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Chlorine in PDB 3afi: Crystal Structure of Dbja (His-Dbja)

Enzymatic activity of Crystal Structure of Dbja (His-Dbja)

All present enzymatic activity of Crystal Structure of Dbja (His-Dbja):
3.8.1.5;

Protein crystallography data

The structure of Crystal Structure of Dbja (His-Dbja), PDB code: 3afi was solved by Y.Sato, T.Senda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.18 / 1.75
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 212.855, 117.843, 55.796, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 19.1

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Dbja (His-Dbja) (pdb code 3afi). 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 Dbja (His-Dbja), PDB code: 3afi:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3afi

Go back to Chlorine Binding Sites List in 3afi
Chlorine binding site 1 out of 4 in the Crystal Structure of Dbja (His-Dbja)


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 Dbja (His-Dbja) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl401

b:16.9
occ:1.00
O E:HOH1162 3.0 24.1 1.0
NE1 E:TRP104 3.2 14.3 1.0
N E:PRO214 3.4 15.1 1.0
CA E:PRO214 3.5 15.1 1.0
ND2 E:ASN38 3.5 15.6 1.0
CD E:PRO214 3.6 15.0 1.0
C E:PHE213 3.7 14.9 1.0
CB E:PHE213 3.7 15.8 1.0
CD1 E:TRP104 3.8 15.6 1.0
CZ E:PHE176 3.8 18.7 1.0
CB E:PRO214 3.9 15.1 1.0
O E:PHE213 4.0 14.7 1.0
CB E:ASN38 4.1 15.7 1.0
CD1 E:LEU217 4.2 16.1 1.0
CE2 E:PHE157 4.2 15.8 1.0
CG E:PRO214 4.3 16.3 1.0
CE1 E:PHE176 4.3 19.1 1.0
CG E:ASN38 4.3 15.3 1.0
CG E:LEU217 4.3 15.8 1.0
CA E:PHE213 4.3 15.5 1.0
CD2 E:LEU217 4.4 16.9 1.0
CE2 E:TRP104 4.5 14.4 1.0
CG E:PHE213 4.7 16.1 1.0
CE2 E:PHE176 4.7 18.7 1.0
C E:PRO214 4.9 15.7 1.0

Chlorine binding site 2 out of 4 in 3afi

Go back to Chlorine Binding Sites List in 3afi
Chlorine binding site 2 out of 4 in the Crystal Structure of Dbja (His-Dbja)


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 Dbja (His-Dbja) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:12.9
occ:1.00
O A:HOH772 3.0 19.3 1.0
NE1 A:TRP104 3.3 9.9 1.0
N A:PRO214 3.4 11.2 1.0
ND2 A:ASN38 3.5 9.7 1.0
CA A:PRO214 3.5 11.2 1.0
CD A:PRO214 3.6 11.4 1.0
C A:PHE213 3.6 10.2 1.0
CB A:PHE213 3.7 10.0 1.0
CZ A:PHE176 3.8 11.8 1.0
CD1 A:TRP104 3.9 10.1 1.0
CB A:PRO214 3.9 11.3 1.0
O A:PHE213 4.0 10.3 1.0
CE1 A:PHE176 4.1 14.1 1.0
CB A:ASN38 4.1 11.5 1.0
CE2 A:PHE157 4.1 9.8 1.0
CD1 A:LEU217 4.2 11.6 1.0
CG A:PRO214 4.3 12.3 1.0
CG A:LEU217 4.3 9.8 1.0
CG A:ASN38 4.3 11.8 1.0
CA A:PHE213 4.3 10.3 1.0
CD2 A:LEU217 4.5 9.9 1.0
CE2 A:TRP104 4.5 9.0 1.0
CG A:PHE213 4.7 10.7 1.0
CE2 A:PHE176 4.9 13.4 1.0
C A:PRO214 4.9 11.2 1.0
CD2 A:PHE157 5.0 11.2 1.0

Chlorine binding site 3 out of 4 in 3afi

Go back to Chlorine Binding Sites List in 3afi
Chlorine binding site 3 out of 4 in the Crystal Structure of Dbja (His-Dbja)


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 Dbja (His-Dbja) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl403

b:14.9
occ:1.00
O B:HOH567 3.0 20.9 1.0
NE1 B:TRP104 3.3 12.4 1.0
N B:PRO214 3.4 13.3 1.0
CA B:PRO214 3.5 13.1 1.0
ND2 B:ASN38 3.6 10.7 1.0
C B:PHE213 3.7 12.7 1.0
CD B:PRO214 3.7 13.4 1.0
CB B:PHE213 3.8 12.0 1.0
CD1 B:TRP104 3.8 13.9 1.0
CZ B:PHE176 3.9 14.1 1.0
CB B:PRO214 3.9 14.2 1.0
O B:PHE213 4.0 13.4 1.0
CD1 B:LEU217 4.1 13.5 1.0
CB B:ASN38 4.2 12.2 1.0
CE2 B:PHE157 4.2 12.8 1.0
CG B:PRO214 4.2 13.9 1.0
CE1 B:PHE176 4.3 16.3 1.0
CG B:LEU217 4.3 12.2 1.0
CA B:PHE213 4.4 12.7 1.0
CG B:ASN38 4.4 13.4 1.0
CD2 B:LEU217 4.5 12.4 1.0
CE2 B:TRP104 4.5 13.0 1.0
CG B:PHE213 4.8 12.5 1.0
CE2 B:PHE176 4.8 16.1 1.0
C B:PRO214 4.9 13.2 1.0

Chlorine binding site 4 out of 4 in 3afi

Go back to Chlorine Binding Sites List in 3afi
Chlorine binding site 4 out of 4 in the Crystal Structure of Dbja (His-Dbja)


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 Dbja (His-Dbja) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl404

b:16.2
occ:1.00
O F:HOH974 3.0 20.3 1.0
NE1 F:TRP104 3.3 12.1 1.0
N F:PRO214 3.4 14.6 1.0
ND2 F:ASN38 3.5 11.7 1.0
CA F:PRO214 3.5 14.8 1.0
CD F:PRO214 3.6 14.1 1.0
C F:PHE213 3.6 13.9 1.0
CB F:PHE213 3.7 14.3 1.0
CZ F:PHE176 3.8 15.4 1.0
CD1 F:TRP104 3.8 12.0 1.0
CB F:PRO214 3.9 14.9 1.0
O F:PHE213 3.9 13.9 1.0
CE1 F:PHE176 4.1 17.4 1.0
CB F:ASN38 4.1 14.0 1.0
CD1 F:LEU217 4.2 14.9 1.0
CE2 F:PHE157 4.2 14.2 1.0
CG F:LEU217 4.3 13.6 1.0
CG F:PRO214 4.3 15.6 1.0
CA F:PHE213 4.3 14.1 1.0
CG F:ASN38 4.3 15.6 1.0
CD2 F:LEU217 4.5 14.1 1.0
CE2 F:TRP104 4.5 12.9 1.0
CG F:PHE213 4.7 13.8 1.0
CE2 F:PHE176 4.8 14.6 1.0
C F:PRO214 4.9 15.1 1.0

Reference:

Z.Prokop, Y.Sato, J.Brezovsky, T.Mozga, R.Chaloupkova, T.Koudelakova, P.Jerabek, V.Stepankova, R.Natsume, J.G.Van Leeuwen, D.B.Janssen, J.Florian, Y.Nagata, T.Senda, J.Damborsky. Enantioselectivity of Haloalkane Dehalogenases and Its Modulation By Surface Loop Engineering Angew.Chem.Int.Ed.Engl. V. 49 6111 2010.
ISSN: ISSN 1433-7851
PubMed: 20645368
DOI: 10.1002/ANIE.201001753
Page generated: Sat Dec 12 09:31:21 2020

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