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Chlorine in PDB 6xy9: Crystal Structure of Haloalkane Dehalogenase Dbea-M1 Loop Variant From Bradyrhizobium Elkanii

Enzymatic activity of Crystal Structure of Haloalkane Dehalogenase Dbea-M1 Loop Variant From Bradyrhizobium Elkanii

All present enzymatic activity of Crystal Structure of Haloalkane Dehalogenase Dbea-M1 Loop Variant From Bradyrhizobium Elkanii:
3.8.1.5;

Protein crystallography data

The structure of Crystal Structure of Haloalkane Dehalogenase Dbea-M1 Loop Variant From Bradyrhizobium Elkanii, PDB code: 6xy9 was solved by T.Prudnikova, P.Rezacova, I.Kuta Smatanova, R.Chaloupkova, J.Damborsky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.60 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 133.750, 75.130, 77.600, 90.00, 91.90, 90.00
R / Rfree (%) 17.5 / 23.5

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Haloalkane Dehalogenase Dbea-M1 Loop Variant From Bradyrhizobium Elkanii (pdb code 6xy9). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Haloalkane Dehalogenase Dbea-M1 Loop Variant From Bradyrhizobium Elkanii, PDB code: 6xy9:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6xy9

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Chlorine binding site 1 out of 4 in the Crystal Structure of Haloalkane Dehalogenase Dbea-M1 Loop Variant From Bradyrhizobium Elkanii


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 Haloalkane Dehalogenase Dbea-M1 Loop Variant From Bradyrhizobium Elkanii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl501

b:25.6
occ:1.00
 O A:HOH604 3.0 33.4 1.0
NE1 A:TRP104 3.3 22.6 1.0
ND2 A:ASN38 3.3 22.8 1.0
N A:PRO214 3.4 28.0 1.0
CZ A:PHE176 3.5 25.5 1.0
CD A:PRO214 3.6 25.0 1.0
CA A:PRO214 3.7 27.1 1.0
CE2 A:PHE176 3.7 27.7 1.0
CD1 A:TRP104 3.7 23.4 1.0
C A:LEU213 3.8 26.0 1.0
CB A:ASN38 3.9 22.3 1.0
CE2 A:PHE157 4.0 24.9 1.0
CB A:LEU213 4.0 22.8 1.0
CB A:PRO214 4.0 27.8 1.0
CG A:ASN38 4.1 22.5 1.0
CD1 A:LEU217 4.2 22.6 1.0
O A:LEU213 4.3 27.4 1.0
CG A:PRO214 4.3 26.2 1.0
CG A:LEU217 4.4 24.1 1.0
CA A:LEU213 4.5 26.1 1.0
CE2 A:TRP104 4.5 21.9 1.0
CD2 A:LEU217 4.7 22.7 1.0
CE1 A:PHE176 4.7 25.9 1.0
CZ A:PHE157 4.8 23.8 1.0
CD2 A:PHE157 4.8 22.8 1.0
O A:HOH757 4.9 40.7 1.0
CD2 A:PHE176 4.9 25.5 1.0
OD1 A:ASP103 5.0 32.4 1.0

Chlorine binding site 2 out of 4 in 6xy9

Go back to Chlorine Binding Sites List in 6xy9
Chlorine binding site 2 out of 4 in the Crystal Structure of Haloalkane Dehalogenase Dbea-M1 Loop Variant From Bradyrhizobium Elkanii


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 Haloalkane Dehalogenase Dbea-M1 Loop Variant From Bradyrhizobium Elkanii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:34.6
occ:1.00
 OG1 A:THR40 3.0 22.6 1.0
N A:GLY37 3.1 19.9 1.0
NE2 A:GLN102 3.2 33.0 1.0
NE2 A:GLN283 3.5 21.9 1.0
CD1 A:ILE44 3.8 24.8 1.0
CA A:HIS36 3.9 21.2 1.0
CA A:GLY37 3.9 23.7 1.0
C A:HIS36 4.0 21.8 1.0
CB A:THR40 4.0 24.8 1.0
CD1 A:TYR281 4.0 23.0 1.0
CB A:HIS36 4.0 21.7 1.0
CG2 A:THR40 4.1 22.5 1.0
CG2 A:ILE44 4.1 18.9 1.0
CD A:GLN102 4.2 32.8 1.0
CE1 A:TYR281 4.3 23.3 1.0
CD A:GLN283 4.4 24.4 1.0
C A:GLY37 4.4 25.1 1.0
OE1 A:GLN283 4.4 22.4 1.0
CB A:GLN102 4.4 27.7 1.0
O A:GLN102 4.4 34.3 1.0
CG A:GLN102 4.5 27.7 1.0
O A:GLY37 4.6 24.4 1.0
CB A:ASP103 4.7 32.9 1.0
CG1 A:ILE44 4.8 21.0 1.0
C A:GLN102 4.9 31.9 1.0
CB A:ILE44 4.9 23.9 1.0

Chlorine binding site 3 out of 4 in 6xy9

Go back to Chlorine Binding Sites List in 6xy9
Chlorine binding site 3 out of 4 in the Crystal Structure of Haloalkane Dehalogenase Dbea-M1 Loop Variant From Bradyrhizobium Elkanii


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 Haloalkane Dehalogenase Dbea-M1 Loop Variant From Bradyrhizobium Elkanii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl501

b:21.8
occ:1.00
 O B:HOH623 3.0 34.1 1.0
NE1 B:TRP104 3.2 24.1 1.0
ND2 B:ASN38 3.3 22.1 1.0
N B:PRO214 3.4 23.0 1.0
CZ B:PHE176 3.6 25.1 1.0
CA B:PRO214 3.6 23.9 1.0
CE2 B:PHE176 3.6 23.2 1.0
CD1 B:TRP104 3.7 22.5 1.0
CD B:PRO214 3.7 22.9 1.0
C B:LEU213 3.7 22.6 1.0
CB B:PRO214 3.9 23.9 1.0
CE2 B:PHE157 4.0 23.0 1.0
CB B:ASN38 4.0 21.4 1.0
O B:LEU213 4.1 23.1 1.0
CB B:LEU213 4.1 21.2 1.0
CG B:ASN38 4.2 25.0 1.0
CD1 B:LEU217 4.2 22.1 1.0
CG B:PRO214 4.4 23.7 1.0
CE2 B:TRP104 4.5 23.5 1.0
CG B:LEU217 4.5 24.7 1.0
CA B:LEU213 4.5 22.0 1.0
CD2 B:LEU217 4.6 17.9 1.0
O B:HOH781 4.7 39.5 1.0
CZ B:PHE157 4.7 23.3 1.0
CE1 B:PHE176 4.8 26.1 1.0
CD2 B:PHE157 4.8 23.1 1.0
CD2 B:PHE176 4.9 23.0 1.0
OD2 B:ASP103 4.9 25.1 1.0
OD1 B:ASP103 4.9 35.8 1.0

Chlorine binding site 4 out of 4 in 6xy9

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Chlorine binding site 4 out of 4 in the Crystal Structure of Haloalkane Dehalogenase Dbea-M1 Loop Variant From Bradyrhizobium Elkanii


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 Haloalkane Dehalogenase Dbea-M1 Loop Variant From Bradyrhizobium Elkanii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:27.4
occ:1.00
 NE2 B:GLN102 3.0 31.1 1.0
OG1 B:THR40 3.1 23.2 1.0
N B:GLY37 3.2 19.8 1.0
NE2 B:GLN283 3.5 22.8 1.0
CD1 B:TYR281 3.9 20.6 1.0
CA B:HIS36 4.0 21.6 1.0
CA B:GLY37 4.0 21.0 1.0
CD1 B:ILE44 4.0 16.3 1.0
C B:HIS36 4.0 22.2 1.0
CD B:GLN102 4.1 30.0 1.0
CG2 B:ILE44 4.1 18.8 1.0
CB B:THR40 4.2 23.5 1.0
CE1 B:TYR281 4.2 22.0 1.0
CG2 B:THR40 4.2 22.8 1.0
CB B:HIS36 4.2 18.8 1.0
CB B:GLN102 4.3 23.0 1.0
CG B:GLN102 4.4 25.5 1.0
C B:GLY37 4.4 21.4 1.0
O B:GLN102 4.4 28.2 1.0
CD B:GLN283 4.4 25.9 1.0
OE1 B:GLN283 4.4 26.4 1.0
CB B:ASP103 4.5 30.2 1.0
O B:GLY37 4.5 22.3 1.0
C B:GLN102 4.8 27.9 1.0
CG1 B:ILE44 4.9 18.7 1.0
CB B:ILE44 5.0 19.7 1.0

Reference:

M.Marek, R.Chaloupkova, T.Prudnikova, Y.Sato, P.Rezacova, Y.Nagata, I.Kuta Smatanova, J.Damborsky. Structural and Catalytic Effects of Surface Loop-Helix Transplantation Within Haloalkane Dehalogenase Family. Comput Struct Biotechnol J V. 18 1352 2020.
ISSN: ISSN 2001-0370
PubMed: 32612758
DOI: 10.1016/J.CSBJ.2020.05.019
Page generated: Sat Jul 12 21:50:29 2025

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