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Chlorine in PDB 3doz: Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3K

Protein crystallography data

The structure of Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3K, PDB code: 3doz was solved by L.Zhang, L.He, X.Liu, H.Liu, X.Shen, H.Jiang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.737, 100.215, 186.564, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 25.5

Other elements in 3doz:

The structure of Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3K also contains other interesting chemical elements:

Bromine (Br) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3K (pdb code 3doz). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3K, PDB code: 3doz:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 3doz

Go back to Chlorine Binding Sites List in 3doz
Chlorine binding site 1 out of 6 in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3K


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 (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl160

b:54.0
occ:1.00
 N A:GLY67 3.3 16.9 1.0
O B:HOH166 3.3 18.9 1.0
O B:HOH201 3.4 18.0 1.0
CE1 A:HIS58 3.5 17.6 1.0
NE2 A:HIS58 3.5 16.8 1.0
O B:HOH212 3.8 25.5 1.0
O B:HOH170 3.9 9.4 1.0
CA A:PRO66 3.9 18.4 1.0
C A:PRO66 4.1 17.6 1.0
CA A:GLY67 4.1 16.7 1.0
O A:PHE65 4.5 18.6 1.0
CAJ B:3BE163 4.5 54.4 1.0
CAH B:3BE163 4.6 55.2 1.0
ND1 A:HIS58 4.8 17.9 1.0
O B:HOH191 4.8 24.2 1.0
CB A:PRO66 4.8 17.2 1.0
CD2 A:HIS58 4.8 18.0 1.0
N A:PRO66 4.8 16.9 1.0
CG2 A:ILE64 4.9 18.4 1.0
O A:HOH184 4.9 21.9 1.0

Chlorine binding site 2 out of 6 in 3doz

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Chlorine binding site 2 out of 6 in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3K


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 (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl160

b:58.5
occ:1.00
 O A:HOH171 2.7 26.2 1.0
O A:HOH168 3.2 11.8 1.0
O A:HOH164 3.6 14.8 1.0
N B:GLY67 3.6 20.5 1.0
CE1 B:HIS58 3.8 13.6 1.0
NE2 B:HIS58 4.1 12.4 1.0
CA B:GLY67 4.3 18.6 1.0
O B:HOH205 4.4 13.9 1.0
CA B:PRO66 4.5 20.9 1.0
C B:PRO66 4.5 20.6 1.0
CD2 A:PHE101 4.7 36.4 1.0
CE2 A:PHE101 4.7 38.0 1.0
CD1 A:TYR100 4.7 33.0 1.0
O B:PHE65 4.8 22.0 1.0
CG2 B:ILE64 4.8 21.3 1.0
N A:PHE101 5.0 29.1 1.0

Chlorine binding site 3 out of 6 in 3doz

Go back to Chlorine Binding Sites List in 3doz
Chlorine binding site 3 out of 6 in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3K


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 (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3K within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl160

b:35.5
occ:1.00
 O D:HOH181 2.9 29.8 1.0
N C:GLY67 3.2 20.1 1.0
O D:HOH165 3.4 14.2 1.0
CE1 C:HIS58 3.9 19.0 1.0
NE2 C:HIS58 3.9 18.9 1.0
CA C:GLY67 3.9 18.5 1.0
N D:PHE101 4.0 27.9 1.0
CB D:PHE101 4.1 28.0 1.0
CD1 D:PHE101 4.2 28.6 1.0
C C:PRO66 4.2 20.1 1.0
O C:HOH173 4.3 20.1 1.0
CA C:PRO66 4.3 19.9 1.0
O D:HOH169 4.3 22.3 1.0
CA D:TYR100 4.7 30.7 1.0
CG D:PHE101 4.7 28.4 1.0
O C:PHE65 4.7 19.4 1.0
CB D:TYR100 4.7 34.3 1.0
CA D:PHE101 4.7 26.6 1.0
C D:TYR100 4.9 28.9 1.0
CG2 C:ILE64 4.9 17.8 1.0

Chlorine binding site 4 out of 6 in 3doz

Go back to Chlorine Binding Sites List in 3doz
Chlorine binding site 4 out of 6 in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3K


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 (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3K within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl160

b:43.0
occ:1.00
 O C:HOH191 3.0 32.4 1.0
O C:HOH167 3.2 12.5 1.0
N D:GLY67 3.4 17.7 1.0
CE1 D:HIS58 3.6 17.9 1.0
NE2 D:HIS58 3.8 16.3 1.0
O D:HOH162 3.8 19.4 1.0
O D:HOH191 4.1 14.9 1.0
CA D:PRO66 4.1 17.2 1.0
CA D:GLY67 4.2 16.1 1.0
C D:PRO66 4.3 17.6 1.0
O D:PHE65 4.6 19.0 1.0
ND1 D:HIS58 4.9 18.6 1.0

Chlorine binding site 5 out of 6 in 3doz

Go back to Chlorine Binding Sites List in 3doz
Chlorine binding site 5 out of 6 in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3K


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3K within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl160

b:44.1
occ:1.00
 O F:HOH208 3.1 36.1 1.0
N E:GLY67 3.2 20.2 1.0
NE2 E:HIS58 3.6 16.9 1.0
CE1 E:HIS58 3.6 17.9 1.0
O F:HOH189 3.6 17.8 1.0
O F:HOH163 3.7 8.8 1.0
CA E:GLY67 4.0 19.8 1.0
CA E:PRO66 4.0 19.6 1.0
CB F:PHE101 4.0 24.5 1.0
C E:PRO66 4.1 19.8 1.0
N F:PHE101 4.1 24.6 1.0
CD2 F:PHE101 4.3 26.5 1.0
O E:PHE65 4.5 20.5 1.0
CG2 E:ILE64 4.6 22.5 1.0
CG F:PHE101 4.7 25.6 1.0
CA F:PHE101 4.7 24.0 1.0
O F:VAL99 4.8 28.0 1.0
O E:HOH180 4.8 15.2 1.0
ND1 E:HIS58 4.9 16.6 1.0
O E:HOH203 4.9 24.1 1.0
CD2 E:HIS58 4.9 18.2 1.0
CA F:TYR100 4.9 27.5 1.0
CB E:PRO66 5.0 20.0 1.0
N E:PRO66 5.0 20.5 1.0

Chlorine binding site 6 out of 6 in 3doz

Go back to Chlorine Binding Sites List in 3doz
Chlorine binding site 6 out of 6 in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3K


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3K within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl160

b:33.6
occ:1.00
 O E:HOH173 2.9 20.4 1.0
O E:HOH171 3.3 24.1 1.0
N F:GLY67 3.4 19.2 1.0
N E:PHE101 3.7 25.6 1.0
CB E:PHE101 3.7 23.8 1.0
O E:HOH165 3.9 25.6 1.0
CA F:GLY67 4.0 18.2 1.0
O E:HOH172 4.1 9.3 1.0
CE1 F:HIS58 4.1 19.9 1.0
CD1 E:PHE101 4.1 23.8 1.0
NE2 F:HIS58 4.3 20.3 1.0
CA E:PHE101 4.3 25.0 1.0
CG E:PHE101 4.4 23.5 1.0
C F:PRO66 4.5 18.8 1.0
CA E:TYR100 4.5 25.7 1.0
C E:TYR100 4.6 25.9 1.0
CA F:PRO66 4.6 20.5 1.0
O E:VAL99 4.6 25.9 1.0
O F:PHE65 4.8 21.6 1.0
CG2 F:ILE64 4.8 19.5 1.0
O F:HOH169 4.9 18.3 1.0

Reference:

L.He, L.Zhang, X.Liu, X.Li, M.Zheng, H.Li, K.Yu, K.Chen, X.Shen, H.Jiang, H.Liu. Discovering Potent Inhibitors Against the Beta-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) of Helicobacter Pylori: Structure-Based Design, Synthesis, Bioassay, and Crystal Structure Determination. J.Med.Chem. V. 52 2465 2009.
ISSN: ISSN 0022-2623
PubMed: 19309082
DOI: 10.1021/JM8015602
Page generated: Sat Jul 20 18:25:57 2024

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