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Iron in PDB 5maa: Pce Reductive Dehalogenase From S. Multivorans in Complex with 3- Bromophenol

Protein crystallography data

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 3- Bromophenol, PDB code: 5maa 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) 47.38 / 1.69
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 73.835, 73.835, 185.360, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 16.7

Other elements in 5maa:

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

Cobalt (Co) 2 atoms
Bromine (Br) 4 atoms

Iron Binding Sites:

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 3- Bromophenol (pdb code 5maa). 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 3- Bromophenol, PDB code: 5maa:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 5maa

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


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 3- Bromophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:18.0
occ:1.00
 FE1 A:SF4501 0.0 18.0 1.0
S2 A:SF4501 2.3 18.2 1.0
S3 A:SF4501 2.3 17.4 1.0
S4 A:SF4501 2.3 16.4 1.0
SG A:CYS390 2.3 17.4 1.0
FE2 A:SF4501 2.7 18.5 1.0
FE4 A:SF4501 2.7 19.0 1.0
FE3 A:SF4501 2.7 18.7 1.0
CB A:CYS390 3.3 16.8 1.0
CA A:CYS390 3.8 20.5 1.0
S1 A:SF4501 3.9 18.4 1.0
CD A:PRO391 4.0 18.6 1.0
CE A:MET292 4.0 15.9 1.0
CD1 A:ILE296 4.1 17.1 1.0
N A:PRO391 4.6 17.4 1.0
C A:CYS390 4.6 19.4 1.0
CD1 A:PHE392 4.7 17.5 1.0
SG A:CYS329 4.7 20.0 1.0
SG A:CYS335 4.8 20.2 1.0
SG A:CYS332 4.9 21.4 1.0

Iron binding site 2 out of 16 in 5maa

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


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 3- Bromophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:18.5
occ:1.00
 FE2 A:SF4501 0.0 18.5 1.0
SG A:CYS329 2.3 20.0 1.0
S1 A:SF4501 2.3 18.4 1.0
S4 A:SF4501 2.3 16.4 1.0
S3 A:SF4501 2.3 17.4 1.0
FE3 A:SF4501 2.7 18.7 1.0
FE1 A:SF4501 2.7 18.0 1.0
FE4 A:SF4501 2.7 19.0 1.0
CB A:CYS329 3.3 19.1 1.0
CA A:CYS329 3.6 19.2 1.0
S2 A:SF4501 3.8 18.2 1.0
CB A:ARG291 4.1 18.5 1.0
N A:ARG291 4.2 20.5 1.0
N A:CYS329 4.3 22.1 1.0
CB A:SER290 4.5 18.9 1.0
CD1 A:ILE296 4.5 17.1 1.0
CB A:CYS332 4.7 23.6 1.0
CA A:ARG291 4.8 18.1 1.0
SG A:CYS332 4.8 21.4 1.0
SG A:CYS390 4.8 17.4 1.0
C A:CYS329 4.8 26.9 1.0
SG A:CYS335 4.8 20.2 1.0
O A:CYS329 5.0 23.4 1.0

Iron binding site 3 out of 16 in 5maa

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


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 3- Bromophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:18.7
occ:1.00
 FE3 A:SF4501 0.0 18.7 1.0
S4 A:SF4501 2.2 16.4 1.0
S2 A:SF4501 2.3 18.2 1.0
S1 A:SF4501 2.3 18.4 1.0
SG A:CYS335 2.3 20.2 1.0
FE2 A:SF4501 2.7 18.5 1.0
FE1 A:SF4501 2.7 18.0 1.0
FE4 A:SF4501 2.7 19.0 1.0
CB A:CYS335 3.3 18.8 1.0
N A:CYS335 3.8 19.6 1.0
S3 A:SF4501 3.9 17.4 1.0
CB A:ARG291 4.1 18.5 1.0
CA A:CYS335 4.2 18.3 1.0
CE A:MET292 4.4 15.9 1.0
N A:MET292 4.5 17.2 1.0
CD A:ARG291 4.6 19.6 1.0
N A:LYS334 4.6 22.7 1.0
SG A:CYS329 4.7 20.0 1.0
CG A:ARG291 4.7 20.3 1.0
SG A:CYS332 4.8 21.4 1.0
CB A:MET292 4.8 16.6 1.0
SG A:CYS390 4.9 17.4 1.0
CA A:ARG291 5.0 18.1 1.0
C A:LYS334 5.0 20.9 1.0
N A:ARG291 5.0 20.5 1.0

Iron binding site 4 out of 16 in 5maa

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


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 3- Bromophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:19.0
occ:1.00
 FE4 A:SF4501 0.0 19.0 1.0
S3 A:SF4501 2.2 17.4 1.0
S2 A:SF4501 2.3 18.2 1.0
S1 A:SF4501 2.3 18.4 1.0
SG A:CYS332 2.3 21.4 1.0
FE1 A:SF4501 2.7 18.0 1.0
FE2 A:SF4501 2.7 18.5 1.0
FE3 A:SF4501 2.7 18.7 1.0
CB A:CYS332 3.1 23.6 1.0
S4 A:SF4501 3.9 16.4 1.0
N A:LYS333 4.0 26.4 1.0
N A:LYS334 4.0 22.7 1.0
CD A:PRO391 4.1 18.6 1.0
CA A:CYS332 4.4 25.0 1.0
C A:CYS332 4.5 27.6 1.0
CB A:LYS334 4.6 23.1 1.0
N A:CYS335 4.7 19.6 1.0
CE2 A:PHE412 4.7 29.8 1.0
SG A:CYS390 4.7 17.4 1.0
SG A:CYS335 4.8 20.2 1.0
SG A:CYS329 4.8 20.0 1.0
CG A:PRO391 4.8 24.1 1.0
CA A:LYS333 4.8 30.7 1.0
CA A:LYS334 4.8 22.0 1.0
CA A:CYS329 4.8 19.2 1.0
C A:LYS333 4.9 29.4 1.0
CD2 A:PHE412 5.0 43.3 1.0

Iron binding site 5 out of 16 in 5maa

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


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 3- Bromophenol 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 19.6 1.0
S2 A:SF4502 2.3 18.2 1.0
S4 A:SF4502 2.3 18.2 1.0
S3 A:SF4502 2.3 16.1 1.0
FE4 A:SF4502 2.6 19.0 1.0
FE3 A:SF4502 2.7 19.1 1.0
FE2 A:SF4502 2.7 18.2 1.0
CB A:CYS383 3.2 17.6 1.0
S1 A:SF4502 3.8 19.4 1.0
N A:GLY384 4.0 16.5 1.0
CD A:PRO340 4.0 20.5 1.0
N A:VAL385 4.1 15.4 1.0
CA A:CYS383 4.5 17.7 1.0
CB A:VAL385 4.5 18.7 1.0
SG A:CYS386 4.6 18.0 1.0
CD2 A:TYR375 4.7 21.5 1.0
SG A:CYS339 4.7 19.7 1.0
SG A:CYS372 4.7 18.4 1.0
N A:CYS386 4.7 16.3 1.0
C A:CYS383 4.7 19.8 1.0
CA A:GLY384 4.9 16.6 1.0
CG A:PRO340 4.9 24.0 1.0
CA A:VAL385 4.9 17.1 1.0
C A:GLY384 4.9 18.6 1.0

Iron binding site 6 out of 16 in 5maa

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


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 3- Bromophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:18.2
occ:1.00
 FE2 A:SF4502 0.0 18.2 1.0
S1 A:SF4502 2.3 19.4 1.0
S3 A:SF4502 2.3 16.1 1.0
SG A:CYS386 2.3 18.0 1.0
S4 A:SF4502 2.3 18.2 1.0
FE1 A:SF4502 2.7 19.3 1.0
FE4 A:SF4502 2.7 19.0 1.0
FE3 A:SF4502 2.7 19.1 1.0
CB A:CYS386 3.3 18.0 1.0
N A:CYS386 3.8 16.3 1.0
S2 A:SF4502 3.9 18.2 1.0
N45 A:OBL503 4.1 30.1 1.0
C42 A:OBL503 4.1 27.4 1.0
C41 A:OBL503 4.2 21.0 1.0
CA A:CYS386 4.2 16.8 1.0
CD1 A:ILE344 4.4 18.2 1.0
SG A:CYS383 4.6 19.6 1.0
C43 A:OBL503 4.7 30.9 1.0
N A:VAL385 4.7 15.4 1.0
SG A:CYS372 4.7 18.4 1.0
SG A:CYS339 4.8 19.7 1.0
N A:GLY384 4.9 16.5 1.0
C8 A:OBL503 4.9 14.9 1.0
C A:GLY384 5.0 18.6 1.0

Iron binding site 7 out of 16 in 5maa

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


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 3- Bromophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:19.1
occ:1.00
 FE3 A:SF4502 0.0 19.1 1.0
S4 A:SF4502 2.2 18.2 1.0
S1 A:SF4502 2.3 19.4 1.0
S2 A:SF4502 2.3 18.2 1.0
SG A:CYS339 2.3 19.7 1.0
FE4 A:SF4502 2.7 19.0 1.0
FE1 A:SF4502 2.7 19.3 1.0
FE2 A:SF4502 2.7 18.2 1.0
CB A:CYS339 3.4 22.8 1.0
S3 A:SF4502 3.9 16.1 1.0
CA A:CYS339 3.9 19.4 1.0
OG A:SER341 3.9 24.1 1.0
CD A:PRO340 4.1 20.5 1.0
N A:PRO340 4.4 19.8 1.0
C A:CYS339 4.5 21.2 1.0
CB A:ALA343 4.5 20.4 1.0
CD1 A:ILE344 4.6 18.2 1.0
CG1 A:ILE344 4.7 19.3 1.0
N A:SER341 4.8 23.9 1.0
SG A:CYS383 4.8 19.6 1.0
SG A:CYS372 4.8 18.4 1.0
SG A:CYS386 4.8 18.0 1.0
N A:ALA343 5.0 22.0 1.0

Iron binding site 8 out of 16 in 5maa

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


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 3- Bromophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:19.0
occ:1.00
 FE4 A:SF4502 0.0 19.0 1.0
S3 A:SF4502 2.2 16.1 1.0
S1 A:SF4502 2.3 19.4 1.0
S2 A:SF4502 2.3 18.2 1.0
SG A:CYS372 2.3 18.4 1.0
FE1 A:SF4502 2.6 19.3 1.0
FE3 A:SF4502 2.7 19.1 1.0
FE2 A:SF4502 2.7 18.2 1.0
CB A:CYS372 3.3 19.6 1.0
S4 A:SF4502 3.8 18.2 1.0
CA A:CYS372 3.8 18.0 1.0
C42 A:OBL503 4.1 27.4 1.0
NE1 A:TRP376 4.4 23.6 1.0
O A:CYS372 4.5 19.4 1.0
C A:CYS372 4.5 20.9 1.0
C41 A:OBL503 4.6 21.0 1.0
SG A:CYS383 4.6 19.6 1.0
OG A:SER341 4.7 24.1 1.0
SG A:CYS339 4.7 19.7 1.0
CB A:CYS383 4.7 17.6 1.0
SG A:CYS386 4.8 18.0 1.0
C8 A:OBL503 4.8 14.9 1.0

Iron binding site 9 out of 16 in 5maa

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


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 3- Bromophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:27.8
occ:1.00
 FE1 B:SF4501 0.0 27.8 1.0
S2 B:SF4501 2.2 31.1 1.0
S3 B:SF4501 2.3 32.1 1.0
S4 B:SF4501 2.3 26.9 1.0
SG B:CYS390 2.3 28.8 1.0
FE2 B:SF4501 2.7 31.4 1.0
FE4 B:SF4501 2.7 31.1 1.0
FE3 B:SF4501 2.7 28.6 1.0
CB B:CYS390 3.3 29.5 1.0
CA B:CYS390 3.8 26.4 1.0
S1 B:SF4501 3.9 31.8 1.0
CD B:PRO391 4.1 32.4 1.0
CD1 B:ILE296 4.1 26.6 1.0
CE B:MET292 4.4 31.4 1.0
SG B:CYS329 4.5 30.1 1.0
N B:PRO391 4.6 30.0 1.0
CD2 B:PHE392 4.6 32.4 1.0
C B:CYS390 4.6 26.4 1.0
SG B:CYS335 4.8 32.4 1.0
SG B:CYS332 4.9 35.2 1.0
N B:CYS390 5.0 27.2 1.0
CB B:CYS335 5.0 31.8 1.0

Iron binding site 10 out of 16 in 5maa

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


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 3- Bromophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:31.4
occ:1.00
 FE2 B:SF4501 0.0 31.4 1.0
SG B:CYS329 2.1 30.1 1.0
S1 B:SF4501 2.3 31.8 1.0
S3 B:SF4501 2.3 32.1 1.0
S4 B:SF4501 2.3 26.9 1.0
FE3 B:SF4501 2.6 28.6 1.0
FE4 B:SF4501 2.6 31.1 1.0
FE1 B:SF4501 2.7 27.8 1.0
CB B:CYS329 3.3 32.6 1.0
CA B:CYS329 3.7 33.5 1.0
S2 B:SF4501 3.8 31.1 1.0
CB B:ARG291 4.1 33.8 1.0
N B:ARG291 4.2 34.7 1.0
N B:CYS329 4.4 36.9 1.0
CD1 B:ILE296 4.6 26.6 1.0
CB B:SER290 4.6 29.2 1.0
CB B:CYS332 4.7 35.6 1.0
SG B:CYS332 4.7 35.2 1.0
SG B:CYS390 4.7 28.8 1.0
SG B:CYS335 4.7 32.4 1.0
CA B:ARG291 4.8 34.0 1.0
C B:CYS329 4.9 38.6 1.0
CD1 B:PHE328 5.0 47.1 1.0
O B:CYS329 5.0 40.0 1.0

Reference:

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
Page generated: Tue Aug 5 23:47:33 2025

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