Iron in PDB 5m8z: Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol, PDB code: 5m8z was solved by C.Kunze, M.Bommer, W.R.Hagen, M.Uksa, H.Dobbek, T.Schubert, G.Diekert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.26 / 1.66
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	73.579, 73.579, 184.962, 90.00, 90.00, 90.00
R / Rfree (%)	13.8 / 16.1

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol also contains other interesting chemical elements:

Fluorine	(F)	8 atoms
Cobalt	(Co)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol (pdb code 5m8z). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol, PDB code: 5m8z:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:18.8 occ:1.00 FE1 A:SF4501 0.0 18.8 1.0 S2 A:SF4501 2.2 19.2 1.0 S3 A:SF4501 2.3 18.2 1.0 S4 A:SF4501 2.3 17.5 1.0 SG A:CYS390 2.3 18.0 1.0 FE4 A:SF4501 2.7 21.6 1.0 FE2 A:SF4501 2.7 19.2 1.0 FE3 A:SF4501 2.7 19.0 1.0 CB A:CYS390 3.3 16.4 1.0 CA A:CYS390 3.8 18.2 1.0 S1 A:SF4501 3.9 19.3 1.0 CD A:PRO391 4.0 16.7 1.0 CE A:MET292 4.1 16.4 1.0 CD1 A:ILE296 4.1 16.3 1.0 N A:PRO391 4.5 18.6 1.0 C A:CYS390 4.6 19.4 1.0 CD2 A:PHE392 4.6 20.3 1.0 SG A:CYS329 4.7 19.6 1.0 SG A:CYS335 4.8 19.4 1.0 SG A:CYS332 4.8 22.9 1.0

Iron binding site 2 out of 16 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:19.2 occ:1.00 FE2 A:SF4501 0.0 19.2 1.0 SG A:CYS329 2.3 19.6 1.0 S1 A:SF4501 2.3 19.3 1.0 S4 A:SF4501 2.3 17.5 1.0 S3 A:SF4501 2.3 18.2 1.0 FE3 A:SF4501 2.7 19.0 1.0 FE1 A:SF4501 2.7 18.8 1.0 FE4 A:SF4501 2.7 21.6 1.0 CB A:CYS329 3.3 19.6 1.0 CA A:CYS329 3.6 19.4 1.0 S2 A:SF4501 3.9 19.2 1.0 CB A:ARG291 4.1 19.5 1.0 N A:ARG291 4.2 18.5 1.0 N A:CYS329 4.3 20.6 1.0 CD1 A:ILE296 4.5 16.3 1.0 CB A:SER290 4.6 18.9 1.0 CB A:CYS332 4.7 25.3 1.0 CA A:ARG291 4.7 18.7 1.0 C A:CYS329 4.8 24.6 1.0 SG A:CYS332 4.8 22.9 1.0 SG A:CYS390 4.8 18.0 1.0 SG A:CYS335 4.8 19.4 1.0 O A:CYS329 4.9 24.3 1.0

Iron binding site 3 out of 16 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:19.0 occ:1.00 FE3 A:SF4501 0.0 19.0 1.0 S4 A:SF4501 2.3 17.5 1.0 S2 A:SF4501 2.3 19.2 1.0 SG A:CYS335 2.3 19.4 1.0 S1 A:SF4501 2.3 19.3 1.0 FE2 A:SF4501 2.7 19.2 1.0 FE4 A:SF4501 2.7 21.6 1.0 FE1 A:SF4501 2.7 18.8 1.0 CB A:CYS335 3.3 17.9 1.0 N A:CYS335 3.8 20.3 1.0 S3 A:SF4501 3.9 18.2 1.0 CB A:ARG291 4.1 19.5 1.0 CA A:CYS335 4.2 19.3 1.0 CE A:MET292 4.4 16.4 1.0 N A:MET292 4.5 19.4 1.0 CD A:ARG291 4.6 17.7 1.0 N A:LYS334 4.6 22.5 1.0 CG A:ARG291 4.7 19.2 1.0 SG A:CYS332 4.8 22.9 1.0 SG A:CYS329 4.8 19.6 1.0 CB A:MET292 4.9 20.3 1.0 SG A:CYS390 4.9 18.0 1.0 CA A:ARG291 5.0 18.7 1.0 N A:LYS333 5.0 30.7 1.0 C A:LYS334 5.0 22.6 1.0

Iron binding site 4 out of 16 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:21.6 occ:1.00 FE4 A:SF4501 0.0 21.6 1.0 S3 A:SF4501 2.2 18.2 1.0 S2 A:SF4501 2.3 19.2 1.0 SG A:CYS332 2.3 22.9 1.0 S1 A:SF4501 2.3 19.3 1.0 FE1 A:SF4501 2.7 18.8 1.0 FE3 A:SF4501 2.7 19.0 1.0 FE2 A:SF4501 2.7 19.2 1.0 CB A:CYS332 3.1 25.3 1.0 S4 A:SF4501 3.9 17.5 1.0 N A:LYS333 4.0 30.7 1.0 N A:LYS334 4.1 22.5 1.0 CD A:PRO391 4.1 16.7 1.0 CA A:CYS332 4.3 24.8 1.0 C A:CYS332 4.4 28.6 1.0 CB A:LYS334 4.6 20.6 1.0 N A:CYS335 4.7 20.3 1.0 SG A:CYS390 4.7 18.0 1.0 SG A:CYS335 4.7 19.4 1.0 CA A:LYS333 4.8 28.8 1.0 CA A:LYS334 4.8 19.9 1.0 C A:LYS333 4.8 27.8 1.0 SG A:CYS329 4.9 19.6 1.0 CA A:CYS329 4.9 19.4 1.0 CE2 A:PHE412 4.9 29.0 1.0 CG A:PRO391 4.9 23.0 1.0

Iron binding site 5 out of 16 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:19.3 occ:1.00 FE1 A:SF4502 0.0 19.3 1.0 SG A:CYS383 2.3 20.1 1.0 S2 A:SF4502 2.3 19.1 1.0 S4 A:SF4502 2.3 18.1 1.0 S3 A:SF4502 2.3 16.2 1.0 FE4 A:SF4502 2.7 19.4 1.0 FE3 A:SF4502 2.7 19.9 1.0 FE2 A:SF4502 2.7 18.1 1.0 CB A:CYS383 3.1 19.8 1.0 S1 A:SF4502 3.9 20.2 1.0 CD A:PRO340 4.0 21.9 1.0 N A:GLY384 4.0 17.4 1.0 N A:VAL385 4.2 17.0 1.0 CA A:CYS383 4.5 16.5 1.0 CB A:VAL385 4.5 19.2 1.0 SG A:CYS386 4.6 18.9 1.0 SG A:CYS339 4.7 19.9 1.0 CD2 A:TYR375 4.7 21.9 1.0 SG A:CYS372 4.7 19.6 1.0 N A:CYS386 4.7 17.6 1.0 C A:CYS383 4.7 21.5 1.0 CG A:PRO340 4.8 24.3 1.0 CA A:GLY384 4.9 15.7 1.0 CA A:VAL385 4.9 16.6 1.0 C A:GLY384 4.9 17.5 1.0

Iron binding site 6 out of 16 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:18.1 occ:1.00 FE2 A:SF4502 0.0 18.1 1.0 S1 A:SF4502 2.3 20.2 1.0 SG A:CYS386 2.3 18.9 1.0 S3 A:SF4502 2.3 16.2 1.0 S4 A:SF4502 2.3 18.1 1.0 FE4 A:SF4502 2.7 19.4 1.0 FE1 A:SF4502 2.7 19.3 1.0 FE3 A:SF4502 2.7 19.9 1.0 CB A:CYS386 3.2 18.1 1.0 N A:CYS386 3.8 17.6 1.0 S2 A:SF4502 3.9 19.1 1.0 C42 A:BVQ503 4.1 25.9 1.0 N45 A:BVQ503 4.1 27.5 1.0 CA A:CYS386 4.2 18.2 1.0 C41 A:BVQ503 4.3 21.6 1.0 CD1 A:ILE344 4.4 18.6 1.0 C43 A:BVQ503 4.5 25.3 1.0 SG A:CYS383 4.7 20.1 1.0 SG A:CYS372 4.7 19.6 1.0 N A:VAL385 4.7 17.0 1.0 SG A:CYS339 4.8 19.9 1.0 N A:GLY384 4.9 17.4 1.0 C8 A:BVQ503 4.9 17.0 1.0

Iron binding site 7 out of 16 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:19.9 occ:1.00 FE3 A:SF4502 0.0 19.9 1.0 S4 A:SF4502 2.2 18.1 1.0 SG A:CYS339 2.3 19.9 1.0 S1 A:SF4502 2.3 20.2 1.0 S2 A:SF4502 2.3 19.1 1.0 FE4 A:SF4502 2.7 19.4 1.0 FE1 A:SF4502 2.7 19.3 1.0 FE2 A:SF4502 2.7 18.1 1.0 CB A:CYS339 3.4 22.9 1.0 CA A:CYS339 3.9 19.8 1.0 S3 A:SF4502 3.9 16.2 1.0 OG A:SER341 4.0 26.4 1.0 CD A:PRO340 4.1 21.9 1.0 N A:PRO340 4.4 19.8 1.0 C A:CYS339 4.4 19.3 1.0 CB A:ALA343 4.5 19.0 1.0 CD1 A:ILE344 4.5 18.6 1.0 CG1 A:ILE344 4.7 17.5 1.0 SG A:CYS372 4.7 19.6 1.0 N A:SER341 4.8 21.9 1.0 SG A:CYS383 4.8 20.1 1.0 SG A:CYS386 4.8 18.9 1.0 N A:ALA343 5.0 23.7 1.0

Iron binding site 8 out of 16 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:19.4 occ:1.00 FE4 A:SF4502 0.0 19.4 1.0 S3 A:SF4502 2.3 16.2 1.0 SG A:CYS372 2.3 19.6 1.0 S1 A:SF4502 2.3 20.2 1.0 S2 A:SF4502 2.3 19.1 1.0 FE3 A:SF4502 2.7 19.9 1.0 FE1 A:SF4502 2.7 19.3 1.0 FE2 A:SF4502 2.7 18.1 1.0 CB A:CYS372 3.3 18.3 1.0 CA A:CYS372 3.8 21.5 1.0 S4 A:SF4502 3.8 18.1 1.0 C42 A:BVQ503 4.2 25.9 1.0 NE1 A:TRP376 4.3 21.3 1.0 C A:CYS372 4.5 24.0 1.0 O A:CYS372 4.5 19.1 1.0 SG A:CYS383 4.7 20.1 1.0 SG A:CYS339 4.7 19.9 1.0 CB A:CYS383 4.7 19.8 1.0 OG A:SER341 4.8 26.4 1.0 C41 A:BVQ503 4.8 21.6 1.0 SG A:CYS386 4.8 18.9 1.0 N45 A:BVQ503 4.8 27.5 1.0 C8 A:BVQ503 4.8 17.0 1.0

Iron binding site 9 out of 16 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:27.6 occ:1.00 FE1 B:SF4501 0.0 27.6 1.0 S2 B:SF4501 2.2 29.7 1.0 S3 B:SF4501 2.3 28.8 1.0 S4 B:SF4501 2.3 25.9 1.0 SG B:CYS390 2.3 28.3 1.0 FE4 B:SF4501 2.7 32.3 1.0 FE2 B:SF4501 2.7 29.1 1.0 FE3 B:SF4501 2.7 27.9 1.0 CB B:CYS390 3.3 30.2 1.0 CA B:CYS390 3.8 26.5 1.0 S1 B:SF4501 3.9 27.6 1.0 CD B:PRO391 4.0 27.7 1.0 CE B:MET292 4.1 23.5 1.0 CD1 B:ILE296 4.1 25.2 1.0 N B:PRO391 4.5 26.4 1.0 SG B:CYS329 4.5 28.9 1.0 C B:CYS390 4.6 27.6 1.0 CD2 B:PHE392 4.6 31.5 1.0 SG B:CYS335 4.8 29.3 1.0 SG B:CYS332 4.8 33.2 1.0 N B:CYS390 5.0 26.6 1.0

Iron binding site 10 out of 16 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:29.1 occ:1.00 FE2 B:SF4501 0.0 29.1 1.0 SG B:CYS329 2.1 28.9 1.0 S1 B:SF4501 2.3 27.6 1.0 S3 B:SF4501 2.3 28.8 1.0 S4 B:SF4501 2.3 25.9 1.0 FE4 B:SF4501 2.7 32.3 1.0 FE3 B:SF4501 2.7 27.9 1.0 FE1 B:SF4501 2.7 27.6 1.0 CB B:CYS329 3.3 30.5 1.0 CA B:CYS329 3.7 30.8 1.0 S2 B:SF4501 3.8 29.7 1.0 CB B:ARG291 4.1 32.0 1.0 N B:ARG291 4.2 29.3 1.0 N B:CYS329 4.4 32.6 1.0 CD1 B:ILE296 4.5 25.2 1.0 CB B:SER290 4.6 25.0 1.0 CB B:CYS332 4.7 36.1 1.0 CA B:ARG291 4.7 29.0 1.0 SG B:CYS332 4.7 33.2 1.0 SG B:CYS390 4.8 28.3 1.0 SG B:CYS335 4.8 29.3 1.0 C B:CYS329 4.8 34.7 1.0 O B:CYS329 4.9 39.9 1.0

C.Kunze, M.Bommer, W.R.Hagen, M.Uksa, H.Dobbek, T.Schubert, G.Diekert. Cobamide-Mediated Enzymatic Reductive Dehalogenation Via Long-Range Electron Transfer. Nat Commun V. 8 15858 2017.
ISSN: ESSN 2041-1723
PubMed: 28671181
DOI: 10.1038/NCOMMS15858