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Iron in PDB 4ur2: Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide

Enzymatic activity of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide

All present enzymatic activity of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide:
1.97.1.8;

Protein crystallography data

The structure of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide, PDB code: 4ur2 was solved by M.Bommer, C.Kunze, J.Fesseler, T.Schubert, G.Diekert, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.047 / 2.10
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 73.243, 73.243, 184.154, 90.00, 90.00, 90.00
R / Rfree (%) 14.2 / 18.59

Other elements in 4ur2:

The structure of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide also contains other interesting chemical elements:

Cobalt (Co) 2 atoms
Iodine (I) 11 atoms

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide (pdb code 4ur2). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide, PDB code: 4ur2:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 4ur2

Go back to Iron Binding Sites List in 4ur2
Iron binding site 1 out of 16 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:23.8
occ:1.00
 FE1 A:SF4501 0.0 23.8 1.0
S3 A:SF4501 2.3 22.5 1.0
S4 A:SF4501 2.3 26.5 1.0
S2 A:SF4501 2.4 21.1 1.0
SG A:CYS390 2.4 24.1 1.0
FE4 A:SF4501 2.7 23.8 1.0
FE3 A:SF4501 2.7 23.6 1.0
FE2 A:SF4501 2.7 22.8 1.0
CB A:CYS390 3.3 19.9 1.0
CA A:CYS390 3.8 20.9 1.0
S1 A:SF4501 3.9 21.3 1.0
CD A:PRO391 4.0 22.4 1.0
CE A:MET292 4.0 24.2 1.0
CD1 A:ILE296 4.1 19.7 1.0
N A:PRO391 4.5 25.7 1.0
C A:CYS390 4.6 22.2 1.0
CD2 A:PHE392 4.7 20.6 1.0
SG A:CYS335 4.7 23.4 1.0
SG A:CYS329 4.7 22.7 1.0
SG A:CYS332 4.9 26.9 1.0
N A:CYS390 5.0 21.2 1.0

Iron binding site 2 out of 16 in 4ur2

Go back to Iron Binding Sites List in 4ur2
Iron binding site 2 out of 16 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:22.8
occ:1.00
 FE2 A:SF4501 0.0 22.8 1.0
S4 A:SF4501 2.2 26.5 1.0
S1 A:SF4501 2.3 21.3 1.0
S3 A:SF4501 2.3 22.5 1.0
SG A:CYS332 2.4 26.9 1.0
FE3 A:SF4501 2.7 23.6 1.0
FE4 A:SF4501 2.7 23.8 1.0
FE1 A:SF4501 2.7 23.8 1.0
CB A:CYS332 3.1 27.7 1.0
S2 A:SF4501 3.9 21.1 1.0
N A:LYS334 4.0 28.2 1.0
N A:LYS333 4.0 26.2 1.0
CD A:PRO391 4.1 22.4 1.0
CA A:CYS332 4.4 29.3 1.0
C A:CYS332 4.4 34.0 1.0
CB A:LYS334 4.4 32.1 1.0
N A:CYS335 4.6 23.2 1.0
SG A:CYS335 4.7 23.4 1.0
CA A:LYS333 4.7 31.0 1.0
CA A:LYS334 4.7 30.0 1.0
SG A:CYS390 4.8 24.1 1.0
SG A:CYS329 4.8 22.7 1.0
CA A:CYS329 4.8 22.1 1.0
C A:LYS333 4.8 30.0 1.0
CE2 A:PHE412 4.8 36.5 1.0
CG A:PRO391 4.9 28.5 1.0
CD2 A:PHE412 5.0 38.2 1.0

Iron binding site 3 out of 16 in 4ur2

Go back to Iron Binding Sites List in 4ur2
Iron binding site 3 out of 16 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:23.6
occ:1.00
 FE3 A:SF4501 0.0 23.6 1.0
S4 A:SF4501 2.3 26.5 1.0
S1 A:SF4501 2.3 21.3 1.0
SG A:CYS329 2.3 22.7 1.0
S2 A:SF4501 2.3 21.1 1.0
FE2 A:SF4501 2.7 22.8 1.0
FE4 A:SF4501 2.7 23.8 1.0
FE1 A:SF4501 2.7 23.8 1.0
CB A:CYS329 3.4 21.4 1.0
CA A:CYS329 3.6 22.1 1.0
S3 A:SF4501 3.8 22.5 1.0
CB A:ARG291 4.1 25.6 1.0
N A:ARG291 4.2 22.7 1.0
N A:CYS329 4.3 26.6 1.0
CB A:SER290 4.6 18.2 1.0
CD1 A:ILE296 4.6 19.7 1.0
C A:CYS329 4.7 29.2 1.0
CB A:CYS332 4.8 27.7 1.0
SG A:CYS335 4.8 23.4 1.0
CA A:ARG291 4.8 23.2 1.0
SG A:CYS332 4.8 26.9 1.0
SG A:CYS390 4.8 24.1 1.0
O A:CYS329 4.8 26.3 1.0

Iron binding site 4 out of 16 in 4ur2

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Iron binding site 4 out of 16 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:23.8
occ:1.00
 FE4 A:SF4501 0.0 23.8 1.0
S3 A:SF4501 2.2 22.5 1.0
S2 A:SF4501 2.3 21.1 1.0
SG A:CYS335 2.3 23.4 1.0
S1 A:SF4501 2.3 21.3 1.0
FE3 A:SF4501 2.7 23.6 1.0
FE1 A:SF4501 2.7 23.8 1.0
FE2 A:SF4501 2.7 22.8 1.0
CB A:CYS335 3.2 24.2 1.0
N A:CYS335 3.8 23.2 1.0
S4 A:SF4501 3.9 26.5 1.0
CA A:CYS335 4.1 26.6 1.0
CB A:ARG291 4.1 25.6 1.0
CE A:MET292 4.5 24.2 1.0
N A:MET292 4.5 19.4 1.0
CD A:ARG291 4.6 22.6 1.0
N A:LYS334 4.6 28.2 1.0
SG A:CYS329 4.7 22.7 1.0
CG A:ARG291 4.7 23.8 1.0
CB A:MET292 4.8 22.8 1.0
SG A:CYS332 4.8 26.9 1.0
C A:LYS334 4.9 29.4 1.0
SG A:CYS390 4.9 24.1 1.0
CA A:ARG291 5.0 23.2 1.0
C A:LYS333 5.0 30.0 1.0

Iron binding site 5 out of 16 in 4ur2

Go back to Iron Binding Sites List in 4ur2
Iron binding site 5 out of 16 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:24.6
occ:1.00
 FE1 A:SF4502 0.0 24.6 1.0
S2 A:SF4502 2.2 22.0 1.0
SG A:CYS383 2.3 24.5 1.0
S3 A:SF4502 2.3 22.6 1.0
S4 A:SF4502 2.3 21.6 1.0
FE3 A:SF4502 2.6 23.4 1.0
FE4 A:SF4502 2.7 24.0 1.0
FE2 A:SF4502 2.8 23.4 1.0
CB A:CYS383 3.2 20.3 1.0
S1 A:SF4502 3.8 21.9 1.0
N A:GLY384 4.0 22.2 1.0
CD A:PRO340 4.0 26.0 1.0
N A:VAL385 4.1 20.3 1.0
CA A:CYS383 4.5 25.8 1.0
CB A:VAL385 4.5 27.5 1.0
CD2 A:TYR375 4.6 22.4 1.0
C A:CYS383 4.7 25.7 1.0
SG A:CYS386 4.7 23.4 1.0
SG A:CYS339 4.7 24.0 1.0
SG A:CYS372 4.7 23.6 1.0
CG A:PRO340 4.8 28.1 1.0
N A:CYS386 4.8 21.2 1.0
CA A:GLY384 4.8 19.8 1.0
CA A:VAL385 4.8 20.8 1.0
C A:GLY384 4.9 26.3 1.0
CG2 A:VAL385 5.0 22.1 1.0

Iron binding site 6 out of 16 in 4ur2

Go back to Iron Binding Sites List in 4ur2
Iron binding site 6 out of 16 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:23.4
occ:1.00
 FE2 A:SF4502 0.0 23.4 1.0
S1 A:SF4502 2.3 21.9 1.0
S4 A:SF4502 2.3 21.6 1.0
SG A:CYS386 2.3 23.4 1.0
S3 A:SF4502 2.3 22.6 1.0
FE4 A:SF4502 2.7 24.0 1.0
FE3 A:SF4502 2.7 23.4 1.0
FE1 A:SF4502 2.8 24.6 1.0
CB A:CYS386 3.3 21.0 1.0
N A:CYS386 3.8 21.2 1.0
S2 A:SF4502 4.0 22.0 1.0
C41 A:BVQ503 4.1 23.8 1.0
N45 A:BVQ503 4.1 29.3 1.0
C42 A:BVQ503 4.1 34.8 1.0
CA A:CYS386 4.2 25.3 1.0
CD1 A:ILE344 4.4 23.4 1.0
C43 A:BVQ503 4.6 34.6 1.0
N A:VAL385 4.6 20.3 1.0
SG A:CYS383 4.7 24.5 1.0
SG A:CYS372 4.8 23.6 1.0
N A:GLY384 4.8 22.2 1.0
C8 A:BVQ503 4.9 23.5 1.0
SG A:CYS339 4.9 24.0 1.0
CA A:GLY384 4.9 19.8 1.0
C A:GLY384 4.9 26.3 1.0
C A:VAL385 5.0 23.3 1.0

Iron binding site 7 out of 16 in 4ur2

Go back to Iron Binding Sites List in 4ur2
Iron binding site 7 out of 16 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:23.4
occ:1.00
 FE3 A:SF4502 0.0 23.4 1.0
S4 A:SF4502 2.2 21.6 1.0
S1 A:SF4502 2.3 21.9 1.0
S2 A:SF4502 2.3 22.0 1.0
SG A:CYS372 2.3 23.6 1.0
FE1 A:SF4502 2.6 24.6 1.0
FE4 A:SF4502 2.7 24.0 1.0
FE2 A:SF4502 2.7 23.4 1.0
CB A:CYS372 3.4 23.7 1.0
S3 A:SF4502 3.9 22.6 1.0
CA A:CYS372 3.9 21.1 1.0
C42 A:BVQ503 4.1 34.8 1.0
NE1 A:TRP376 4.4 28.0 1.0
C A:CYS372 4.5 26.2 1.0
O A:CYS372 4.5 26.6 1.0
C41 A:BVQ503 4.5 23.8 1.0
SG A:CYS383 4.7 24.5 1.0
OG A:SER341 4.7 28.8 1.0
SG A:CYS339 4.7 24.0 1.0
CB A:CYS383 4.7 20.3 1.0
C8 A:BVQ503 4.7 23.5 1.0
SG A:CYS386 4.9 23.4 1.0

Iron binding site 8 out of 16 in 4ur2

Go back to Iron Binding Sites List in 4ur2
Iron binding site 8 out of 16 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:24.0
occ:1.00
 FE4 A:SF4502 0.0 24.0 1.0
S1 A:SF4502 2.3 21.9 1.0
S3 A:SF4502 2.3 22.6 1.0
SG A:CYS339 2.3 24.0 1.0
S2 A:SF4502 2.3 22.0 1.0
FE1 A:SF4502 2.7 24.6 1.0
FE3 A:SF4502 2.7 23.4 1.0
FE2 A:SF4502 2.7 23.4 1.0
CB A:CYS339 3.3 24.1 1.0
S4 A:SF4502 3.9 21.6 1.0
CA A:CYS339 3.9 24.6 1.0
OG A:SER341 3.9 28.8 1.0
CD A:PRO340 4.1 26.0 1.0
N A:PRO340 4.4 25.4 1.0
C A:CYS339 4.4 27.9 1.0
CB A:ALA343 4.5 22.6 1.0
CD1 A:ILE344 4.5 23.4 1.0
CG1 A:ILE344 4.7 22.2 1.0
N A:SER341 4.7 26.7 1.0
SG A:CYS372 4.8 23.6 1.0
SG A:CYS383 4.8 24.5 1.0
SG A:CYS386 4.8 23.4 1.0
N A:ALA343 5.0 29.0 1.0

Iron binding site 9 out of 16 in 4ur2

Go back to Iron Binding Sites List in 4ur2
Iron binding site 9 out of 16 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:32.0
occ:1.00
 FE1 B:SF4501 0.0 32.0 1.0
S3 B:SF4501 2.3 29.9 1.0
S4 B:SF4501 2.4 36.0 1.0
S2 B:SF4501 2.4 31.1 1.0
SG B:CYS390 2.4 30.1 1.0
FE3 B:SF4501 2.7 36.0 1.0
FE2 B:SF4501 2.7 37.7 1.0
FE4 B:SF4501 2.7 32.3 1.0
CB B:CYS390 3.2 31.1 1.0
CA B:CYS390 3.8 32.1 1.0
CD B:PRO391 3.9 38.9 1.0
S1 B:SF4501 4.0 38.9 1.0
CE B:MET292 4.1 35.5 1.0
CD1 B:ILE296 4.1 28.6 1.0
N B:PRO391 4.5 31.4 1.0
C B:CYS390 4.5 31.3 1.0
SG B:CYS329 4.6 33.0 1.0
CD2 B:PHE392 4.6 35.0 1.0
SG B:CYS335 4.8 35.4 1.0
SG B:CYS332 4.9 41.9 1.0
N B:CYS390 4.9 30.2 1.0

Iron binding site 10 out of 16 in 4ur2

Go back to Iron Binding Sites List in 4ur2
Iron binding site 10 out of 16 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:37.7
occ:1.00
 FE2 B:SF4501 0.0 37.7 1.0
S4 B:SF4501 2.3 36.0 1.0
S3 B:SF4501 2.3 29.9 1.0
S1 B:SF4501 2.3 38.9 1.0
SG B:CYS332 2.4 41.9 1.0
FE3 B:SF4501 2.7 36.0 1.0
FE1 B:SF4501 2.7 32.0 1.0
FE4 B:SF4501 2.7 32.3 1.0
CB B:CYS332 3.1 37.3 1.0
S2 B:SF4501 3.9 31.1 1.0
CD B:PRO391 4.0 38.9 1.0
N B:LYS333 4.1 43.5 1.0
N B:LYS334 4.2 47.6 1.0
CA B:CYS332 4.4 45.6 1.0
CB B:LYS334 4.5 52.1 1.0
C B:CYS332 4.5 49.4 1.0
CE1 B:PHE328 4.5 49.0 1.0
CD1 B:PHE328 4.6 52.7 1.0
N B:CYS335 4.7 36.2 1.0
CG B:PRO391 4.7 34.3 1.0
SG B:CYS329 4.7 33.0 1.0
SG B:CYS335 4.7 35.4 1.0
SG B:CYS390 4.8 30.1 1.0
CA B:LYS334 4.8 45.0 1.0
CA B:LYS333 4.9 42.5 1.0
CA B:CYS329 4.9 39.4 1.0
C B:LYS333 5.0 43.0 1.0

Reference:

M.Bommer, C.Kunze, J.Fesseler, T.Schubert, G.Diekert, H.Dobbek. Structural Basis For Organohalide Respiration. Science V. 346 455 2014.
ISSN: ISSN 0036-8075
PubMed: 25278505
DOI: 10.1126/SCIENCE.1258118
Page generated: Mon Aug 5 14:05:31 2024

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