Cobalt in PDB 4ras: Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation

The structure of Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation, PDB code: 4ras was solved by C.P.Quezada, K.A.P.Payne, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	76.90 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	177.340, 171.510, 109.020, 90.00, 98.87, 90.00
R / Rfree (%)	18.1 / 20.7

The structure of Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation also contains other interesting chemical elements:

Iron	(Fe)	24 atoms
Chlorine	(Cl)	3 atoms
Sodium	(Na)	3 atoms

The binding sites of Cobalt atom in the Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation (pdb code 4ras). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation, PDB code: 4ras:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation within 5.0Å range: probe atom residue distance (Å) B Occ A:Co803 b:28.8 occ:1.00 CO A:B12803 0.0 28.8 1.0 N21 A:B12803 1.9 28.4 1.0 N24 A:B12803 1.9 29.8 1.0 N23 A:B12803 1.9 29.2 1.0 N22 A:B12803 1.9 29.0 1.0 CL A:CL804 2.6 55.0 1.0 C9 A:B12803 2.8 29.2 1.0 C1 A:B12803 2.8 29.3 1.0 C11 A:B12803 2.8 28.9 1.0 C19 A:B12803 2.8 29.6 1.0 C14 A:B12803 2.9 29.9 1.0 C4 A:B12803 2.9 29.6 1.0 C16 A:B12803 2.9 29.9 1.0 C6 A:B12803 2.9 29.7 1.0 C10 A:B12803 3.2 29.3 1.0 C15 A:B12803 3.3 30.3 1.0 C20 A:B12803 3.3 27.7 1.0 C5 A:B12803 3.3 28.4 1.0 C8 A:B12803 4.1 29.6 1.0 C2 A:B12803 4.1 30.0 1.0 C18 A:B12803 4.2 29.8 1.0 C12 A:B12803 4.2 29.2 1.0 C3 A:B12803 4.2 29.0 1.0 C7 A:B12803 4.2 30.6 1.0 C13 A:B12803 4.2 29.8 1.0 C17 A:B12803 4.2 29.6 1.0 C26 A:B12803 4.7 29.6 1.0 C41 A:B12803 4.7 29.6 1.0 C37 A:B12803 4.7 32.6 1.0 C53 A:B12803 4.8 30.6 1.0 C35 A:B12803 4.8 27.4 1.0 NH2 A:ARG552 4.8 35.3 1.0 C54 A:B12803 4.9 28.0 1.0 C46 A:B12803 5.0 30.3 1.0

Cobalt binding site 2 out of 3 in the Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation within 5.0Å range: probe atom residue distance (Å) B Occ B:Co803 b:35.5 occ:1.00 CO B:B12803 0.0 35.5 1.0 N21 B:B12803 1.9 33.2 1.0 N24 B:B12803 1.9 33.6 1.0 N22 B:B12803 1.9 34.4 1.0 N23 B:B12803 1.9 34.3 1.0 CL B:CL804 2.6 63.2 1.0 C9 B:B12803 2.7 36.0 1.0 C1 B:B12803 2.8 33.2 1.0 C19 B:B12803 2.8 33.3 1.0 C11 B:B12803 2.8 34.6 1.0 C6 B:B12803 2.9 34.7 1.0 C4 B:B12803 2.9 32.5 1.0 C16 B:B12803 2.9 35.0 1.0 C14 B:B12803 3.0 35.1 1.0 C10 B:B12803 3.1 34.7 1.0 C20 B:B12803 3.3 33.9 1.0 C5 B:B12803 3.3 33.6 1.0 C15 B:B12803 3.4 35.2 1.0 C8 B:B12803 4.1 36.3 1.0 C7 B:B12803 4.1 36.3 1.0 C18 B:B12803 4.1 34.1 1.0 C2 B:B12803 4.1 32.7 1.0 C3 B:B12803 4.2 33.0 1.0 C17 B:B12803 4.2 35.5 1.0 C12 B:B12803 4.2 34.6 1.0 C13 B:B12803 4.3 34.9 1.0 C26 B:B12803 4.5 31.8 1.0 C37 B:B12803 4.6 37.4 1.0 C41 B:B12803 4.8 37.1 1.0 C35 B:B12803 4.8 33.0 1.0 NH2 B:ARG552 4.8 41.9 1.0 C54 B:B12803 4.8 32.4 1.0 C53 B:B12803 4.9 35.2 1.0

Cobalt binding site 3 out of 3 in the Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation within 5.0Å range: probe atom residue distance (Å) B Occ C:Co803 b:46.6 occ:1.00 CO C:B12803 0.0 46.6 1.0 N21 C:B12803 1.9 44.7 1.0 N24 C:B12803 1.9 47.1 1.0 N23 C:B12803 1.9 45.6 1.0 N22 C:B12803 1.9 45.6 1.0 CL C:CL804 2.5 62.9 1.0 C1 C:B12803 2.8 45.7 1.0 C19 C:B12803 2.8 46.2 1.0 C4 C:B12803 2.8 45.0 1.0 C9 C:B12803 2.9 46.7 1.0 C11 C:B12803 2.9 46.0 1.0 C14 C:B12803 2.9 45.6 1.0 C16 C:B12803 2.9 46.8 1.0 C6 C:B12803 3.0 45.9 1.0 C10 C:B12803 3.3 45.4 1.0 C5 C:B12803 3.3 46.0 1.0 C15 C:B12803 3.3 46.7 1.0 C20 C:B12803 3.4 45.9 1.0 C18 C:B12803 4.1 47.0 1.0 C2 C:B12803 4.1 45.7 1.0 C3 C:B12803 4.1 45.1 1.0 C17 C:B12803 4.2 47.9 1.0 C12 C:B12803 4.2 45.6 1.0 C8 C:B12803 4.2 45.6 1.0 C7 C:B12803 4.2 45.8 1.0 C13 C:B12803 4.3 46.1 1.0 C26 C:B12803 4.5 46.0 1.0 C37 C:B12803 4.6 47.0 1.0 C35 C:B12803 4.8 44.8 1.0 C53 C:B12803 4.8 47.2 1.0 NH2 C:ARG552 4.8 52.8 1.0 C41 C:B12803 4.9 45.8 1.0 C54 C:B12803 4.9 47.9 1.0 C30 C:B12803 5.0 45.5 1.0

K.A.P.Payne, C.P.Quezada, K.Fisher, M.S.Dunstan, F.A.Collins, H.Sjuts, C.Levy, S.Hay, S.E.J.Rigby, D.Leys. Reductive Dehalogenase Structure Suggests A Mechanism For B12-Dependent Dehalogenation Nature 2014.
ISSN: ESSN 1476-4687
DOI: 10.1038/NATURE13901