Chlorine 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:

Cobalt	(Co)	3 atoms
Iron	(Fe)	24 atoms
Sodium	(Na)	3 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation, PDB code: 4ras:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl804 b:55.0 occ:1.00 CO A:B12803 2.6 28.8 1.0 N22 A:B12803 3.1 29.0 1.0 O A:HOH996 3.2 38.1 1.0 NH2 A:ARG552 3.3 35.3 1.0 N21 A:B12803 3.3 28.4 1.0 N24 A:B12803 3.4 29.8 1.0 NZ A:LYS488 3.4 40.3 1.0 OH A:TYR426 3.4 37.2 1.0 N23 A:B12803 3.4 29.2 1.0 C6 A:B12803 3.5 29.7 1.0 C9 A:B12803 3.8 29.2 1.0 C4 A:B12803 3.9 29.6 1.0 C19 A:B12803 3.9 29.6 1.0 C5 A:B12803 3.9 28.4 1.0 C37 A:B12803 4.0 32.6 1.0 CE2 A:PHE291 4.1 38.3 1.0 C11 A:B12803 4.1 28.9 1.0 C14 A:B12803 4.1 29.9 1.0 C16 A:B12803 4.1 29.9 1.0 C10 A:B12803 4.2 29.3 1.0 C1 A:B12803 4.2 29.3 1.0 CZ A:ARG552 4.2 36.1 1.0 C7 A:B12803 4.3 30.6 1.0 C15 A:B12803 4.4 30.3 1.0 CZ A:PHE291 4.4 41.8 1.0 NH1 A:ARG552 4.4 37.7 1.0 O39 A:B12803 4.5 34.7 1.0 C38 A:B12803 4.6 35.5 1.0 CZ A:TYR426 4.7 35.9 1.0 C8 A:B12803 4.7 29.6 1.0 C26 A:B12803 4.8 29.6 1.0 CE A:LYS488 4.9 41.5 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl804 b:63.2 occ:1.00 CO B:B12803 2.6 35.5 1.0 N24 B:B12803 3.2 33.6 1.0 OH B:TYR426 3.3 45.0 1.0 N23 B:B12803 3.3 34.3 1.0 NH2 B:ARG552 3.4 41.9 1.0 N21 B:B12803 3.5 33.2 1.0 NZ B:LYS488 3.5 47.4 1.0 N22 B:B12803 3.5 34.4 1.0 C19 B:B12803 3.7 33.3 1.0 CE2 B:PHE291 3.9 47.9 1.0 C6 B:B12803 3.9 34.7 1.0 C16 B:B12803 3.9 35.0 1.0 C9 B:B12803 4.0 36.0 1.0 C14 B:B12803 4.0 35.1 1.0 C4 B:B12803 4.1 32.5 1.0 C11 B:B12803 4.1 34.6 1.0 C37 B:B12803 4.2 37.4 1.0 C5 B:B12803 4.2 33.6 1.0 C15 B:B12803 4.2 35.2 1.0 C1 B:B12803 4.2 33.2 1.0 CZ B:PHE291 4.3 47.0 1.0 C10 B:B12803 4.3 34.7 1.0 CZ B:ARG552 4.4 40.1 1.0 C7 B:B12803 4.6 36.3 1.0 CZ B:TYR426 4.6 42.2 1.0 C54 B:B12803 4.6 32.4 1.0 NH1 B:ARG552 4.6 40.5 1.0 C26 B:B12803 4.7 31.8 1.0 C17 B:B12803 4.9 35.5 1.0 C38 B:B12803 5.0 38.8 1.0 C18 B:B12803 5.0 34.1 1.0 CE B:LYS488 5.0 44.2 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl804 b:62.9 occ:1.00 CO C:B12803 2.5 46.6 1.0 N24 C:B12803 3.0 47.1 1.0 N23 C:B12803 3.1 45.6 1.0 N22 C:B12803 3.2 45.6 1.0 NH2 C:ARG552 3.3 52.8 1.0 N21 C:B12803 3.4 44.7 1.0 OH C:TYR426 3.5 63.1 1.0 NZ C:LYS488 3.6 59.2 1.0 C6 C:B12803 3.7 45.9 1.0 C19 C:B12803 3.7 46.2 1.0 C16 C:B12803 3.8 46.8 1.0 C14 C:B12803 3.8 45.6 1.0 C9 C:B12803 3.8 46.7 1.0 C11 C:B12803 3.9 46.0 1.0 C4 C:B12803 3.9 45.0 1.0 CE2 C:PHE291 3.9 54.6 1.0 C15 C:B12803 4.0 46.7 1.0 C5 C:B12803 4.0 46.0 1.0 C37 C:B12803 4.1 47.0 1.0 C10 C:B12803 4.2 45.4 1.0 C1 C:B12803 4.2 45.7 1.0 CZ C:PHE291 4.3 55.4 1.0 CZ C:ARG552 4.4 52.8 1.0 C7 C:B12803 4.6 45.8 1.0 C26 C:B12803 4.6 46.0 1.0 NH1 C:ARG552 4.6 53.0 1.0 CZ C:TYR426 4.7 59.7 1.0 C38 C:B12803 4.8 48.2 1.0 O39 C:B12803 4.8 47.7 1.0 C54 C:B12803 4.8 47.9 1.0 C17 C:B12803 4.9 47.9 1.0 C8 C:B12803 4.9 45.6 1.0 C13 C:B12803 5.0 46.1 1.0 C2 C:B12803 5.0 45.7 1.0 C12 C:B12803 5.0 45.6 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