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Bromine in PDB 1k6e: Complex of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,2-Propanediol (Product of Dehalogenation of 1,2-Dibromopropane) at 1.85A

Enzymatic activity of Complex of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,2-Propanediol (Product of Dehalogenation of 1,2-Dibromopropane) at 1.85A

All present enzymatic activity of Complex of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,2-Propanediol (Product of Dehalogenation of 1,2-Dibromopropane) at 1.85A:
3.8.1.5;

Protein crystallography data

The structure of Complex of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,2-Propanediol (Product of Dehalogenation of 1,2-Dibromopropane) at 1.85A, PDB code: 1k6e was solved by V.A.Streltsov, Z.Prokop, J.Damborsky, Y.Nagata, A.Oakley, M.C.J.Wilce, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.69 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.410, 68.330, 80.980, 90.00, 90.00, 90.00
R / Rfree (%) 14.2 / 20.1

Other elements in 1k6e:

The structure of Complex of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,2-Propanediol (Product of Dehalogenation of 1,2-Dibromopropane) at 1.85A also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Chlorine (Cl) 2 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Complex of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,2-Propanediol (Product of Dehalogenation of 1,2-Dibromopropane) at 1.85A (pdb code 1k6e). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Complex of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,2-Propanediol (Product of Dehalogenation of 1,2-Dibromopropane) at 1.85A, PDB code: 1k6e:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 1k6e

Go back to Bromine Binding Sites List in 1k6e
Bromine binding site 1 out of 4 in the Complex of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,2-Propanediol (Product of Dehalogenation of 1,2-Dibromopropane) at 1.85A


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Complex of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,2-Propanediol (Product of Dehalogenation of 1,2-Dibromopropane) at 1.85A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1001

b:27.8
occ:0.75
 CL A:CL1003 0.0 46.3 0.2
O1 A:PGO2001 3.2 13.8 0.5
NE1 A:TRP109 3.3 8.0 1.0
ND2 A:ASN38 3.4 6.7 1.0
C3 A:1BP2003 3.5 41.9 0.2
N A:PRO208 3.5 5.9 1.0
C1 A:PGO2001 3.5 28.0 0.5
O A:HOH2004 3.6 39.2 1.0
CA A:PRO208 3.6 11.6 1.0
CZ A:PHE169 3.7 11.9 1.0
O2 A:1BP2002 3.7 45.7 0.3
CD A:PRO208 3.8 5.4 1.0
CD1 A:TRP109 3.8 5.3 1.0
C A:TRP207 3.8 10.3 1.0
CD1 A:ILE211 3.9 8.1 1.0
CE2 A:PHE169 3.9 11.0 1.0
CB A:PRO208 3.9 7.9 1.0
CB A:TRP207 3.9 8.3 1.0
CB A:ASN38 4.0 6.1 1.0
O A:TRP207 4.1 6.0 1.0
CE2 A:PHE151 4.2 9.1 1.0
CG A:ASN38 4.2 12.8 1.0
CG1 A:ILE211 4.3 6.0 1.0
CA A:TRP207 4.5 9.8 1.0
CE2 A:TRP109 4.6 7.1 1.0
CG A:PRO208 4.6 5.6 1.0
C2 A:1BP2002 4.6 42.2 0.3
C2 A:1BP2003 4.7 38.8 0.2
CE1 A:PHE169 4.7 11.8 1.0
OD2 A:ASP108 4.8 8.9 1.0
OD1 A:ASP108 4.8 24.8 1.0
C3 A:1BP2002 4.9 43.4 0.3
C A:PRO208 5.0 11.2 1.0

Bromine binding site 2 out of 4 in 1k6e

Go back to Bromine Binding Sites List in 1k6e
Bromine binding site 2 out of 4 in the Complex of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,2-Propanediol (Product of Dehalogenation of 1,2-Dibromopropane) at 1.85A


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Complex of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,2-Propanediol (Product of Dehalogenation of 1,2-Dibromopropane) at 1.85A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1002

b:31.4
occ:0.75
 CL A:CL1004 0.3 44.8 0.2
O A:HOH2348 3.1 21.6 1.0
N A:ALA218 3.1 8.8 1.0
CG2 A:THR216 3.3 17.6 1.0
O A:HOH2435 3.5 30.5 1.0
CA A:PRO217 3.7 9.7 1.0
CB A:ALA218 3.8 8.3 1.0
C A:PRO217 3.9 10.4 1.0
CA A:ALA218 4.1 7.8 1.0
CB A:THR216 4.3 18.8 1.0
CA A:THR216 4.3 10.5 1.0
CB A:PRO217 4.5 12.6 1.0
OG1 A:THR216 4.5 24.7 1.0
O A:GLY215 4.7 13.3 1.0
N A:PRO217 4.8 10.6 1.0

Bromine binding site 3 out of 4 in 1k6e

Go back to Bromine Binding Sites List in 1k6e
Bromine binding site 3 out of 4 in the Complex of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,2-Propanediol (Product of Dehalogenation of 1,2-Dibromopropane) at 1.85A


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Complex of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,2-Propanediol (Product of Dehalogenation of 1,2-Dibromopropane) at 1.85A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br2002

b:37.5
occ:0.30
 BR A:1BP2002 0.0 37.5 0.3
O2 A:PGO2001 1.8 28.6 0.5
C1 A:1BP2002 1.9 41.3 0.3
C1 A:1BP2003 2.0 38.2 0.2
C2 A:1BP2002 2.8 42.2 0.3
C2 A:1BP2003 2.8 38.8 0.2
O2 A:1BP2003 2.9 41.5 0.2
C2 A:PGO2001 2.9 25.7 0.5
C3 A:1BP2002 3.2 43.4 0.3
O A:HOH2005 3.3 28.6 1.0
C3 A:PGO2001 3.3 32.2 0.5
BR A:1BP2003 3.3 31.4 0.2
CD1 A:LEU177 3.8 11.2 1.0
CG A:PRO144 3.8 21.1 1.0
O2 A:1BP2002 4.1 45.7 0.3
CB A:ALA247 4.1 12.7 1.0
C1 A:PGO2001 4.1 28.0 0.5
CG A:HIS272 4.2 13.6 1.0
C3 A:1BP2003 4.3 41.9 0.2
ND1 A:HIS272 4.3 9.4 1.0
CB A:HIS272 4.4 11.1 1.0
CZ A:PHE143 4.5 15.5 1.0
CD2 A:HIS272 4.7 16.1 1.0
CZ A:PHE151 4.7 7.1 1.0
CD A:PRO144 4.7 13.8 1.0
CE1 A:HIS272 4.8 14.2 1.0
N A:LEU248 4.8 9.5 1.0
CE1 A:PHE151 4.9 9.9 1.0
CB A:LEU248 4.9 12.6 1.0
CB A:PRO144 4.9 13.8 1.0
CD2 A:LEU177 5.0 11.3 1.0
CE2 A:PHE143 5.0 14.8 1.0

Bromine binding site 4 out of 4 in 1k6e

Go back to Bromine Binding Sites List in 1k6e
Bromine binding site 4 out of 4 in the Complex of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,2-Propanediol (Product of Dehalogenation of 1,2-Dibromopropane) at 1.85A


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Complex of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,2-Propanediol (Product of Dehalogenation of 1,2-Dibromopropane) at 1.85A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br2003

b:31.4
occ:0.20
 BR A:1BP2003 0.0 31.4 0.2
C3 A:1BP2002 0.9 43.4 0.3
C1 A:1BP2003 1.9 38.2 0.2
O2 A:PGO2001 2.3 28.6 0.5
C2 A:1BP2002 2.3 42.2 0.3
C2 A:1BP2003 2.9 38.8 0.2
C1 A:PGO2001 3.1 28.0 0.5
C1 A:1BP2002 3.1 41.3 0.3
C2 A:PGO2001 3.2 25.7 0.5
O A:HOH2004 3.2 39.2 1.0
O2 A:1BP2002 3.3 45.7 0.3
C3 A:1BP2003 3.3 41.9 0.2
BR A:1BP2002 3.3 37.5 0.3
CD1 A:LEU177 3.5 11.2 1.0
CD2 A:HIS272 3.5 16.1 1.0
CG1 A:VAL173 3.7 11.2 1.0
CZ A:PHE151 3.8 7.1 1.0
CZ A:PHE273 3.8 10.5 1.0
CE1 A:PHE273 4.0 8.3 1.0
NE2 A:HIS272 4.0 10.4 1.0
CE1 A:PHE169 4.0 11.8 1.0
CZ A:PHE169 4.0 11.9 1.0
CG A:HIS272 4.1 13.6 1.0
O2 A:1BP2003 4.1 41.5 0.2
O1 A:PGO2001 4.4 13.8 0.5
C3 A:PGO2001 4.5 32.2 0.5
CE1 A:PHE151 4.6 9.9 1.0
CE2 A:PHE151 4.6 9.1 1.0
CB A:HIS272 4.6 11.1 1.0
CE1 A:HIS272 4.7 14.2 1.0
OD1 A:ASP108 4.7 24.8 1.0
ND1 A:HIS272 4.7 9.4 1.0
CE2 A:PHE273 5.0 12.7 1.0
CG A:LEU177 5.0 9.8 1.0

Reference:

V.A.Streltsov, Z.Prokop, J.Damborsky, Y.Nagata, A.Oakley, M.C.J.Wilce. Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26: X-Ray Crystallographic Studies of Dehalogenation of Brominated Substrates. Biochemistry V. 42 10104 2003.
ISSN: ISSN 0006-2960
PubMed: 12939138
DOI: 10.1021/BI027280A
Page generated: Wed Jul 10 16:47:46 2024

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