Cobalt in PDB 5m2q: Structure of Cobinamide-Bound Btuf Mutant W66F, the Periplasmic Vitamin B12 Binding Protein in E.Coli

The structure of Structure of Cobinamide-Bound Btuf Mutant W66F, the Periplasmic Vitamin B12 Binding Protein in E.Coli, PDB code: 5m2q 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)	19.71 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	136.560, 90.670, 50.810, 90.00, 110.87, 90.00
R / Rfree (%)	20.9 / 24.9

The binding sites of Cobalt atom in the Structure of Cobinamide-Bound Btuf Mutant W66F, the Periplasmic Vitamin B12 Binding Protein in E.Coli (pdb code 5m2q). 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 W66F, the Periplasmic Vitamin B12 Binding Protein in E.Coli, PDB code: 5m2q:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Structure of Cobinamide-Bound Btuf Mutant W66F, 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 W66F, the Periplasmic Vitamin B12 Binding Protein in E.Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Co301 b:24.0 occ:1.00 CO A:CBY301 0.0 24.0 1.0 N21 A:CBY301 1.9 25.7 1.0 N24 A:CBY301 1.9 27.8 1.0 N23 A:CBY301 1.9 24.1 1.0 C A:CYN302 1.9 28.1 1.0 N22 A:CBY301 2.0 23.6 1.0 C19 A:CBY301 2.8 27.6 1.0 C1 A:CBY301 2.8 26.8 1.0 C4 A:CBY301 2.9 26.1 1.0 C14 A:CBY301 2.9 24.9 1.0 C16 A:CBY301 3.0 27.2 1.0 O A:HOH550 3.0 50.5 1.0 C11 A:CBY301 3.0 23.4 1.0 C6 A:CBY301 3.0 23.4 1.0 N A:CYN302 3.0 29.0 1.0 C9 A:CBY301 3.0 22.4 1.0 C5 A:CBY301 3.4 25.0 1.0 C20 A:CBY301 3.4 27.0 1.0 C15 A:CBY301 3.4 25.3 1.0 C10 A:CBY301 3.5 22.6 1.0 C18 A:CBY301 4.0 29.3 1.0 C2 A:CBY301 4.0 26.9 1.0 C3 A:CBY301 4.1 27.7 1.0 C13 A:CBY301 4.2 25.4 1.0 C17 A:CBY301 4.2 29.7 1.0 C12 A:CBY301 4.3 23.9 1.0 C8 A:CBY301 4.3 21.9 1.0 C7 A:CBY301 4.3 23.0 1.0 OE1 A:GLU245 4.5 33.7 1.0 C26 A:CBY301 4.5 28.7 1.0 O A:HOH415 4.8 46.5 1.0 C48 A:CBY301 4.8 28.4 1.0 CE2 A:PHE66 4.8 42.5 1.0 C37 A:CBY301 4.8 23.9 1.0 C47 A:CBY301 4.9 22.9 1.0 C35 A:CBY301 4.9 24.1 1.0 C53 A:CBY301 5.0 24.7 1.0 C54 A:CBY301 5.0 28.8 1.0

Cobalt binding site 2 out of 2 in the Structure of Cobinamide-Bound Btuf Mutant W66F, 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 W66F, the Periplasmic Vitamin B12 Binding Protein in E.Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Co301 b:27.8 occ:1.00 CO B:CBY301 0.0 27.8 1.0 O B:HOH406 1.6 30.4 1.0 N21 B:CBY301 1.9 28.5 1.0 N24 B:CBY301 1.9 29.1 1.0 N22 B:CBY301 1.9 26.8 1.0 N23 B:CBY301 1.9 27.6 1.0 C B:CYN302 2.0 30.4 1.0 C19 B:CBY301 2.7 30.4 1.0 C1 B:CBY301 2.8 29.9 1.0 C4 B:CBY301 2.9 29.2 1.0 C9 B:CBY301 2.9 26.6 1.0 C14 B:CBY301 3.0 28.1 1.0 C6 B:CBY301 3.0 26.9 1.0 C11 B:CBY301 3.0 27.8 1.0 N B:CYN302 3.0 37.3 1.0 C16 B:CBY301 3.0 29.8 1.0 C10 B:CBY301 3.3 26.3 1.0 C5 B:CBY301 3.4 28.2 1.0 C15 B:CBY301 3.4 28.8 1.0 C20 B:CBY301 3.5 30.1 1.0 O B:HOH559 3.8 45.9 1.0 C2 B:CBY301 4.0 30.4 1.0 C18 B:CBY301 4.1 31.7 1.0 C3 B:CBY301 4.2 30.4 1.0 C17 B:CBY301 4.2 32.0 1.0 C13 B:CBY301 4.2 29.0 1.0 C12 B:CBY301 4.2 27.8 1.0 C8 B:CBY301 4.2 26.1 1.0 C7 B:CBY301 4.3 26.8 1.0 C26 B:CBY301 4.5 31.7 1.0 C48 B:CBY301 4.7 30.9 1.0 CE2 B:PHE66 4.8 51.3 1.0 C47 B:CBY301 4.8 27.9 1.0 C35 B:CBY301 4.8 27.9 1.0 C37 B:CBY301 4.8 27.0 1.0 OE1 B:GLU245 4.8 56.1 1.0 C53 B:CBY301 4.9 28.2 1.0 C54 B:CBY301 4.9 32.0 1.0 C41 B:CBY301 5.0 25.7 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