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Bromine in PDB 3wj8: Crystal Structure of Dl-2-Haloacid Dehalogenase Mutant with 2-Bromo-2- Methylpropionate

Enzymatic activity of Crystal Structure of Dl-2-Haloacid Dehalogenase Mutant with 2-Bromo-2- Methylpropionate

All present enzymatic activity of Crystal Structure of Dl-2-Haloacid Dehalogenase Mutant with 2-Bromo-2- Methylpropionate:
3.8.1.10;

Protein crystallography data

The structure of Crystal Structure of Dl-2-Haloacid Dehalogenase Mutant with 2-Bromo-2- Methylpropionate, PDB code: 3wj8 was solved by A.Siwek, R.Omi, K.Hirotsu, K.Jitsumori, N.Esaki, T.Kurihara, P.Paneth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.70
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 186.309, 186.309, 114.315, 90.00, 90.00, 120.00
R / Rfree (%) 18.7 / 26.9

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of Dl-2-Haloacid Dehalogenase Mutant with 2-Bromo-2- Methylpropionate (pdb code 3wj8). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 6 binding sites of Bromine where determined in the Crystal Structure of Dl-2-Haloacid Dehalogenase Mutant with 2-Bromo-2- Methylpropionate, PDB code: 3wj8:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6;

Bromine binding site 1 out of 6 in 3wj8

Go back to Bromine Binding Sites List in 3wj8
Bromine binding site 1 out of 6 in the Crystal Structure of Dl-2-Haloacid Dehalogenase Mutant with 2-Bromo-2- Methylpropionate


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 Dl-2-Haloacid Dehalogenase Mutant with 2-Bromo-2- Methylpropionate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br401

b:7.0
occ:1.00
 BR A:B2P401 0.0 7.0 1.0
CA A:B2P401 1.5 7.9 1.0
CM A:B2P401 2.2 8.0 1.0
CB A:B2P401 2.6 8.2 1.0
N A:GLY41 2.6 11.6 1.0
C A:B2P401 2.8 8.9 1.0
N A:PHE40 3.2 11.9 1.0
OXT A:B2P401 3.3 9.6 1.0
CB A:PHE40 3.4 13.5 1.0
C A:PHE40 3.5 12.3 1.0
CA A:PHE40 3.5 12.6 1.0
CA A:GLY41 3.6 11.3 1.0
CD1 A:TYR270 3.7 8.5 1.0
CE1 A:TYR270 3.7 8.7 1.0
O A:B2P401 3.8 9.3 1.0
C A:ALA39 3.8 11.6 1.0
CB A:ALA39 3.8 10.5 1.0
CG1 A:ILE274 4.2 7.0 1.0
CA A:ALA39 4.2 11.3 1.0
CD1 A:ILE274 4.2 6.9 1.0
CD2 A:PHE273 4.4 7.6 1.0
CG A:PHE40 4.5 14.6 1.0
CE2 A:PHE273 4.6 7.7 1.0
O A:ALA39 4.6 11.4 1.0
O A:PHE40 4.7 12.7 1.0
C A:GLY41 4.8 11.6 1.0
CG A:TYR270 4.8 8.6 1.0
CD2 A:PHE40 4.8 14.7 1.0
CZ A:TYR270 4.8 8.9 1.0
N A:ILE42 4.9 11.5 1.0

Bromine binding site 2 out of 6 in 3wj8

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Bromine binding site 2 out of 6 in the Crystal Structure of Dl-2-Haloacid Dehalogenase Mutant with 2-Bromo-2- Methylpropionate


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 Dl-2-Haloacid Dehalogenase Mutant with 2-Bromo-2- Methylpropionate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br401

b:6.7
occ:1.00
 BR B:B2P401 0.0 6.7 1.0
CA B:B2P401 1.6 7.8 1.0
CM B:B2P401 2.5 7.9 1.0
CB B:B2P401 2.6 7.7 1.0
C B:B2P401 2.7 8.2 1.0
N B:GLY41 3.2 13.8 1.0
OXT B:B2P401 3.4 8.4 1.0
CB B:PHE40 3.5 13.3 1.0
CG1 B:ILE274 3.6 7.9 1.0
N B:PHE40 3.7 12.5 1.0
O B:B2P401 3.7 8.4 1.0
CD1 B:TYR270 3.8 9.1 1.0
CA B:PHE40 3.9 13.1 1.0
CB B:ALA39 3.9 11.2 1.0
CE1 B:TYR270 4.0 9.2 1.0
CD1 B:ILE274 4.0 8.0 1.0
CA B:GLY41 4.0 13.6 1.0
C B:PHE40 4.1 13.3 1.0
CD2 B:PHE273 4.2 7.4 1.0
CE2 B:PHE273 4.3 7.2 1.0
C B:ALA39 4.3 12.2 1.0
CA B:ALA39 4.5 11.7 1.0
CG B:PHE40 4.6 13.7 1.0
CD2 B:PHE40 4.8 13.8 1.0
CG B:TYR270 4.8 9.1 1.0

Bromine binding site 3 out of 6 in 3wj8

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Bromine binding site 3 out of 6 in the Crystal Structure of Dl-2-Haloacid Dehalogenase Mutant with 2-Bromo-2- Methylpropionate


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 Dl-2-Haloacid Dehalogenase Mutant with 2-Bromo-2- Methylpropionate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br401

b:8.4
occ:1.00
 BR D:B2P401 0.0 8.4 1.0
CA D:B2P401 1.6 9.7 1.0
CB D:B2P401 2.4 10.0 1.0
CM D:B2P401 2.6 10.0 1.0
C D:B2P401 2.7 10.6 1.0
N D:GLY41 3.0 16.5 1.0
CB D:PHE40 3.2 17.7 1.0
O D:B2P401 3.4 11.1 1.0
CE1 D:TYR270 3.5 12.8 1.0
N D:PHE40 3.6 16.4 1.0
OXT D:B2P401 3.6 10.6 1.0
CD1 D:TYR270 3.6 12.7 1.0
CA D:PHE40 3.7 17.0 1.0
CD2 D:PHE273 3.7 10.7 1.0
C D:PHE40 3.8 16.7 1.0
CE2 D:PHE273 3.8 10.8 1.0
CA D:GLY41 3.9 16.3 1.0
CG D:PHE40 4.1 18.0 1.0
CG1 D:ILE274 4.1 9.2 1.0
CD2 D:PHE40 4.2 18.1 1.0
C D:ALA39 4.3 15.8 1.0
CD1 D:ILE274 4.3 9.2 1.0
CB D:ALA39 4.6 15.0 1.0
CZ D:TYR270 4.6 12.9 1.0
CG D:TYR270 4.8 12.5 1.0
CA D:ALA39 4.8 15.6 1.0
O D:ALA39 4.9 15.9 1.0
O D:PHE40 4.9 17.6 1.0
CG D:PHE273 5.0 10.6 1.0

Bromine binding site 4 out of 6 in 3wj8

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Bromine binding site 4 out of 6 in the Crystal Structure of Dl-2-Haloacid Dehalogenase Mutant with 2-Bromo-2- Methylpropionate


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 Dl-2-Haloacid Dehalogenase Mutant with 2-Bromo-2- Methylpropionate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Br401

b:10.9
occ:1.00
 BR E:B2P401 0.0 10.9 1.0
CA E:B2P401 1.6 12.6 1.0
CM E:B2P401 2.4 13.7 1.0
CB E:B2P401 2.5 13.8 1.0
N E:GLY41 2.7 14.9 1.0
C E:B2P401 2.7 13.6 1.0
CB E:PHE40 3.2 15.9 1.0
N E:PHE40 3.4 14.2 1.0
CA E:GLY41 3.5 14.7 1.0
O E:B2P401 3.5 13.9 1.0
OXT E:B2P401 3.6 13.6 1.0
C E:PHE40 3.6 15.1 1.0
CD1 E:TYR270 3.6 15.8 1.0
CE1 E:TYR270 3.6 16.3 1.0
CA E:PHE40 3.6 14.8 1.0
C E:ALA39 4.0 13.8 1.0
CG1 E:ILE274 4.2 10.7 1.0
CG E:PHE40 4.2 17.2 1.0
CD2 E:PHE273 4.3 10.9 1.0
CB E:ALA39 4.3 12.7 1.0
CD1 E:ILE274 4.3 10.6 1.0
CE2 E:PHE273 4.3 11.0 1.0
CA E:ALA39 4.4 13.5 1.0
CD2 E:PHE40 4.4 17.8 1.0
CG E:TYR270 4.7 15.2 1.0
CZ E:TYR270 4.7 17.4 1.0
O E:PHE40 4.7 16.0 1.0
O E:ALA39 4.8 13.9 1.0
C E:GLY41 4.8 14.8 1.0

Bromine binding site 5 out of 6 in 3wj8

Go back to Bromine Binding Sites List in 3wj8
Bromine binding site 5 out of 6 in the Crystal Structure of Dl-2-Haloacid Dehalogenase Mutant with 2-Bromo-2- Methylpropionate


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Crystal Structure of Dl-2-Haloacid Dehalogenase Mutant with 2-Bromo-2- Methylpropionate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Br401

b:11.2
occ:1.00
 BR F:B2P401 0.0 11.2 1.0
CA F:B2P401 1.6 13.5 1.0
CB F:B2P401 2.3 13.8 1.0
CM F:B2P401 2.6 14.1 1.0
C F:B2P401 2.7 14.9 1.0
N F:GLY41 3.2 18.7 1.0
CB F:PHE40 3.3 19.1 1.0
O F:B2P401 3.4 15.3 1.0
CE1 F:TYR270 3.5 14.4 1.0
CD1 F:TYR270 3.6 13.7 1.0
N F:PHE40 3.6 17.7 1.0
OXT F:B2P401 3.7 15.9 1.0
CE2 F:PHE273 3.8 10.3 1.0
CA F:PHE40 3.8 18.9 1.0
CD2 F:PHE273 3.8 10.3 1.0
C F:PHE40 3.9 19.3 1.0
CG1 F:ILE274 4.0 10.4 1.0
CA F:GLY41 4.0 18.3 1.0
CG F:PHE40 4.2 20.2 1.0
CD1 F:ILE274 4.3 10.4 1.0
CD2 F:PHE40 4.3 20.4 1.0
C F:ALA39 4.4 17.2 1.0
CB F:ALA39 4.4 15.7 1.0
CZ F:TYR270 4.5 15.0 1.0
CG F:TYR270 4.7 13.4 1.0
CA F:ALA39 4.8 16.5 1.0
O F:PHE40 5.0 21.5 1.0

Bromine binding site 6 out of 6 in 3wj8

Go back to Bromine Binding Sites List in 3wj8
Bromine binding site 6 out of 6 in the Crystal Structure of Dl-2-Haloacid Dehalogenase Mutant with 2-Bromo-2- Methylpropionate


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Crystal Structure of Dl-2-Haloacid Dehalogenase Mutant with 2-Bromo-2- Methylpropionate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Br401

b:9.3
occ:1.00
 BR G:B2P401 0.0 9.3 1.0
CA G:B2P401 1.6 10.7 1.0
CB G:B2P401 2.3 11.4 1.0
CM G:B2P401 2.6 11.3 1.0
C G:B2P401 2.8 11.7 1.0
N G:GLY41 3.3 14.4 1.0
CD1 G:TYR270 3.4 12.4 1.0
CB G:PHE40 3.5 15.8 1.0
CE1 G:TYR270 3.5 12.7 1.0
O G:B2P401 3.5 11.6 1.0
OXT G:B2P401 3.6 12.2 1.0
CD2 G:PHE273 3.6 11.4 1.0
CE2 G:PHE273 3.7 11.3 1.0
N G:PHE40 3.8 14.9 1.0
CA G:PHE40 3.9 15.4 1.0
CG1 G:ILE274 4.0 11.3 1.0
C G:PHE40 4.1 15.3 1.0
CA G:GLY41 4.1 14.7 1.0
CG G:PHE40 4.4 16.9 1.0
CD2 G:PHE40 4.4 17.0 1.0
C G:ALA39 4.5 14.3 1.0
CB G:ALA39 4.6 14.2 1.0
CD1 G:ILE274 4.6 11.2 1.0
CG G:TYR270 4.6 12.3 1.0
CZ G:TYR270 4.8 13.2 1.0
CG G:PHE273 4.8 11.6 1.0
CA G:ALA39 4.8 14.1 1.0

Reference:

A.Siwek, R.Omi, K.Hirotsu, K.Jitsumori, N.Esaki, T.Kurihara, P.Paneth. Binding Modes of Dl-2-Haloacid Dehalogenase Revealed By Crystallography, Modeling and Isotope Effects Studies. Arch.Biochem.Biophys. V. 540 26 2013.
ISSN: ISSN 0003-9861
PubMed: 24071515
DOI: 10.1016/J.ABB.2013.09.012
Page generated: Wed Jul 10 20:37:25 2024

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