Cobalt in PDB 4jgi: 1.5 Angstrom Crystal Structure of A Novel Cobalamin-Binding Protein From Desulfitobacterium Hafniense Dcb-2

The structure of 1.5 Angstrom Crystal Structure of A Novel Cobalamin-Binding Protein From Desulfitobacterium Hafniense Dcb-2, PDB code: 4jgi was solved by H.Sjuts, M.S.Dunstan, K.Fisher, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.69 / 1.50
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	69.990, 69.990, 91.680, 90.00, 90.00, 120.00
R / Rfree (%)	14.7 / 19.4

The binding sites of Cobalt atom in the 1.5 Angstrom Crystal Structure of A Novel Cobalamin-Binding Protein From Desulfitobacterium Hafniense Dcb-2 (pdb code 4jgi). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the 1.5 Angstrom Crystal Structure of A Novel Cobalamin-Binding Protein From Desulfitobacterium Hafniense Dcb-2, PDB code: 4jgi:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the 1.5 Angstrom Crystal Structure of A Novel Cobalamin-Binding Protein From Desulfitobacterium Hafniense Dcb-2


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of 1.5 Angstrom Crystal Structure of A Novel Cobalamin-Binding Protein From Desulfitobacterium Hafniense Dcb-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co301 b:21.0 occ:1.00 CO A:COB301 0.0 21.0 1.0 N21 A:COB301 1.9 22.1 1.0 N24 A:COB301 1.9 19.2 1.0 N23 A:COB301 1.9 19.0 1.0 N22 A:COB301 1.9 18.9 1.0 NE2 A:HIS102 2.6 25.3 1.0 C19 A:COB301 2.8 18.0 1.0 C9 A:COB301 2.9 18.8 1.0 C1 A:COB301 2.9 19.3 1.0 C11 A:COB301 2.9 19.3 1.0 C4 A:COB301 2.9 20.8 1.0 C16 A:COB301 3.0 18.7 1.0 C14 A:COB301 3.0 18.4 1.0 C6 A:COB301 3.0 19.5 1.0 C10 A:COB301 3.3 19.7 1.0 C5 A:COB301 3.4 21.6 1.0 C15 A:COB301 3.4 18.1 1.0 C20 A:COB301 3.4 20.1 1.0 CE1 A:HIS102 3.5 27.2 1.0 CD2 A:HIS102 3.6 23.1 1.0 C18 A:COB301 4.1 18.4 1.0 C2 A:COB301 4.2 21.0 1.0 C3 A:COB301 4.2 22.1 1.0 C7 A:COB301 4.2 21.4 1.0 C8 A:COB301 4.2 21.0 1.0 C17 A:COB301 4.2 19.9 1.0 C13 A:COB301 4.2 18.4 1.0 C12 A:COB301 4.3 20.7 1.0 ND1 A:HIS102 4.6 25.6 1.0 C26 A:COB301 4.6 22.2 1.0 CG A:HIS102 4.7 23.2 1.0 C37 A:COB301 4.8 21.8 1.0 C41 A:COB301 4.8 24.3 1.0 C35 A:COB301 4.9 23.2 1.0 C53 A:COB301 4.9 17.7 1.0 C46 A:COB301 4.9 23.3 1.0 C48 A:COB301 5.0 20.0 1.0 C54 A:COB301 5.0 19.6 1.0

Cobalt binding site 2 out of 2 in the 1.5 Angstrom Crystal Structure of A Novel Cobalamin-Binding Protein From Desulfitobacterium Hafniense Dcb-2


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of 1.5 Angstrom Crystal Structure of A Novel Cobalamin-Binding Protein From Desulfitobacterium Hafniense Dcb-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co301 b:17.6 occ:1.00 CO B:COB301 0.0 17.6 1.0 N21 B:COB301 1.8 15.6 1.0 N24 B:COB301 1.9 18.1 1.0 N22 B:COB301 1.9 16.6 1.0 N23 B:COB301 1.9 15.8 1.0 NE2 B:HIS102 2.5 20.8 1.0 C11 B:COB301 2.9 15.5 1.0 C9 B:COB301 2.9 15.6 1.0 C1 B:COB301 2.9 18.2 1.0 C19 B:COB301 2.9 17.0 1.0 C14 B:COB301 2.9 17.2 1.0 C4 B:COB301 2.9 15.9 1.0 C16 B:COB301 2.9 17.2 1.0 C6 B:COB301 2.9 17.5 1.0 C10 B:COB301 3.2 16.6 1.0 C5 B:COB301 3.3 18.9 1.0 C15 B:COB301 3.3 16.4 1.0 CE1 B:HIS102 3.4 21.6 1.0 CD2 B:HIS102 3.5 22.4 1.0 C20 B:COB301 3.5 16.2 1.0 C18 B:COB301 4.1 18.4 1.0 C2 B:COB301 4.1 18.5 1.0 C8 B:COB301 4.2 17.4 1.0 C3 B:COB301 4.2 19.7 1.0 C7 B:COB301 4.2 16.1 1.0 C13 B:COB301 4.2 15.5 1.0 C12 B:COB301 4.2 15.8 1.0 C17 B:COB301 4.2 16.9 1.0 ND1 B:HIS102 4.6 21.9 1.0 CG B:HIS102 4.6 19.1 1.0 C26 B:COB301 4.6 20.0 1.0 C41 B:COB301 4.8 19.8 1.0 C35 B:COB301 4.8 20.6 1.0 C37 B:COB301 4.8 18.2 1.0 C53 B:COB301 4.9 19.0 1.0 C46 B:COB301 4.9 18.4 1.0 C48 B:COB301 5.0 17.6 1.0 C54 B:COB301 5.0 17.3 1.0

H.Sjuts, M.S.Dunstan, K.Fisher, D.Leys. Structure of the Cobalamin-Binding Protein of A Putative O-Demethylase From Desulfitobacterium Hafniense Dcb-2. Acta Crystallogr.,Sect.D V. 69 1609 2013.
ISSN: ISSN 0907-4449
PubMed: 23897483
DOI: 10.1107/S0907444913011323