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

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron 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 Iron atom.
In total 24 binding sites of Iron where determined in the Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation, PDB code: 4ras:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in the Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe801 b:28.1 occ:1.00 FE1 A:SF4801 0.0 28.1 1.0 S3 A:SF4801 2.1 28.7 1.0 S4 A:SF4801 2.1 29.0 1.0 S2 A:SF4801 2.1 27.4 1.0 SG A:CYS518 2.3 34.5 1.0 FE3 A:SF4801 2.6 28.4 1.0 FE4 A:SF4801 2.6 27.4 1.0 FE2 A:SF4801 2.7 28.9 1.0 CB A:CYS518 3.2 32.4 1.0 S1 A:SF4801 3.7 29.4 1.0 CB A:ARG473 3.9 29.5 1.0 N A:CYS518 4.0 32.8 1.0 CG1 A:ILE474 4.2 30.5 1.0 CA A:CYS518 4.2 31.6 1.0 CD A:ARG473 4.5 28.9 1.0 N A:ILE474 4.5 29.7 1.0 CG A:ARG473 4.5 29.6 1.0 SG A:CYS512 4.6 31.4 1.0 SG A:CYS568 4.6 27.8 1.0 SG A:CYS515 4.6 31.1 1.0 CD1 A:ILE474 4.7 31.6 1.0 CA A:ARG473 4.8 30.7 1.0 N A:ARG473 4.8 29.3 1.0 N A:LYS517 4.9 31.6 1.0 C A:ARG473 5.0 30.1 1.0

Iron binding site 2 out of 24 in the Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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 A:Fe801 b:28.9 occ:1.00 FE2 A:SF4801 0.0 28.9 1.0 S4 A:SF4801 2.1 29.0 1.0 S3 A:SF4801 2.1 28.7 1.0 S1 A:SF4801 2.2 29.4 1.0 SG A:CYS515 2.3 31.1 1.0 FE3 A:SF4801 2.6 28.4 1.0 FE4 A:SF4801 2.6 27.4 1.0 FE1 A:SF4801 2.7 28.1 1.0 CB A:CYS515 3.1 34.2 1.0 S2 A:SF4801 3.7 27.4 1.0 CD A:PRO569 4.0 32.8 1.0 N A:LYS517 4.3 31.6 1.0 CA A:CYS515 4.4 34.0 1.0 C A:CYS515 4.4 34.8 1.0 SG A:CYS568 4.5 27.8 1.0 SG A:CYS518 4.6 34.5 1.0 CG A:PRO569 4.6 31.4 1.0 N A:ARG516 4.6 33.4 1.0 CE1 A:PHE511 4.7 31.3 1.0 CB A:LYS517 4.7 30.2 1.0 SG A:CYS512 4.7 31.4 1.0 O A:CYS515 4.7 36.1 1.0 N A:CYS518 4.8 32.8 1.0 CD1 A:PHE511 4.9 30.8 1.0 CA A:CYS512 5.0 32.5 1.0

Iron binding site 3 out of 24 in the Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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 A:Fe801 b:28.4 occ:1.00 FE3 A:SF4801 0.0 28.4 1.0 S2 A:SF4801 2.1 27.4 1.0 S1 A:SF4801 2.2 29.4 1.0 S4 A:SF4801 2.2 29.0 1.0 SG A:CYS568 2.2 27.8 1.0 FE4 A:SF4801 2.5 27.4 1.0 FE1 A:SF4801 2.6 28.1 1.0 FE2 A:SF4801 2.6 28.9 1.0 CB A:CYS568 3.5 30.9 1.0 S3 A:SF4801 3.5 28.7 1.0 CD A:PRO569 3.9 32.8 1.0 CA A:CYS568 4.0 32.1 1.0 CD1 A:LEU479 4.1 32.9 1.0 CD1 A:TRP570 4.5 28.3 1.0 N A:PRO569 4.6 31.5 1.0 SG A:CYS512 4.6 31.4 1.0 SG A:CYS518 4.7 34.5 1.0 SG A:CYS515 4.7 31.1 1.0 C A:CYS568 4.7 31.6 1.0 CD1 A:ILE474 4.8 31.6 1.0 CB A:CYS518 4.9 32.4 1.0

Iron binding site 4 out of 24 in the Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:27.4 occ:1.00 FE4 A:SF4801 0.0 27.4 1.0 S3 A:SF4801 2.1 28.7 1.0 S2 A:SF4801 2.1 27.4 1.0 S1 A:SF4801 2.1 29.4 1.0 SG A:CYS512 2.3 31.4 1.0 FE3 A:SF4801 2.5 28.4 1.0 FE2 A:SF4801 2.6 28.9 1.0 FE1 A:SF4801 2.6 28.1 1.0 CB A:CYS512 3.5 30.8 1.0 S4 A:SF4801 3.6 29.0 1.0 CA A:CYS512 3.8 32.5 1.0 CB A:ARG473 4.3 29.5 1.0 N A:ARG473 4.3 29.3 1.0 SG A:CYS568 4.6 27.8 1.0 N A:CYS512 4.6 32.5 1.0 SG A:CYS515 4.7 31.1 1.0 CD1 A:LEU479 4.7 32.9 1.0 CB A:SER472 4.7 30.0 1.0 CB A:CYS515 4.7 34.2 1.0 SG A:CYS518 4.8 34.5 1.0 CA A:ARG473 4.9 30.7 1.0 C A:CYS512 5.0 33.4 1.0 CD1 A:PHE511 5.0 30.8 1.0

Iron binding site 5 out of 24 in the Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe802 b:31.1 occ:1.00 FE1 A:SF4802 0.0 31.1 1.0 S4 A:SF4802 2.1 32.0 1.0 S3 A:SF4802 2.1 34.2 1.0 S2 A:SF4802 2.2 30.3 1.0 SG A:CYS548 2.3 32.0 1.0 FE4 A:SF4802 2.5 31.2 1.0 FE2 A:SF4802 2.6 31.5 1.0 FE3 A:SF4802 2.6 28.8 1.0 CB A:CYS548 3.5 32.2 1.0 S1 A:SF4802 3.6 32.7 1.0 CA A:CYS548 4.1 32.2 1.0 C42 A:B12803 4.4 32.5 1.0 CD A:ARG552 4.4 32.7 1.0 CG A:ARG552 4.4 34.8 1.0 SG A:CYS522 4.7 31.5 1.0 O A:CYS548 4.7 29.7 1.0 SG A:CYS561 4.7 31.9 1.0 SG A:CYS564 4.8 30.9 1.0 C A:CYS548 4.8 31.7 1.0 C8 A:B12803 4.9 29.6 1.0 N45 A:B12803 4.9 33.3 1.0

Iron binding site 6 out of 24 in the Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe802 b:31.5 occ:1.00 FE2 A:SF4802 0.0 31.5 1.0 S3 A:SF4802 2.1 34.2 1.0 S1 A:SF4802 2.2 32.7 1.0 S4 A:SF4802 2.2 32.0 1.0 SG A:CYS561 2.3 31.9 1.0 FE4 A:SF4802 2.6 31.2 1.0 FE1 A:SF4802 2.6 31.1 1.0 FE3 A:SF4802 2.7 28.8 1.0 CB A:CYS561 3.3 33.3 1.0 S2 A:SF4802 3.7 30.3 1.0 CD A:PRO523 4.2 35.5 1.0 N A:ARG563 4.2 28.7 1.0 C A:CYS561 4.3 31.2 1.0 CA A:CYS561 4.4 33.5 1.0 N A:GLY562 4.5 31.5 1.0 O A:CYS561 4.6 30.1 1.0 SG A:CYS564 4.6 30.9 1.0 SG A:CYS522 4.6 31.5 1.0 CB A:ARG563 4.6 31.1 1.0 CD2 A:TYR551 4.7 35.0 1.0 SG A:CYS548 4.7 32.0 1.0 CA A:GLY562 4.7 29.5 1.0 C A:GLY562 4.9 29.2 1.0 N A:CYS564 4.9 29.8 1.0 CG A:ARG552 4.9 34.8 1.0 CG A:PRO523 4.9 37.4 1.0 CA A:ARG563 4.9 30.1 1.0 CE2 A:TYR551 5.0 36.1 1.0

Iron binding site 7 out of 24 in the Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe802 b:28.8 occ:1.00 FE3 A:SF4802 0.0 28.8 1.0 S2 A:SF4802 2.1 30.3 1.0 S4 A:SF4802 2.1 32.0 1.0 S1 A:SF4802 2.2 32.7 1.0 SG A:CYS564 2.3 30.9 1.0 FE4 A:SF4802 2.6 31.2 1.0 FE1 A:SF4802 2.6 31.1 1.0 FE2 A:SF4802 2.7 31.5 1.0 CB A:CYS564 3.3 31.1 1.0 S3 A:SF4802 3.7 34.2 1.0 N A:CYS564 3.9 29.8 1.0 CA A:CYS564 4.3 29.5 1.0 CD1 A:ILE527 4.5 27.0 1.0 C42 A:B12803 4.5 32.5 1.0 C41 A:B12803 4.6 29.6 1.0 SG A:CYS548 4.6 32.0 1.0 SG A:CYS561 4.7 31.9 1.0 N A:ARG563 4.7 28.7 1.0 N45 A:B12803 4.7 33.3 1.0 SG A:CYS522 4.8 31.5 1.0 C8 A:B12803 4.9 29.6 1.0 C A:GLY562 5.0 29.2 1.0 CA A:GLY562 5.0 29.5 1.0 C43 A:B12803 5.0 32.1 1.0

Iron binding site 8 out of 24 in the Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe802 b:31.2 occ:1.00 FE4 A:SF4802 0.0 31.2 1.0 S1 A:SF4802 2.0 32.7 1.0 S3 A:SF4802 2.2 34.2 1.0 S2 A:SF4802 2.2 30.3 1.0 SG A:CYS522 2.4 31.5 1.0 FE1 A:SF4802 2.5 31.1 1.0 FE2 A:SF4802 2.6 31.5 1.0 FE3 A:SF4802 2.6 28.8 1.0 CB A:CYS522 3.4 31.2 1.0 S4 A:SF4802 3.5 32.0 1.0 CA A:CYS522 4.0 33.0 1.0 CD A:PRO523 4.1 35.5 1.0 SG A:CYS524 4.5 42.7 1.0 SG A:CYS548 4.6 32.0 1.0 N A:PRO523 4.6 34.7 1.0 C A:CYS522 4.7 34.4 1.0 CB A:ALA526 4.7 34.5 1.0 CD1 A:ILE527 4.7 27.0 1.0 SG A:CYS561 4.7 31.9 1.0 SG A:CYS564 4.7 30.9 1.0 CG1 A:ILE527 4.8 27.4 1.0

Iron binding site 9 out of 24 in the Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe801 b:38.3 occ:1.00 FE1 B:SF4801 0.0 38.3 1.0 S4 B:SF4801 2.1 38.4 1.0 S2 B:SF4801 2.1 37.5 1.0 S3 B:SF4801 2.2 38.3 1.0 SG B:CYS518 2.3 45.3 1.0 FE4 B:SF4801 2.5 37.4 1.0 FE3 B:SF4801 2.6 36.8 1.0 FE2 B:SF4801 2.6 38.8 1.0 CB B:CYS518 3.3 42.2 1.0 S1 B:SF4801 3.6 39.5 1.0 CB B:ARG473 3.9 38.5 1.0 N B:CYS518 4.0 42.3 1.0 CA B:CYS518 4.3 41.9 1.0 CG1 B:ILE474 4.3 44.3 1.0 SG B:CYS512 4.4 40.7 1.0 CD B:ARG473 4.5 38.6 1.0 N B:ILE474 4.6 41.2 1.0 CG B:ARG473 4.6 38.5 1.0 SG B:CYS515 4.6 44.3 1.0 SG B:CYS568 4.7 42.9 1.0 CA B:ARG473 4.8 39.0 1.0 CD1 B:ILE474 4.8 42.2 1.0 N B:LYS517 4.8 44.4 1.0 N B:ARG473 4.9 39.1 1.0 C B:ARG473 5.0 39.1 1.0

Iron binding site 10 out of 24 in the Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Reductive Dehalogenase Structure Suggests A Mechanism For B12- Dependent Dehalogenation within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe801 b:38.8 occ:1.00 FE2 B:SF4801 0.0 38.8 1.0 S1 B:SF4801 2.1 39.5 1.0 S4 B:SF4801 2.1 38.4 1.0 S3 B:SF4801 2.1 38.3 1.0 SG B:CYS515 2.3 44.3 1.0 FE4 B:SF4801 2.6 37.4 1.0 FE1 B:SF4801 2.6 38.3 1.0 FE3 B:SF4801 2.6 36.8 1.0 CB B:CYS515 3.1 45.7 1.0 S2 B:SF4801 3.7 37.5 1.0 CD B:PRO569 4.1 41.4 1.0 CA B:CYS515 4.3 48.4 1.0 C B:CYS515 4.3 48.9 1.0 N B:LYS517 4.3 44.4 1.0 SG B:CYS568 4.5 42.9 1.0 SG B:CYS512 4.5 40.7 1.0 SG B:CYS518 4.6 45.3 1.0 N B:ARG516 4.6 48.9 1.0 CG B:PRO569 4.6 42.2 1.0 O B:CYS515 4.6 57.1 1.0 CE1 B:PHE511 4.7 41.6 1.0 CB B:LYS517 4.7 44.4 1.0 N B:CYS518 4.8 42.3 1.0 CD1 B:PHE511 4.9 42.2 1.0 CA B:CYS512 4.9 43.7 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