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

Protein crystallography data

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

Cobalt Binding Sites:

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 4jgi

Go back to Cobalt Binding Sites List in 4jgi
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 4jgi

Go back to Cobalt Binding Sites List in 4jgi
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

Reference:

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
Page generated: Sun Dec 13 10:44:51 2020

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