Bromine in PDB 4ur1: Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Dibromoethene
Enzymatic activity of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Dibromoethene
All present enzymatic activity of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Dibromoethene:
1.97.1.8;
Protein crystallography data
The structure of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Dibromoethene, PDB code: 4ur1
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)
|
47.335 /
1.65
|
Space group
|
P 41
|
Cell size a, b, c (Å), α, β, γ (°)
|
73.703,
73.703,
185.264,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
13.42 /
15.73
|
Other elements in 4ur1:
The structure of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Dibromoethene also contains other interesting chemical elements:
Bromine Binding Sites:
The binding sites of Bromine atom in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Dibromoethene
(pdb code 4ur1). This binding sites where shown within
5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the
Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Dibromoethene, PDB code: 4ur1:
Jump to Bromine binding site number:
1;
2;
3;
4;
Bromine binding site 1 out
of 4 in 4ur1
Go back to
Bromine Binding Sites List in 4ur1
Bromine binding site 1 out
of 4 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Dibromoethene
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 1 of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Dibromoethene within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Br505
b:39.3
occ:0.38
|
BR1
|
A:CB0505
|
0.0
|
39.3
|
0.4
|
C02
|
A:CB0505
|
1.9
|
35.9
|
0.4
|
C03
|
A:CB0505
|
3.0
|
30.6
|
0.4
|
O
|
A:HOH2325
|
3.3
|
24.4
|
1.0
|
CH2
|
A:TRP376
|
3.7
|
20.8
|
1.0
|
BR4
|
A:CB0505
|
3.7
|
36.5
|
0.4
|
O39
|
A:BVQ503
|
3.7
|
22.8
|
1.0
|
CG2
|
A:THR242
|
3.8
|
19.6
|
1.0
|
C38
|
A:BVQ503
|
3.9
|
21.3
|
1.0
|
CE2
|
A:TYR246
|
3.9
|
20.2
|
1.0
|
CZ3
|
A:TRP376
|
3.9
|
22.4
|
1.0
|
CB
|
A:TYR382
|
4.0
|
17.8
|
1.0
|
OH
|
A:TYR246
|
4.0
|
21.5
|
1.0
|
NH2
|
A:ARG305
|
4.1
|
18.1
|
1.0
|
CG
|
A:TYR382
|
4.2
|
21.0
|
1.0
|
C37
|
A:BVQ503
|
4.2
|
18.6
|
1.0
|
CZ
|
A:TYR246
|
4.4
|
19.8
|
1.0
|
N40
|
A:BVQ503
|
4.4
|
20.4
|
1.0
|
CH2
|
A:TRP96
|
4.5
|
17.9
|
1.0
|
CD2
|
A:TYR382
|
4.6
|
21.6
|
1.0
|
CD1
|
A:TYR382
|
4.6
|
23.4
|
1.0
|
CZ2
|
A:TRP96
|
4.8
|
17.7
|
1.0
|
CZ2
|
A:TRP376
|
4.8
|
20.1
|
1.0
|
CZ
|
A:ARG305
|
4.8
|
20.2
|
1.0
|
CZ
|
A:PHE38
|
4.9
|
26.6
|
1.0
|
CD2
|
A:TYR246
|
5.0
|
17.2
|
1.0
|
|
Bromine binding site 2 out
of 4 in 4ur1
Go back to
Bromine Binding Sites List in 4ur1
Bromine binding site 2 out
of 4 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Dibromoethene
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 2 of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Dibromoethene within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Br505
b:36.5
occ:0.38
|
BR4
|
A:CB0505
|
0.0
|
36.5
|
0.4
|
C03
|
A:CB0505
|
1.9
|
30.6
|
0.4
|
C02
|
A:CB0505
|
3.0
|
35.9
|
0.4
|
CH2
|
A:TRP56
|
3.5
|
29.1
|
1.0
|
CD1
|
A:TYR102
|
3.6
|
25.4
|
1.0
|
CG
|
A:TYR102
|
3.7
|
21.0
|
1.0
|
CB
|
A:TYR102
|
3.7
|
19.6
|
1.0
|
BR1
|
A:CB0505
|
3.7
|
39.3
|
0.4
|
CE1
|
A:TYR382
|
3.8
|
25.2
|
1.0
|
CD1
|
A:TYR382
|
3.8
|
23.4
|
1.0
|
CZ2
|
A:TRP96
|
3.9
|
17.7
|
1.0
|
CH2
|
A:TRP96
|
3.9
|
17.9
|
1.0
|
CZ3
|
A:TRP376
|
3.9
|
22.4
|
1.0
|
CZ2
|
A:TRP56
|
4.1
|
27.3
|
1.0
|
CE1
|
A:TYR102
|
4.4
|
25.4
|
1.0
|
CZ
|
A:TYR382
|
4.4
|
21.1
|
1.0
|
CG
|
A:TYR382
|
4.5
|
21.0
|
1.0
|
CD2
|
A:TYR102
|
4.5
|
20.4
|
1.0
|
CZ3
|
A:TRP56
|
4.6
|
28.1
|
1.0
|
O
|
A:HOH2167
|
4.7
|
25.0
|
1.0
|
CE3
|
A:TRP376
|
4.7
|
23.9
|
1.0
|
CA
|
A:TYR102
|
4.8
|
19.6
|
1.0
|
CZ
|
A:PHE38
|
4.8
|
26.6
|
1.0
|
CH2
|
A:TRP376
|
4.9
|
20.8
|
1.0
|
CE1
|
A:PHE38
|
4.9
|
22.2
|
1.0
|
CE2
|
A:TRP96
|
4.9
|
19.6
|
1.0
|
CE2
|
A:TYR382
|
5.0
|
20.7
|
1.0
|
|
Bromine binding site 3 out
of 4 in 4ur1
Go back to
Bromine Binding Sites List in 4ur1
Bromine binding site 3 out
of 4 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Dibromoethene
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 3 of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Dibromoethene within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Br505
b:42.9
occ:0.38
|
BR1
|
B:CB0505
|
0.0
|
42.9
|
0.4
|
C02
|
B:CB0505
|
1.9
|
35.9
|
0.4
|
C03
|
B:CB0505
|
2.9
|
33.5
|
0.4
|
O
|
B:HOH2280
|
3.3
|
26.9
|
1.0
|
BR4
|
B:CB0505
|
3.6
|
36.9
|
0.4
|
CH2
|
B:TRP376
|
3.8
|
24.0
|
1.0
|
CG2
|
B:THR242
|
3.8
|
21.6
|
1.0
|
O39
|
B:BVQ503
|
3.8
|
23.9
|
1.0
|
C38
|
B:BVQ503
|
3.9
|
24.1
|
1.0
|
CE2
|
B:TYR246
|
3.9
|
20.6
|
1.0
|
CZ3
|
B:TRP376
|
3.9
|
24.7
|
1.0
|
CB
|
B:TYR382
|
4.0
|
21.5
|
1.0
|
OH
|
B:TYR246
|
4.1
|
22.8
|
1.0
|
CG
|
B:TYR382
|
4.1
|
24.2
|
1.0
|
NH2
|
B:ARG305
|
4.2
|
20.2
|
1.0
|
C37
|
B:BVQ503
|
4.2
|
21.7
|
1.0
|
N40
|
B:BVQ503
|
4.4
|
20.8
|
1.0
|
CD2
|
B:TYR382
|
4.4
|
25.2
|
1.0
|
CZ
|
B:TYR246
|
4.4
|
20.6
|
1.0
|
CH2
|
B:TRP96
|
4.5
|
19.2
|
1.0
|
CD1
|
B:TYR382
|
4.6
|
25.8
|
1.0
|
CZ2
|
B:TRP96
|
4.7
|
20.4
|
1.0
|
CZ
|
B:PHE38
|
4.8
|
28.6
|
1.0
|
CZ2
|
B:TRP376
|
4.9
|
23.2
|
1.0
|
CZ
|
B:ARG305
|
4.9
|
20.4
|
1.0
|
CD2
|
B:TYR246
|
4.9
|
19.9
|
1.0
|
|
Bromine binding site 4 out
of 4 in 4ur1
Go back to
Bromine Binding Sites List in 4ur1
Bromine binding site 4 out
of 4 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Dibromoethene
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 4 of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Dibromoethene within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Br505
b:36.9
occ:0.38
|
BR4
|
B:CB0505
|
0.0
|
36.9
|
0.4
|
C03
|
B:CB0505
|
1.9
|
33.5
|
0.4
|
C02
|
B:CB0505
|
2.9
|
35.9
|
0.4
|
BR1
|
B:CB0505
|
3.6
|
42.9
|
0.4
|
CD1
|
B:TYR102
|
3.7
|
24.8
|
1.0
|
CH2
|
B:TRP56
|
3.7
|
37.2
|
1.0
|
CG
|
B:TYR102
|
3.7
|
25.4
|
1.0
|
CB
|
B:TYR102
|
3.8
|
22.9
|
1.0
|
CE1
|
B:TYR382
|
3.8
|
26.8
|
1.0
|
CD1
|
B:TYR382
|
3.8
|
25.8
|
1.0
|
CZ2
|
B:TRP96
|
3.9
|
20.4
|
1.0
|
CZ3
|
B:TRP376
|
4.0
|
24.7
|
1.0
|
CH2
|
B:TRP96
|
4.0
|
19.2
|
1.0
|
CZ2
|
B:TRP56
|
4.3
|
34.8
|
1.0
|
CE1
|
B:TYR102
|
4.4
|
23.9
|
1.0
|
CZ
|
B:TYR382
|
4.4
|
25.3
|
1.0
|
CG
|
B:TYR382
|
4.5
|
24.2
|
1.0
|
CD2
|
B:TYR102
|
4.5
|
22.8
|
1.0
|
CE3
|
B:TRP376
|
4.7
|
26.6
|
1.0
|
O
|
B:HOH2134
|
4.7
|
29.5
|
1.0
|
CZ3
|
B:TRP56
|
4.7
|
36.0
|
1.0
|
CZ
|
B:PHE38
|
4.8
|
28.6
|
1.0
|
CA
|
B:TYR102
|
4.8
|
21.4
|
1.0
|
CE1
|
B:PHE38
|
4.9
|
26.3
|
1.0
|
CH2
|
B:TRP376
|
4.9
|
24.0
|
1.0
|
CE2
|
B:TRP96
|
5.0
|
20.6
|
1.0
|
CE2
|
B:TYR382
|
5.0
|
23.4
|
1.0
|
OH
|
B:TYR382
|
5.0
|
26.1
|
1.0
|
CD2
|
B:TYR382
|
5.0
|
25.2
|
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: Wed Jul 10 22:48:33 2024
|