 1.9 18.0 1.0 N21 A:CBY302 1.9 16.2 1.0 N23 A:CBY302 1.9 14.5 1.0 N22 A:CBY302 1.9 15.3 1.0 N A:CYN301 2.8 23.9 0.8 C19 A:CBY302 2.8 19.1 1.0 C1 A:CBY302 2.9 19.9 1.0 C11 A:CBY302 3.0 15.2 1.0 C9 A:CBY302 3.0 14.9 1.0 C6 A:CBY302 3.0 15.2 1.0 C4 A:CBY302 3.0 17.2 1.0 C16 A:CBY302 3.0 18.6 1.0 C14 A:CBY302 3.0 17.3 1.0 N A:CYN303 3.1 25.9 1.0 C10 A:CBY302 3.3 13.5 1.0 C5 A:CBY302 3.4 14.7 1.0 C15 A:CBY302 3.4 17.2 1.0 C20 A:CBY302 3.4 20.9 1.0 C18 A:CBY302 4.1 21.4 1.0 C2 A:CBY302 4.2 21.1 1.0 C17 A:CBY302 4.2 20.2 1.0 C8 A:CBY302 4.3 14.3 1.0 C12 A:CBY302 4.3 16.2 1.0 C7 A:CBY302 4.3 16.0 1.0 C3 A:CBY302 4.3 19.1 1.0 C13 A:CBY302 4.3 17.0 1.0 C26 A:CBY302 4.6 25.0 1.0 C47 A:CBY302 4.7 15.6 1.0 O A:HOH414 4.8 51.5 1.0 C37 A:CBY302 4.8 16.8 1.0 C35 A:CBY302 4.9 16.1 1.0 C48 A:CBY302 4.9 21.8 1.0 C54 A:CBY302 4.9 21.2 1.0 C53 A:CBY302 4.9 18.5 1.0 O A:HOH553 5.0 35.8 1.0 OE1 A:GLU245 5.0 29.3 1.0 O1 A:GOL304 5.0 44.0 1.0

Cobalt binding site 2 out of 2 in the Structure of Cobinamide-Bound Btuf Mutant W66L, the Periplasmic Vitamin B12 Binding Protein in E.Coli


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of Cobinamide-Bound Btuf Mutant W66L, the Periplasmic Vitamin B12 Binding Protein in E.Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Co301 b:19.4 occ:1.00 CO B:CBY301 0.0 19.4 1.0 N21 B:CBY301 1.8 16.9 1.0 C B:CYN302 1.9 26.8 1.0 N24 B:CBY301 1.9 20.4 1.0 N23 B:CBY301 1.9 17.8 1.0 N22 B:CBY301 2.0 18.2 1.0 C19 B:CBY301 2.8 23.1 1.0 C1 B:CBY301 2.8 21.4 1.0 C4 B:CBY301 2.9 17.4 1.0 C9 B:CBY301 2.9 17.9 1.0 C11 B:CBY301 3.0 20.2 1.0 C6 B:CBY301 3.0 17.5 1.0 C14 B:CBY301 3.0 20.0 1.0 C16 B:CBY301 3.0 22.3 1.0 N B:CYN302 3.1 31.9 1.0 C10 B:CBY301 3.3 18.9 1.0 O B:HOH406 3.3 33.5 1.0 C5 B:CBY301 3.4 17.0 1.0 C20 B:CBY301 3.4 20.9 1.0 C15 B:CBY301 3.4 20.4 1.0 C2 B:CBY301 4.1 23.1 1.0 C18 B:CBY301 4.1 24.2 1.0 C3 B:CBY301 4.2 20.3 1.0 C17 B:CBY301 4.2 24.1 1.0 C8 B:CBY301 4.2 16.5 1.0 C12 B:CBY301 4.2 19.6 1.0 C7 B:CBY301 4.2 18.5 1.0 C13 B:CBY301 4.3 20.3 1.0 O3 B:GOL303 4.6 39.5 0.5 C26 B:CBY301 4.6 24.8 1.0 C37 B:CBY301 4.7 18.4 1.0 C47 B:CBY301 4.8 20.7 1.0 C48 B:CBY301 4.8 21.7 1.0 C35 B:CBY301 4.9 17.6 1.0 C53 B:CBY301 4.9 19.6 1.0 C54 B:CBY301 4.9 24.3 1.0

S.A.Mireku, M.Ruetz, T.Zhou, V.M.Korkhov, B.Krautler, K.P.Locher. Conformational Change of A Tryptophan Residue in Btuf Facilitates Binding and Transport of Cobinamide By the Vitamin B12 Transporter Btucd-F. Sci Rep V. 7 41575 2017.
ISSN: ESSN 2045-2322
PubMed: 28128319
DOI: 10.1038/SREP41575