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Iron in PDB 4ur3: Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form

Enzymatic activity of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form

All present enzymatic activity of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form:
1.97.1.8;

Protein crystallography data

The structure of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form, PDB code: 4ur3 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) 48.763 / 2.24
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.315, 110.601, 178.792, 90.00, 95.91, 90.00
R / Rfree (%) 17.93 / 21.77

Other elements in 4ur3:

The structure of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form also contains other interesting chemical elements:

Cobalt (Co) 6 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 48;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form (pdb code 4ur3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 48 binding sites of Iron where determined in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form, PDB code: 4ur3:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 48 in 4ur3

Go back to Iron Binding Sites List in 4ur3
Iron binding site 1 out of 48 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form


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 P2(1) Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:33.7
occ:1.00
FE1 A:SF4501 0.0 33.7 1.0
S2 A:SF4501 2.2 28.2 1.0
S4 A:SF4501 2.3 34.4 1.0
SG A:CYS329 2.3 30.1 1.0
S3 A:SF4501 2.3 30.5 1.0
FE3 A:SF4501 2.7 34.3 1.0
FE4 A:SF4501 2.7 32.3 1.0
FE2 A:SF4501 2.7 38.9 1.0
CB A:CYS329 3.3 36.5 1.0
CA A:CYS329 3.6 39.7 1.0
S1 A:SF4501 3.9 32.0 1.0
CB A:ARG291 4.2 32.6 1.0
N A:ARG291 4.3 28.4 1.0
N A:CYS329 4.4 34.5 1.0
CB A:SER290 4.5 34.8 1.0
CD1 A:ILE296 4.7 33.2 1.0
SG A:CYS390 4.8 30.2 1.0
SG A:CYS335 4.8 29.8 1.0
SG A:CYS332 4.8 35.6 1.0
C A:CYS329 4.9 42.0 1.0
CA A:ARG291 4.9 29.4 1.0
O A:CYS332 5.0 51.2 1.0

Iron binding site 2 out of 48 in 4ur3

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Iron binding site 2 out of 48 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form


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 P2(1) Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:38.9
occ:1.00
FE2 A:SF4501 0.0 38.9 1.0
S1 A:SF4501 2.2 32.0 1.0
S3 A:SF4501 2.3 30.5 1.0
S4 A:SF4501 2.3 34.4 1.0
SG A:CYS332 2.4 35.6 1.0
FE4 A:SF4501 2.7 32.3 1.0
FE3 A:SF4501 2.7 34.3 1.0
FE1 A:SF4501 2.7 33.7 1.0
CB A:CYS332 3.4 41.6 1.0
S2 A:SF4501 3.9 28.2 1.0
C A:CYS332 4.2 44.3 1.0
O A:CYS332 4.2 51.2 1.0
N A:LYS334 4.2 39.2 1.0
CD A:PRO391 4.3 37.1 1.0
CA A:CYS332 4.4 37.9 1.0
CB A:LYS334 4.4 41.6 1.0
N A:LYS333 4.6 44.8 1.0
SG A:CYS335 4.7 29.8 1.0
SG A:CYS390 4.7 30.2 1.0
N A:CYS335 4.8 36.1 1.0
SG A:CYS329 4.8 30.1 1.0
CA A:CYS329 4.9 39.7 1.0
CA A:LYS334 4.9 42.3 1.0

Iron binding site 3 out of 48 in 4ur3

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Iron binding site 3 out of 48 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form


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 P2(1) Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:34.3
occ:1.00
FE3 A:SF4501 0.0 34.3 1.0
S2 A:SF4501 2.2 28.2 1.0
S4 A:SF4501 2.3 34.4 1.0
SG A:CYS335 2.3 29.8 1.0
S1 A:SF4501 2.3 32.0 1.0
FE1 A:SF4501 2.7 33.7 1.0
FE4 A:SF4501 2.7 32.3 1.0
FE2 A:SF4501 2.7 38.9 1.0
CB A:CYS335 3.4 32.6 1.0
S3 A:SF4501 3.9 30.5 1.0
N A:CYS335 3.9 36.1 1.0
CB A:ARG291 4.2 32.6 1.0
CA A:CYS335 4.3 34.7 1.0
N A:MET292 4.6 29.4 1.0
CE A:MET292 4.6 28.4 1.0
CD A:ARG291 4.7 38.6 1.0
CG A:ARG291 4.7 30.8 1.0
SG A:CYS332 4.8 35.6 1.0
SG A:CYS329 4.8 30.1 1.0
N A:LYS334 4.8 39.2 1.0
SG A:CYS390 4.8 30.2 1.0
CB A:MET292 4.9 25.7 1.0

Iron binding site 4 out of 48 in 4ur3

Go back to Iron Binding Sites List in 4ur3
Iron binding site 4 out of 48 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form


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 P2(1) Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:32.3
occ:1.00
FE4 A:SF4501 0.0 32.3 1.0
S1 A:SF4501 2.3 32.0 1.0
S2 A:SF4501 2.3 28.2 1.0
S3 A:SF4501 2.3 30.5 1.0
SG A:CYS390 2.3 30.2 1.0
FE1 A:SF4501 2.7 33.7 1.0
FE3 A:SF4501 2.7 34.3 1.0
FE2 A:SF4501 2.7 38.9 1.0
CB A:CYS390 3.3 27.8 1.0
S4 A:SF4501 3.9 34.4 1.0
CA A:CYS390 3.9 29.8 1.0
CD1 A:ILE296 4.2 33.2 1.0
CD A:PRO391 4.2 37.1 1.0
CE A:MET292 4.2 28.4 1.0
CD2 A:PHE392 4.5 30.2 1.0
SG A:CYS329 4.7 30.1 1.0
C A:CYS390 4.7 38.1 1.0
N A:PRO391 4.7 36.6 1.0
SG A:CYS335 4.7 29.8 1.0
SG A:CYS332 4.9 35.6 1.0

Iron binding site 5 out of 48 in 4ur3

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Iron binding site 5 out of 48 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form


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 P2(1) Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:33.2
occ:1.00
FE1 A:SF4502 0.0 33.2 1.0
S2 A:SF4502 2.2 29.3 1.0
S4 A:SF4502 2.3 33.4 1.0
S3 A:SF4502 2.3 36.2 1.0
SG A:CYS339 2.3 31.1 1.0
FE3 A:SF4502 2.7 32.1 1.0
FE4 A:SF4502 2.7 35.3 1.0
FE2 A:SF4502 2.7 32.8 1.0
CB A:CYS339 3.2 25.2 1.0
S1 A:SF4502 3.8 29.5 1.0
CA A:CYS339 3.9 33.4 1.0
OG A:SER341 4.0 29.0 1.0
CD A:PRO340 4.2 37.3 1.0
C A:CYS339 4.5 33.7 1.0
N A:PRO340 4.5 37.6 1.0
CD1 A:ILE344 4.5 28.9 1.0
CB A:ALA343 4.5 32.2 1.0
CG1 A:ILE344 4.7 30.6 1.0
SG A:CYS386 4.7 32.7 1.0
N A:SER341 4.8 37.5 1.0
SG A:CYS372 4.8 32.1 1.0
SG A:CYS383 4.9 33.4 1.0

Iron binding site 6 out of 48 in 4ur3

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Iron binding site 6 out of 48 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form


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 P2(1) Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:32.8
occ:1.00
FE2 A:SF4502 0.0 32.8 1.0
S1 A:SF4502 2.2 29.5 1.0
S3 A:SF4502 2.3 36.2 1.0
S4 A:SF4502 2.3 33.4 1.0
SG A:CYS372 2.3 32.1 1.0
FE4 A:SF4502 2.7 35.3 1.0
FE3 A:SF4502 2.7 32.1 1.0
FE1 A:SF4502 2.7 33.2 1.0
CB A:CYS372 3.3 34.8 1.0
CA A:CYS372 3.8 33.2 1.0
S2 A:SF4502 3.8 29.3 1.0
C42 A:BVQ503 4.4 33.3 1.0
NE1 A:TRP376 4.4 31.2 1.0
O A:CYS372 4.4 35.7 1.0
C A:CYS372 4.4 36.7 1.0
SG A:CYS383 4.6 33.4 1.0
OG A:SER341 4.7 29.0 1.0
C41 A:BVQ503 4.7 27.9 1.0
SG A:CYS339 4.7 31.1 1.0
CB A:CYS383 4.8 33.4 1.0
C8 A:BVQ503 4.9 37.2 1.0
SG A:CYS386 4.9 32.7 1.0
CB A:ALA343 4.9 32.2 1.0

Iron binding site 7 out of 48 in 4ur3

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Iron binding site 7 out of 48 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form


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 P2(1) Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:32.1
occ:1.00
FE3 A:SF4502 0.0 32.1 1.0
S2 A:SF4502 2.2 29.3 1.0
S1 A:SF4502 2.2 29.5 1.0
S4 A:SF4502 2.3 33.4 1.0
SG A:CYS386 2.3 32.7 1.0
FE1 A:SF4502 2.7 33.2 1.0
FE4 A:SF4502 2.7 35.3 1.0
FE2 A:SF4502 2.7 32.8 1.0
CB A:CYS386 3.4 27.2 1.0
S3 A:SF4502 3.8 36.2 1.0
N A:CYS386 3.9 23.4 1.0
N45 A:BVQ503 4.0 35.0 1.0
C41 A:BVQ503 4.1 27.9 1.0
C42 A:BVQ503 4.2 33.3 1.0
CA A:CYS386 4.3 24.7 1.0
CD1 A:ILE344 4.4 28.9 1.0
N A:VAL385 4.7 28.7 1.0
SG A:CYS383 4.7 33.4 1.0
C43 A:BVQ503 4.7 38.8 1.0
SG A:CYS372 4.7 32.1 1.0
SG A:CYS339 4.8 31.1 1.0
C8 A:BVQ503 4.9 37.2 1.0
N A:GLY384 4.9 27.6 1.0
CA A:GLY384 5.0 28.1 1.0

Iron binding site 8 out of 48 in 4ur3

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Iron binding site 8 out of 48 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form


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 P2(1) Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:35.3
occ:1.00
FE4 A:SF4502 0.0 35.3 1.0
S1 A:SF4502 2.2 29.5 1.0
S2 A:SF4502 2.3 29.3 1.0
SG A:CYS383 2.3 33.4 1.0
S3 A:SF4502 2.3 36.2 1.0
FE1 A:SF4502 2.7 33.2 1.0
FE3 A:SF4502 2.7 32.1 1.0
FE2 A:SF4502 2.7 32.8 1.0
CB A:CYS383 3.3 33.4 1.0
S4 A:SF4502 3.8 33.4 1.0
N A:GLY384 4.0 27.6 1.0
N A:VAL385 4.1 28.7 1.0
CD A:PRO340 4.1 37.3 1.0
CB A:VAL385 4.5 35.6 1.0
SG A:CYS386 4.6 32.7 1.0
CA A:CYS383 4.6 31.8 1.0
CD2 A:TYR375 4.7 34.1 1.0
SG A:CYS339 4.7 31.1 1.0
N A:CYS386 4.7 23.4 1.0
SG A:CYS372 4.8 32.1 1.0
CA A:GLY384 4.8 28.1 1.0
C A:CYS383 4.8 29.7 1.0
CA A:VAL385 4.8 28.9 1.0
CG2 A:VAL385 4.9 25.1 1.0
C A:GLY384 4.9 28.0 1.0
CG A:PRO340 4.9 33.8 1.0

Iron binding site 9 out of 48 in 4ur3

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Iron binding site 9 out of 48 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form


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 P2(1) Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:24.2
occ:1.00
FE1 B:SF4501 0.0 24.2 1.0
S4 B:SF4501 2.3 20.1 1.0
S3 B:SF4501 2.3 25.8 1.0
S2 B:SF4501 2.3 22.3 1.0
SG B:CYS329 2.3 23.3 1.0
FE3 B:SF4501 2.7 23.3 1.0
FE4 B:SF4501 2.7 24.2 1.0
FE2 B:SF4501 2.7 28.3 1.0
CB B:CYS329 3.4 20.9 1.0
CA B:CYS329 3.7 26.0 1.0
S1 B:SF4501 3.8 24.1 1.0
CB B:ARG291 4.2 21.0 1.0
N B:ARG291 4.3 16.6 1.0
N B:CYS329 4.5 27.6 1.0
CB B:SER290 4.6 21.3 1.0
CD1 B:ILE296 4.7 20.0 1.0
SG B:CYS390 4.7 22.6 1.0
SG B:CYS332 4.8 29.2 1.0
SG B:CYS335 4.8 23.4 1.0
C B:CYS329 4.9 28.9 1.0
CB B:CYS332 4.9 24.6 1.0
CA B:ARG291 4.9 21.1 1.0
O B:CYS329 4.9 26.3 1.0

Iron binding site 10 out of 48 in 4ur3

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Iron binding site 10 out of 48 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form


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 P2(1) Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:28.3
occ:1.00
FE2 B:SF4501 0.0 28.3 1.0
S1 B:SF4501 2.2 24.1 1.0
S3 B:SF4501 2.3 25.8 1.0
SG B:CYS332 2.3 29.2 1.0
S4 B:SF4501 2.3 20.1 1.0
FE4 B:SF4501 2.7 24.2 1.0
FE3 B:SF4501 2.7 23.3 1.0
FE1 B:SF4501 2.7 24.2 1.0
CB B:CYS332 3.2 24.6 1.0
S2 B:SF4501 3.9 22.3 1.0
CD B:PRO391 4.0 24.5 1.0
C B:CYS332 4.2 30.3 1.0
N B:LYS334 4.3 28.9 1.0
O B:CYS332 4.3 35.8 1.0
CA B:CYS332 4.3 29.4 1.0
CB B:LYS334 4.5 33.1 1.0
CG B:PRO391 4.6 32.1 1.0
SG B:CYS390 4.6 22.6 1.0
N B:LYS333 4.7 26.9 1.0
CE1 B:PHE328 4.7 37.0 1.0
N B:CYS335 4.7 24.3 1.0
SG B:CYS335 4.7 23.4 1.0
CD1 B:PHE328 4.8 30.6 1.0
SG B:CYS329 4.9 23.3 1.0
CA B:LYS334 4.9 28.5 1.0
CA B:CYS329 5.0 26.0 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: Sun Dec 13 15:50:03 2020

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