Cobalt in PDB 5m29: Structure of Cobinamide-Bound Btuf, the Periplasmic Vitamin B12 Binding Protein in E.Coli

The structure of Structure of Cobinamide-Bound Btuf, the Periplasmic Vitamin B12 Binding Protein in E.Coli, PDB code: 5m29 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)	29.39 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	138.150, 90.560, 50.840, 90.00, 110.90, 90.00
R / Rfree (%)	17.9 / 21.3

The binding sites of Cobalt atom in the Structure of Cobinamide-Bound Btuf, the Periplasmic Vitamin B12 Binding Protein in E.Coli (pdb code 5m29). 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, the Periplasmic Vitamin B12 Binding Protein in E.Coli, PDB code: 5m29:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Structure of Cobinamide-Bound Btuf, 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, the Periplasmic Vitamin B12 Binding Protein in E.Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Co301 b:21.1 occ:1.00 CO A:CBY301 0.0 21.1 1.0 N21 A:CBY301 1.9 21.9 1.0 N23 A:CBY301 1.9 20.1 1.0 C A:CYN302 1.9 30.3 1.0 N24 A:CBY301 2.0 23.2 1.0 N22 A:CBY301 2.0 18.6 1.0 O A:HOH421 2.7 35.1 1.0 C19 A:CBY301 2.8 22.6 1.0 C1 A:CBY301 2.8 23.8 1.0 C14 A:CBY301 2.9 22.6 1.0 C4 A:CBY301 2.9 24.6 1.0 C11 A:CBY301 2.9 20.3 1.0 C9 A:CBY301 3.0 18.1 1.0 C6 A:CBY301 3.0 19.2 1.0 C16 A:CBY301 3.0 22.6 1.0 N A:CYN302 3.2 30.8 1.0 C10 A:CBY301 3.3 19.1 1.0 C15 A:CBY301 3.4 21.7 1.0 C5 A:CBY301 3.4 23.3 1.0 C20 A:CBY301 3.5 24.8 1.0 C2 A:CBY301 4.1 24.8 1.0 C18 A:CBY301 4.1 25.7 1.0 C3 A:CBY301 4.2 26.0 1.0 C13 A:CBY301 4.2 22.6 1.0 C12 A:CBY301 4.2 20.6 1.0 C17 A:CBY301 4.2 25.0 1.0 C8 A:CBY301 4.3 17.1 1.0 C7 A:CBY301 4.3 18.7 1.0 OE1 A:GLU245 4.3 33.8 1.0 O A:HOH563 4.4 45.7 1.0 C26 A:CBY301 4.5 26.8 1.0 C37 A:CBY301 4.8 19.5 1.0 C47 A:CBY301 4.9 20.8 1.0 O A:HOH588 4.9 48.5 1.0 C48 A:CBY301 4.9 26.1 1.0 C53 A:CBY301 4.9 23.0 1.0 C35 A:CBY301 4.9 23.1 1.0 CZ2 A:TRP66 5.0 33.6 1.0 C54 A:CBY301 5.0 25.9 1.0 NE1 A:TRP66 5.0 42.1 1.0

Cobalt binding site 2 out of 2 in the Structure of Cobinamide-Bound Btuf, 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, the Periplasmic Vitamin B12 Binding Protein in E.Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Co301 b:23.2 occ:1.00 CO B:CBY301 0.0 23.2 1.0 C B:CYN303 1.7 12.1 1.0 N21 B:CBY301 1.9 23.8 1.0 C B:CYN302 1.9 21.6 0.8 N23 B:CBY301 1.9 23.5 1.0 N24 B:CBY301 1.9 25.9 1.0 N22 B:CBY301 2.0 23.2 1.0 C19 B:CBY301 2.8 26.4 1.0 C1 B:CBY301 2.8 24.9 1.0 C14 B:CBY301 2.9 22.1 1.0 C11 B:CBY301 3.0 23.7 1.0 C4 B:CBY301 3.0 26.5 1.0 C9 B:CBY301 3.0 21.7 1.0 C6 B:CBY301 3.0 23.1 1.0 C16 B:CBY301 3.0 26.3 1.0 N B:CYN303 3.1 18.0 0.5 N B:CYN302 3.2 25.4 0.6 C10 B:CBY301 3.3 22.7 1.0 C5 B:CBY301 3.4 26.4 1.0 C15 B:CBY301 3.4 24.5 1.0 C20 B:CBY301 3.4 26.7 1.0 C2 B:CBY301 4.1 28.4 1.0 C18 B:CBY301 4.1 28.4 1.0 C3 B:CBY301 4.2 25.6 1.0 C13 B:CBY301 4.2 24.1 1.0 C12 B:CBY301 4.3 21.3 1.0 C7 B:CBY301 4.3 22.1 1.0 C17 B:CBY301 4.3 27.8 1.0 C8 B:CBY301 4.3 20.2 1.0 C26 B:CBY301 4.5 28.3 1.0 OE1 B:GLU245 4.7 41.4 1.0 C37 B:CBY301 4.7 23.5 1.0 C48 B:CBY301 4.8 25.4 1.0 O B:HOH487 4.8 46.6 1.0 C47 B:CBY301 4.8 22.8 1.0 CZ2 B:TRP66 4.9 43.1 1.0 C35 B:CBY301 4.9 24.9 1.0 C53 B:CBY301 4.9 24.1 1.0 O B:HOH544 5.0 49.0 1.0 C54 B:CBY301 5.0 27.9 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