Cobalt in PDB 5m34: Structure of Cobinamide-Bound Btuf Mutant W66Y, the Periplasmic Vitamin B12 Binding Protein in E.Coli

The structure of Structure of Cobinamide-Bound Btuf Mutant W66Y, the Periplasmic Vitamin B12 Binding Protein in E.Coli, PDB code: 5m34 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)	29.48 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	139.830, 90.800, 51.070, 90.00, 111.25, 90.00
R / Rfree (%)	19.1 / 23.3

The binding sites of Cobalt atom in the Structure of Cobinamide-Bound Btuf Mutant W66Y, the Periplasmic Vitamin B12 Binding Protein in E.Coli (pdb code 5m34). 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 W66Y, the Periplasmic Vitamin B12 Binding Protein in E.Coli, PDB code: 5m34:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Structure of Cobinamide-Bound Btuf Mutant W66Y, 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 W66Y, the Periplasmic Vitamin B12 Binding Protein in E.Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Co301 b:25.9 occ:1.00 CO A:CBY301 0.0 25.9 1.0 N21 A:CBY301 1.9 25.4 1.0 N23 A:CBY301 1.9 23.7 1.0 N24 A:CBY301 1.9 26.2 1.0 N22 A:CBY301 1.9 23.2 1.0 C A:CYN302 1.9 28.0 1.0 C19 A:CBY301 2.8 27.8 1.0 C1 A:CBY301 2.8 27.4 1.0 C14 A:CBY301 2.9 24.1 1.0 C4 A:CBY301 2.9 27.4 1.0 C6 A:CBY301 3.0 23.9 1.0 C11 A:CBY301 3.0 22.6 1.0 C9 A:CBY301 3.0 22.3 1.0 C16 A:CBY301 3.0 25.5 1.0 O A:HOH558 3.1 36.3 1.0 N A:CYN302 3.3 36.7 1.0 C5 A:CBY301 3.3 27.2 1.0 C15 A:CBY301 3.4 24.4 1.0 C10 A:CBY301 3.4 18.4 1.0 C20 A:CBY301 3.5 23.3 1.0 C2 A:CBY301 4.1 27.6 1.0 C18 A:CBY301 4.1 30.3 1.0 C3 A:CBY301 4.2 27.9 1.0 C12 A:CBY301 4.2 20.4 1.0 C13 A:CBY301 4.2 22.9 1.0 C17 A:CBY301 4.3 28.5 1.0 C8 A:CBY301 4.3 20.7 1.0 C7 A:CBY301 4.3 23.7 1.0 O A:HOH480 4.6 42.6 1.0 C26 A:CBY301 4.6 34.2 1.0 C47 A:CBY301 4.8 20.1 1.0 C37 A:CBY301 4.8 24.2 1.0 C35 A:CBY301 4.8 26.3 1.0 OE1 A:GLU245 4.9 41.4 1.0 C53 A:CBY301 4.9 24.5 1.0 C48 A:CBY301 4.9 24.3 1.0

Cobalt binding site 2 out of 2 in the Structure of Cobinamide-Bound Btuf Mutant W66Y, 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 W66Y, the Periplasmic Vitamin B12 Binding Protein in E.Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Co302 b:26.5 occ:1.00 CO B:CBY302 0.0 26.5 1.0 N21 B:CBY302 1.9 30.9 1.0 N24 B:CBY302 1.9 33.4 1.0 C B:CYN303 1.9 18.7 1.0 C B:CYN301 1.9 21.5 1.0 N23 B:CBY302 1.9 27.7 1.0 N22 B:CBY302 2.0 29.5 1.0 C19 B:CBY302 2.8 30.1 1.0 C1 B:CBY302 2.8 29.6 1.0 C14 B:CBY302 3.0 24.8 1.0 C6 B:CBY302 3.0 23.4 1.0 C9 B:CBY302 3.0 21.7 1.0 C4 B:CBY302 3.0 25.9 1.0 C16 B:CBY302 3.0 27.5 1.0 C11 B:CBY302 3.0 26.0 1.0 N B:CYN303 3.0 38.9 1.0 N B:CYN301 3.2 29.0 1.0 C10 B:CBY302 3.4 22.5 1.0 C5 B:CBY302 3.4 29.4 1.0 C15 B:CBY302 3.4 29.9 1.0 C20 B:CBY302 3.5 26.9 1.0 C2 B:CBY302 4.1 27.3 1.0 C18 B:CBY302 4.1 31.9 1.0 C3 B:CBY302 4.2 27.2 1.0 C17 B:CBY302 4.2 33.8 1.0 C8 B:CBY302 4.3 24.7 1.0 C13 B:CBY302 4.3 27.7 1.0 C7 B:CBY302 4.3 27.1 1.0 C12 B:CBY302 4.3 23.1 1.0 C26 B:CBY302 4.6 31.8 1.0 O B:HOH465 4.7 48.2 1.0 O B:HOH502 4.7 49.9 1.0 C37 B:CBY302 4.7 28.0 1.0 C48 B:CBY302 4.7 26.7 1.0 C47 B:CBY302 4.9 23.1 1.0 C35 B:CBY302 4.9 25.4 1.0 C53 B:CBY302 4.9 24.4 1.0 C54 B:CBY302 5.0 32.8 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