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Chlorine in PDB 4zd6: Halohydrin Hydrogen-Halide-Lyase, Hheb

Protein crystallography data

The structure of Halohydrin Hydrogen-Halide-Lyase, Hheb, PDB code: 4zd6 was solved by F.Watanabe, F.Yu, A.Ohtaki, Y.Yamanaka, K.Noguchi, M.Yohda, M.Odaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.31 / 1.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 121.484, 216.380, 104.517, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 20.7

Other elements in 4zd6:

The structure of Halohydrin Hydrogen-Halide-Lyase, Hheb also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Halohydrin Hydrogen-Halide-Lyase, Hheb (pdb code 4zd6). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Halohydrin Hydrogen-Halide-Lyase, Hheb, PDB code: 4zd6:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4zd6

Go back to Chlorine Binding Sites List in 4zd6
Chlorine binding site 1 out of 6 in the Halohydrin Hydrogen-Halide-Lyase, Hheb


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Halohydrin Hydrogen-Halide-Lyase, Hheb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:18.0
occ:1.00
 O A:HOH520 3.1 24.3 1.0
ND2 A:ASN166 3.3 15.7 1.0
NE2 A:GLN161 3.3 14.6 1.0
N A:THR164 3.6 13.3 1.0
CE1 A:PHE170 3.7 16.2 1.0
O A:THR164 3.7 18.1 1.0
CA A:HIS162 3.8 13.6 1.0
CB A:THR164 3.8 16.0 1.0
CD1 A:PHE170 3.8 13.7 1.0
C A:HIS162 3.9 13.0 1.0
N A:TRP163 3.9 13.2 1.0
CG A:GLN161 4.0 12.8 1.0
N A:HIS162 4.0 12.4 1.0
CA A:THR164 4.1 12.2 1.0
CD A:GLN161 4.2 13.1 1.0
OG1 A:THR164 4.2 15.1 1.0
C A:GLN161 4.3 12.4 1.0
O A:GLN161 4.3 14.6 1.0
C A:THR164 4.4 17.7 1.0
CG A:ASN166 4.4 16.1 1.0
CD1 A:TYR169 4.5 15.4 1.0
O A:HIS162 4.5 13.1 1.0
OH A:TYR19 4.6 13.7 1.0
CB A:GLN161 4.6 13.9 1.0
OD1 A:ASN166 4.6 17.4 1.0
C A:TRP163 4.7 14.0 1.0
CB A:TYR169 4.7 15.3 1.0
ND1 A:HIS162 4.7 22.3 1.0
CA A:TRP163 4.8 13.2 1.0
CE1 A:TYR19 4.8 15.1 1.0
CZ A:PHE170 4.9 19.8 1.0
CG A:TYR169 5.0 15.4 1.0

Chlorine binding site 2 out of 6 in 4zd6

Go back to Chlorine Binding Sites List in 4zd6
Chlorine binding site 2 out of 6 in the Halohydrin Hydrogen-Halide-Lyase, Hheb


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Halohydrin Hydrogen-Halide-Lyase, Hheb within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:14.2
occ:1.00
 O B:HOH556 3.1 20.1 1.0
O B:HOH438 3.1 17.6 1.0
ND2 B:ASN166 3.3 14.7 1.0
NE2 B:GLN161 3.4 9.9 1.0
N B:THR164 3.6 10.2 1.0
CB B:THR164 3.7 9.6 1.0
CA B:HIS162 3.7 10.6 1.0
CE2 B:PHE170 3.7 13.0 1.0
O B:THR164 3.7 13.5 1.0
C B:HIS162 3.8 10.5 1.0
N B:TRP163 3.8 10.2 1.0
CG B:GLN161 3.9 10.5 1.0
N B:HIS162 4.0 10.8 1.0
CA B:THR164 4.1 10.7 1.0
CD2 B:PHE170 4.1 12.3 1.0
C B:GLN161 4.2 9.1 1.0
O B:GLN161 4.2 10.6 1.0
CD B:GLN161 4.2 11.9 1.0
OG1 B:THR164 4.2 12.1 1.0
C B:THR164 4.3 11.5 1.0
O B:HIS162 4.4 10.8 1.0
CG B:ASN166 4.4 12.4 1.0
O B:HOH503 4.4 17.9 1.0
CB B:GLN161 4.5 13.0 1.0
C B:TRP163 4.6 10.7 1.0
CD2 B:TYR169 4.7 11.9 1.0
OD1 B:ASN166 4.7 13.4 1.0
CA B:TRP163 4.7 11.0 1.0
OH B:TYR19 4.8 13.4 1.0
CG2 B:THR164 4.8 12.7 1.0
O B:HOH405 4.8 21.6 1.0
ND1 B:HIS162 4.8 12.8 1.0
CZ B:PHE170 4.9 13.0 1.0
CB B:TYR169 4.9 13.4 1.0

Chlorine binding site 3 out of 6 in 4zd6

Go back to Chlorine Binding Sites List in 4zd6
Chlorine binding site 3 out of 6 in the Halohydrin Hydrogen-Halide-Lyase, Hheb


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Halohydrin Hydrogen-Halide-Lyase, Hheb within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl301

b:20.4
occ:1.00
 O C:HOH506 2.9 23.9 1.0
ND2 C:ASN166 3.2 19.0 1.0
NE2 C:GLN161 3.4 12.8 1.0
N C:THR164 3.6 13.8 1.0
CE2 C:PHE170 3.7 17.3 1.0
O C:HOH453 3.7 26.7 1.0
O C:THR164 3.7 19.2 1.0
CB C:THR164 3.7 14.2 1.0
CA C:HIS162 3.7 13.0 1.0
CD2 C:PHE170 3.8 15.4 1.0
N C:TRP163 3.9 14.4 1.0
C C:HIS162 3.9 11.8 1.0
CG C:GLN161 4.0 13.6 1.0
N C:HIS162 4.1 14.6 1.0
CA C:THR164 4.1 16.4 1.0
CD C:GLN161 4.2 13.9 1.0
OG1 C:THR164 4.2 16.7 1.0
O C:GLN161 4.3 15.1 1.0
C C:GLN161 4.3 14.6 1.0
CG C:ASN166 4.4 16.0 1.0
C C:THR164 4.4 17.0 1.0
CD2 C:TYR169 4.4 17.1 1.0
O C:HIS162 4.5 15.6 1.0
CB C:TYR169 4.6 17.8 1.0
OD1 C:ASN166 4.6 21.0 1.0
C C:TRP163 4.7 14.7 1.0
OH C:TYR19 4.7 17.2 1.0
CB C:GLN161 4.7 13.6 1.0
ND1 C:HIS162 4.7 21.3 1.0
CA C:TRP163 4.8 14.9 1.0
CE1 C:TYR19 4.8 14.5 1.0
CG2 C:THR164 4.9 15.2 1.0
CG C:TYR169 4.9 17.6 1.0
CZ C:PHE170 5.0 18.0 1.0

Chlorine binding site 4 out of 6 in 4zd6

Go back to Chlorine Binding Sites List in 4zd6
Chlorine binding site 4 out of 6 in the Halohydrin Hydrogen-Halide-Lyase, Hheb


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Halohydrin Hydrogen-Halide-Lyase, Hheb within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl301

b:19.1
occ:1.00
 O D:HOH512 3.0 26.2 1.0
ND2 D:ASN166 3.3 17.2 1.0
NE2 D:GLN161 3.3 16.0 1.0
CE1 D:PHE170 3.6 18.9 1.0
N D:THR164 3.7 13.4 1.0
CA D:HIS162 3.8 15.1 1.0
CB D:THR164 3.8 16.9 1.0
O D:THR164 3.8 19.0 1.0
CG D:GLN161 3.9 13.7 1.0
C D:HIS162 3.9 13.7 1.0
CD1 D:PHE170 3.9 19.5 1.0
N D:TRP163 4.0 15.6 1.0
N D:HIS162 4.1 12.0 1.0
CD D:GLN161 4.1 13.5 1.0
CA D:THR164 4.2 17.5 1.0
C D:GLN161 4.2 13.9 1.0
O D:GLN161 4.3 14.2 1.0
OG1 D:THR164 4.3 17.7 1.0
CG D:ASN166 4.4 17.0 1.0
C D:THR164 4.4 18.1 1.0
CD2 D:TYR169 4.5 16.4 1.0
CB D:GLN161 4.5 14.8 1.0
O D:HIS162 4.6 15.5 1.0
OD1 D:ASN166 4.6 19.0 1.0
OH D:TYR19 4.7 16.6 1.0
C D:TRP163 4.7 15.9 1.0
CB D:TYR169 4.7 17.2 1.0
ND1 D:HIS162 4.8 20.6 1.0
CZ D:PHE170 4.8 19.8 1.0
CA D:TRP163 4.8 11.6 1.0
CE1 D:TYR19 4.9 15.4 1.0
CG2 D:THR164 4.9 16.2 1.0

Chlorine binding site 5 out of 6 in 4zd6

Go back to Chlorine Binding Sites List in 4zd6
Chlorine binding site 5 out of 6 in the Halohydrin Hydrogen-Halide-Lyase, Hheb


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Halohydrin Hydrogen-Halide-Lyase, Hheb within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl302

b:14.5
occ:1.00
 O E:HOH568 3.1 18.1 1.0
ND2 E:ASN166 3.3 11.8 1.0
NE2 E:GLN161 3.3 12.5 1.0
N E:THR164 3.7 11.5 1.0
CB E:THR164 3.7 10.4 1.0
O E:THR164 3.7 12.3 1.0
CD2 E:PHE170 3.7 10.5 1.0
CE2 E:PHE170 3.8 13.0 1.0
CA E:HIS162 3.8 11.9 1.0
C E:HIS162 3.9 12.6 1.0
N E:TRP163 4.0 10.0 1.0
CG E:GLN161 4.0 11.0 1.0
N E:HIS162 4.1 10.0 1.0
CA E:THR164 4.1 11.4 1.0
CD E:GLN161 4.2 11.1 1.0
OG1 E:THR164 4.2 11.4 1.0
C E:GLN161 4.3 10.4 1.0
C E:THR164 4.3 12.5 1.0
CD2 E:TYR169 4.3 12.5 1.0
CG E:ASN166 4.4 13.1 1.0
O E:GLN161 4.4 10.8 1.0
CB E:TYR169 4.5 12.0 1.0
O E:HIS162 4.6 12.3 1.0
OH E:TYR19 4.6 12.8 1.0
OD1 E:ASN166 4.6 14.7 1.0
CB E:GLN161 4.7 9.8 1.0
C E:TRP163 4.7 10.9 1.0
CE1 E:TYR19 4.8 10.5 1.0
CG2 E:THR164 4.8 11.7 1.0
ND1 E:HIS162 4.8 20.7 1.0
CG E:TYR169 4.8 13.7 1.0
CA E:TRP163 4.9 11.9 1.0

Chlorine binding site 6 out of 6 in 4zd6

Go back to Chlorine Binding Sites List in 4zd6
Chlorine binding site 6 out of 6 in the Halohydrin Hydrogen-Halide-Lyase, Hheb


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Halohydrin Hydrogen-Halide-Lyase, Hheb within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl301

b:17.8
occ:1.00
 O F:HOH533 3.1 23.9 1.0
ND2 F:ASN166 3.2 16.8 1.0
NE2 F:GLN161 3.4 14.9 1.0
CE1 F:PHE170 3.7 14.7 1.0
N F:THR164 3.7 12.6 1.0
O F:THR164 3.7 16.4 1.0
CA F:HIS162 3.8 11.3 1.0
CB F:THR164 3.8 14.8 1.0
CD1 F:PHE170 3.8 16.2 1.0
CG F:GLN161 3.9 14.7 1.0
C F:HIS162 3.9 11.9 1.0
N F:TRP163 3.9 13.7 1.0
O F:HOH432 3.9 24.9 1.0
N F:HIS162 4.1 12.2 1.0
CD F:GLN161 4.1 13.1 1.0
CA F:THR164 4.2 14.1 1.0
OG1 F:THR164 4.2 14.5 1.0
C F:GLN161 4.3 12.0 1.0
O F:GLN161 4.3 13.3 1.0
CG F:ASN166 4.4 15.9 1.0
C F:THR164 4.4 15.9 1.0
CD2 F:TYR169 4.5 14.4 1.0
O F:HIS162 4.5 14.6 1.0
OH F:TYR19 4.6 16.1 1.0
CB F:TYR169 4.6 16.2 1.0
CB F:GLN161 4.6 11.9 1.0
OD1 F:ASN166 4.7 21.1 1.0
C F:TRP163 4.7 12.5 1.0
ND1 F:HIS162 4.8 21.2 1.0
CA F:TRP163 4.8 11.7 1.0
CE1 F:TYR19 4.8 14.2 1.0
CG2 F:THR164 4.9 15.1 1.0
CZ F:PHE170 4.9 18.3 1.0
CG F:TYR169 5.0 16.4 1.0

Reference:

F.Watanabe, F.Yu, A.Ohtaki, Y.Yamanaka, K.Noguchi, M.Yohda, M.Odaka. Crystal Structures of Halohydrin Hydrogen-Halide-Lyases From Corynebacterium Sp. N-1074 Proteins V. 83 2230 2015.
ISSN: ESSN 1097-0134
PubMed: 26422370
DOI: 10.1002/PROT.24938
Page generated: Fri Jul 26 04:32:12 2024

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