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Chlorine in PDB 4ur0: Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Trichloroethene

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

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

Protein crystallography data

The structure of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Trichloroethene, PDB code: 4ur0 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) 45.548 / 1.80
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 73.956, 73.956, 185.421, 90.00, 90.00, 90.00
R / Rfree (%) 13.59 / 16.49

Other elements in 4ur0:

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

Cobalt (Co) 2 atoms
Iron (Fe) 16 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Trichloroethene (pdb code 4ur0). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Trichloroethene, PDB code: 4ur0:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4ur0

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Chlorine binding site 1 out of 6 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Trichloroethene


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Trichloroethene within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl505

b:45.7
occ:0.50
 CL1 B:TCV505 0.0 45.7 0.5
C2 B:TCV505 1.7 30.8 0.2
C2 B:TCV505 1.7 29.1 0.5
O B:HOH2131 2.5 23.9 1.0
C3 B:TCV505 2.5 32.7 0.2
C3 B:TCV505 2.6 37.6 0.5
CL4 B:TCV505 2.8 48.8 0.2
CL1 B:TCV505 3.0 29.7 0.2
O B:TYR102 3.1 26.7 1.0
CL5 B:TCV505 3.1 48.6 0.5
O B:HOH2132 3.2 23.7 1.0
CE2 B:PHE38 3.4 22.4 1.0
CZ B:PHE38 3.4 26.0 1.0
CB B:TYR102 3.4 21.6 1.0
CD2 B:PHE38 3.8 19.5 1.0
C B:TYR102 3.8 23.9 1.0
CE1 B:PHE38 4.0 22.9 1.0
CL5 B:TCV505 4.1 49.3 0.2
CL4 B:TCV505 4.2 53.0 0.5
CA B:TYR102 4.2 21.3 1.0
CG B:PHE38 4.3 21.2 1.0
O B:HOH2019 4.3 27.1 1.0
CD1 B:PHE38 4.4 22.8 1.0
CG B:TYR102 4.5 22.8 1.0
CZ2 B:TRP56 4.7 33.7 1.0
O1 B:GOL513 4.8 49.7 1.0
CH2 B:TRP56 4.9 31.4 1.0
N B:GLY103 4.9 20.9 1.0
ND2 B:ASN272 4.9 19.0 1.0
O B:HOH2278 4.9 21.4 0.5

Chlorine binding site 2 out of 6 in 4ur0

Go back to Chlorine Binding Sites List in 4ur0
Chlorine binding site 2 out of 6 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Trichloroethene


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Trichloroethene within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl505

b:29.7
occ:0.20
 CL1 B:TCV505 0.0 29.7 0.2
C2 B:TCV505 1.7 30.8 0.2
C2 B:TCV505 1.7 29.1 0.5
C3 B:TCV505 2.7 37.6 0.5
C3 B:TCV505 2.7 32.7 0.2
CL1 B:TCV505 3.0 45.7 0.5
CL4 B:TCV505 3.0 53.0 0.5
CL5 B:TCV505 3.2 49.3 0.2
CD1 B:TYR102 3.7 24.6 1.0
CG B:TYR102 3.8 22.8 1.0
CB B:TYR102 3.8 21.6 1.0
CH2 B:TRP56 3.9 31.4 1.0
CE1 B:TYR382 3.9 22.3 1.0
CZ3 B:TRP376 3.9 23.6 1.0
CD1 B:TYR382 3.9 23.3 1.0
CH2 B:TRP96 4.0 20.6 1.0
CZ2 B:TRP96 4.0 18.6 1.0
CL5 B:TCV505 4.2 48.6 0.5
CL4 B:TCV505 4.2 48.8 0.2
CE1 B:TYR102 4.4 26.8 1.0
CZ B:TYR382 4.5 22.0 1.0
CZ2 B:TRP56 4.6 33.7 1.0
CG B:TYR382 4.6 23.6 1.0
CD2 B:TYR102 4.6 22.1 1.0
O B:HOH2131 4.7 23.9 1.0
CE3 B:TRP376 4.7 18.7 1.0
CZ B:PHE38 4.7 26.0 1.0
CH2 B:TRP376 4.8 18.5 1.0
CZ3 B:TRP56 4.8 31.1 1.0
CA B:TYR102 4.8 21.3 1.0
CE1 B:PHE38 4.9 22.9 1.0

Chlorine binding site 3 out of 6 in 4ur0

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Chlorine binding site 3 out of 6 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Trichloroethene


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Trichloroethene within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl505

b:53.0
occ:0.50
 CL4 B:TCV505 0.0 53.0 0.5
CL5 B:TCV505 0.3 49.3 0.2
C3 B:TCV505 1.7 37.6 0.5
C3 B:TCV505 1.8 32.7 0.2
C2 B:TCV505 2.6 29.1 0.5
C2 B:TCV505 2.7 30.8 0.2
CL5 B:TCV505 2.8 48.6 0.5
CL1 B:TCV505 3.0 29.7 0.2
CL4 B:TCV505 3.1 48.8 0.2
O B:HOH2278 3.6 21.4 0.5
CG2 B:THR242 3.8 18.6 1.0
CG B:TYR382 3.9 23.6 1.0
CH2 B:TRP376 3.9 18.5 1.0
CZ3 B:TRP376 3.9 23.6 1.0
CB B:TYR382 4.0 20.2 1.0
CE2 B:TYR246 4.0 21.7 1.0
CH2 B:TRP96 4.0 20.6 1.0
CD2 B:TYR382 4.2 22.9 1.0
CL1 B:TCV505 4.2 45.7 0.5
CD1 B:TYR382 4.2 23.3 1.0
O39 B:BVQ503 4.3 22.7 1.0
CZ2 B:TRP96 4.3 18.6 1.0
OH B:TYR246 4.3 21.3 1.0
C38 B:BVQ503 4.4 24.2 1.0
CZ B:TYR246 4.5 19.1 1.0
NH2 B:ARG305 4.6 17.9 1.0
N40 B:BVQ503 4.8 20.7 1.0
C37 B:BVQ503 4.8 22.5 1.0
CE2 B:TYR382 4.8 20.9 1.0
CE1 B:TYR382 4.8 22.3 1.0
CD2 B:TYR246 4.9 18.2 1.0
CZ B:PHE38 5.0 26.0 1.0

Chlorine binding site 4 out of 6 in 4ur0

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Chlorine binding site 4 out of 6 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Trichloroethene


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Trichloroethene within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl505

b:48.8
occ:0.20
 CL4 B:TCV505 0.0 48.8 0.2
CL5 B:TCV505 0.3 48.6 0.5
C3 B:TCV505 1.7 32.7 0.2
C3 B:TCV505 1.7 37.6 0.5
O B:HOH2278 2.4 21.4 0.5
C2 B:TCV505 2.6 29.1 0.5
C2 B:TCV505 2.6 30.8 0.2
OH B:TYR246 2.7 21.3 1.0
CL5 B:TCV505 2.8 49.3 0.2
CL1 B:TCV505 2.8 45.7 0.5
CL4 B:TCV505 3.1 53.0 0.5
ND2 B:ASN272 3.4 19.0 1.0
CZ B:TYR246 3.5 19.1 1.0
CE2 B:PHE38 3.7 22.4 1.0
O B:HOH2132 3.8 23.7 1.0
CZ B:PHE38 3.8 26.0 1.0
CE2 B:TYR246 4.0 21.7 1.0
CL1 B:TCV505 4.2 29.7 0.2
CE1 B:TYR246 4.4 18.3 1.0
NH2 B:ARG305 4.5 17.9 1.0
CG B:ASN272 4.7 20.4 1.0
N24 B:BVQ503 4.7 20.8 1.0
CO B:BVQ503 4.8 19.9 1.0
CD2 B:PHE38 4.8 19.5 1.0
O B:TYR102 4.8 26.7 1.0
C19 B:BVQ503 5.0 19.7 1.0

Chlorine binding site 5 out of 6 in 4ur0

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Chlorine binding site 5 out of 6 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Trichloroethene


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Trichloroethene within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl505

b:48.6
occ:0.50
 CL5 B:TCV505 0.0 48.6 0.5
CL4 B:TCV505 0.3 48.8 0.2
C3 B:TCV505 1.6 32.7 0.2
C3 B:TCV505 1.7 37.6 0.5
O B:HOH2278 2.2 21.4 0.5
CL5 B:TCV505 2.6 49.3 0.2
OH B:TYR246 2.6 21.3 1.0
C2 B:TCV505 2.6 29.1 0.5
C2 B:TCV505 2.7 30.8 0.2
CL4 B:TCV505 2.8 53.0 0.5
CL1 B:TCV505 3.1 45.7 0.5
CZ B:TYR246 3.4 19.1 1.0
ND2 B:ASN272 3.6 19.0 1.0
CE2 B:PHE38 3.8 22.4 1.0
CE2 B:TYR246 3.9 21.7 1.0
CZ B:PHE38 3.9 26.0 1.0
O B:HOH2132 4.1 23.7 1.0
NH2 B:ARG305 4.2 17.9 1.0
CL1 B:TCV505 4.2 29.7 0.2
CE1 B:TYR246 4.4 18.3 1.0
CO B:BVQ503 4.7 19.9 1.0
N24 B:BVQ503 4.7 20.8 1.0
CH2 B:TRP376 4.8 18.5 1.0
CG B:ASN272 4.9 20.4 1.0
C19 B:BVQ503 5.0 19.7 1.0
CD2 B:PHE38 5.0 19.5 1.0

Chlorine binding site 6 out of 6 in 4ur0

Go back to Chlorine Binding Sites List in 4ur0
Chlorine binding site 6 out of 6 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Trichloroethene


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Trichloroethene within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl505

b:49.3
occ:0.20
 CL5 B:TCV505 0.0 49.3 0.2
CL4 B:TCV505 0.3 53.0 0.5
C3 B:TCV505 1.5 37.6 0.5
C3 B:TCV505 1.7 32.7 0.2
C2 B:TCV505 2.6 29.1 0.5
CL5 B:TCV505 2.6 48.6 0.5
C2 B:TCV505 2.6 30.8 0.2
CL4 B:TCV505 2.8 48.8 0.2
CL1 B:TCV505 3.2 29.7 0.2
O B:HOH2278 3.4 21.4 0.5
CE2 B:TYR246 3.9 21.7 1.0
CG2 B:THR242 3.9 18.6 1.0
CH2 B:TRP376 3.9 18.5 1.0
CZ3 B:TRP376 4.0 23.6 1.0
OH B:TYR246 4.1 21.3 1.0
CG B:TYR382 4.1 23.6 1.0
CL1 B:TCV505 4.1 45.7 0.5
CH2 B:TRP96 4.1 20.6 1.0
CB B:TYR382 4.2 20.2 1.0
O39 B:BVQ503 4.2 22.7 1.0
CZ B:TYR246 4.3 19.1 1.0
C38 B:BVQ503 4.4 24.2 1.0
NH2 B:ARG305 4.4 17.9 1.0
CD2 B:TYR382 4.4 22.9 1.0
CZ2 B:TRP96 4.4 18.6 1.0
CD1 B:TYR382 4.5 23.3 1.0
C37 B:BVQ503 4.7 22.5 1.0
N40 B:BVQ503 4.8 20.7 1.0
CD2 B:TYR246 4.8 18.2 1.0
CZ B:PHE38 4.9 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: Fri Jul 26 02:25:19 2024

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