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Bromine in PDB 1d07: Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,3-Propanediol, A Product of Debromidation of Dibrompropane, at 2.0A Resolution

Enzymatic activity of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,3-Propanediol, A Product of Debromidation of Dibrompropane, at 2.0A Resolution

All present enzymatic activity of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,3-Propanediol, A Product of Debromidation of Dibrompropane, at 2.0A Resolution:
3.8.1.5;

Protein crystallography data

The structure of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,3-Propanediol, A Product of Debromidation of Dibrompropane, at 2.0A Resolution, PDB code: 1d07 was solved by J.Marek, J.Vevodova, J.Damborsky, I.Smatanova, L.A.Svensson, J.Newman, Y.Nagata, M.Takagi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 50.227, 71.721, 73.319, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 27.4

Bromine Binding Sites:

The binding sites of Bromine atom in the Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,3-Propanediol, A Product of Debromidation of Dibrompropane, at 2.0A Resolution (pdb code 1d07). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,3-Propanediol, A Product of Debromidation of Dibrompropane, at 2.0A Resolution, PDB code: 1d07:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in 1d07

Go back to Bromine Binding Sites List in 1d07
Bromine binding site 1 out of 2 in the Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,3-Propanediol, A Product of Debromidation of Dibrompropane, at 2.0A Resolution


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,3-Propanediol, A Product of Debromidation of Dibrompropane, at 2.0A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br901

b:23.8
occ:0.71
 C3 A:PDO903 3.2 40.6 0.7
NE1 A:TRP109 3.5 16.3 1.0
N A:PRO208 3.5 11.3 1.0
CZ A:PHE169 3.6 17.5 1.0
CA A:PRO208 3.6 7.2 1.0
ND2 A:ASN38 3.7 6.9 1.0
C2 A:PDO903 3.8 42.8 0.7
CD A:PRO208 3.8 13.4 1.0
CE2 A:PHE169 3.9 18.4 1.0
CD1 A:TRP109 3.9 13.2 1.0
C A:TRP207 3.9 12.1 1.0
CB A:PRO208 3.9 13.5 1.0
CD1 A:ILE211 3.9 18.0 1.0
CE2 A:PHE151 4.0 13.4 1.0
CB A:ASN38 4.1 13.9 1.0
CB A:TRP207 4.1 15.3 1.0
O A:TRP207 4.3 14.9 1.0
CG1 A:ILE211 4.3 26.6 1.0
CG A:ASN38 4.4 9.6 1.0
O3 A:PDO903 4.4 39.0 0.7
CG A:PRO208 4.5 16.3 1.0
C1 A:PDO903 4.5 45.2 0.7
CE1 A:PHE169 4.6 12.7 1.0
CZ A:PHE151 4.6 23.0 1.0
OD2 A:ASP108 4.7 16.4 1.0
CA A:TRP207 4.7 5.6 1.0
OD1 A:ASP108 4.7 25.0 1.0
CE2 A:TRP109 4.8 20.3 1.0
CD2 A:PHE151 5.0 17.2 1.0

Bromine binding site 2 out of 2 in 1d07

Go back to Bromine Binding Sites List in 1d07
Bromine binding site 2 out of 2 in the Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,3-Propanediol, A Product of Debromidation of Dibrompropane, at 2.0A Resolution


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,3-Propanediol, A Product of Debromidation of Dibrompropane, at 2.0A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br902

b:29.6
occ:0.71
 O A:HOH1007 2.3 23.9 1.0
O A:PRO175 2.4 15.2 1.0
O A:ILE178 2.4 18.5 1.0
O A:HOH1028 2.7 25.5 1.0
C A:PRO175 3.5 14.3 1.0
C A:ILE178 3.6 26.2 1.0
N A:ILE178 4.2 16.7 1.0
N A:GLY176 4.3 12.2 1.0
CA A:GLY176 4.3 11.1 1.0
CA A:ILE178 4.4 17.2 1.0
C A:GLY176 4.4 19.0 1.0
CA A:PRO175 4.5 20.3 1.0
O A:ARG180 4.5 20.6 1.0
O A:HOH1041 4.6 14.9 1.0
CB A:ILE178 4.6 13.2 1.0
N A:LEU179 4.7 26.4 1.0
N A:LEU177 4.8 19.3 1.0
O A:GLY176 4.8 28.2 1.0
CA A:LEU179 4.8 20.8 1.0
C A:LEU179 4.8 23.4 1.0
CB A:PRO175 4.9 18.9 1.0

Reference:

J.Marek, J.Vevodova, I.K.Smatanova, Y.Nagata, L.A.Svensson, J.Newman, M.Takagi, J.Damborsky. Crystal Structure of the Haloalkane Dehalogenase From Sphingomonas Paucimobilis UT26. Biochemistry V. 39 14082 2000.
ISSN: ISSN 0006-2960
PubMed: 11087355
DOI: 10.1021/BI001539C
Page generated: Sun Jan 24 08:27:02 2021

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