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Chlorine in PDB 3dp1: Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3N

Protein crystallography data

The structure of Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3N, PDB code: 3dp1 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 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.853, 100.210, 186.112, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 23.5

Other elements in 3dp1:

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

Bromine (Br) 4 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 3N (pdb code 3dp1). 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 3N, PDB code: 3dp1:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 3dp1

Go back to Chlorine Binding Sites List in 3dp1
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 3N


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 3N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl160

b:29.3
occ:1.00
 N A:GLY67 3.0 10.2 1.0
O B:HOH173 3.2 11.8 1.0
O B:HOH241 3.3 27.3 1.0
CE1 A:HIS58 3.6 13.7 1.0
NE2 A:HIS58 3.6 12.6 1.0
CA A:PRO66 3.8 11.2 1.0
C A:PRO66 3.9 11.1 1.0
O B:HOH180 3.9 15.1 1.0
CA A:GLY67 3.9 10.4 1.0
O B:HOH205 4.0 31.6 1.0
O A:HOH221 4.0 23.3 1.0
O A:PHE65 4.4 12.8 1.0
N A:PRO66 4.7 11.0 1.0
CB A:PRO66 4.7 9.6 1.0
ND1 A:HIS58 4.8 10.9 1.0
CG2 A:ILE64 4.9 12.8 1.0
C A:PHE65 4.9 11.8 1.0
CD2 A:HIS58 5.0 12.4 1.0

Chlorine binding site 2 out of 6 in 3dp1

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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 3N


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 3N within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl160

b:49.3
occ:1.00
 O B:HOH212 3.0 24.0 1.0
N B:GLY67 3.1 11.1 1.0
O A:HOH166 3.1 9.3 1.0
CE1 B:HIS58 3.4 11.7 1.0
NE2 B:HIS58 3.6 12.1 1.0
CA B:PRO66 3.8 9.9 1.0
C B:PRO66 3.9 11.4 1.0
CA B:GLY67 3.9 9.7 1.0
O A:HOH161 4.0 10.6 1.0
O B:HOH209 4.3 18.8 1.0
O B:PHE65 4.3 13.4 1.0
CD1 A:PHE101 4.3 33.8 1.0
CE1 A:PHE101 4.5 34.5 1.0
ND1 B:HIS58 4.7 9.2 1.0
N B:PRO66 4.8 10.1 1.0
CB B:PRO66 4.8 9.6 1.0
CG2 B:ILE64 4.9 16.2 1.0
CD2 B:HIS58 4.9 9.7 1.0
C B:PHE65 4.9 11.9 1.0

Chlorine binding site 3 out of 6 in 3dp1

Go back to Chlorine Binding Sites List in 3dp1
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 3N


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 3N within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl160

b:30.3
occ:1.00
 O D:HOH228 3.0 35.2 1.0
N C:GLY67 3.2 14.2 1.0
O D:HOH163 3.3 11.7 1.0
CB D:PHE101 3.7 22.8 1.0
CA C:GLY67 3.9 14.1 1.0
CE1 C:HIS58 3.9 14.0 1.0
CD1 D:PHE101 4.0 23.0 1.0
N D:PHE101 4.0 24.6 1.0
NE2 C:HIS58 4.1 13.6 1.0
O D:HOH168 4.1 15.5 1.0
C C:PRO66 4.2 14.0 1.0
CA C:PRO66 4.3 13.6 1.0
CG D:PHE101 4.4 23.3 1.0
O C:HOH202 4.5 14.4 1.0
CA D:PHE101 4.5 23.0 1.0
O C:PHE65 4.6 14.7 1.0
CG2 C:ILE64 4.9 18.6 1.0

Chlorine binding site 4 out of 6 in 3dp1

Go back to Chlorine Binding Sites List in 3dp1
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 3N


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 3N within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl160

b:42.3
occ:1.00
 N D:GLY67 3.1 12.3 1.0
O C:HOH162 3.1 10.9 1.0
CE1 D:HIS58 3.6 12.7 1.0
NE2 D:HIS58 3.7 13.1 1.0
CA D:PRO66 3.8 13.1 1.0
CA D:GLY67 3.9 12.0 1.0
C D:PRO66 3.9 12.7 1.0
O C:HOH166 4.1 15.8 1.0
O D:HOH206 4.3 18.1 1.0
O C:HOH227 4.5 28.4 1.0
O D:PHE65 4.5 15.4 1.0
CB D:PRO66 4.8 12.3 1.0
ND1 D:HIS58 4.8 14.2 1.0
N D:PRO66 4.8 11.2 1.0

Chlorine binding site 5 out of 6 in 3dp1

Go back to Chlorine Binding Sites List in 3dp1
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 3N


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 3N within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl160

b:47.3
occ:1.00
 O F:HOH223 2.8 27.5 1.0
N E:GLY67 3.4 12.0 1.0
CE1 E:HIS58 3.6 13.9 1.0
O F:HOH170 3.7 19.1 1.0
NE2 E:HIS58 3.8 12.6 1.0
O F:HOH171 3.8 15.3 1.0
N F:PHE101 3.8 22.0 1.0
CB F:PHE101 3.9 20.7 1.0
O F:HOH213 4.0 32.5 1.0
CA E:GLY67 4.2 11.8 1.0
CA E:PRO66 4.3 12.2 1.0
C E:PRO66 4.3 12.1 1.0
CD2 F:PHE101 4.4 20.8 1.0
O E:HOH207 4.5 21.8 1.0
CA F:PHE101 4.5 21.4 1.0
CA F:TYR100 4.6 24.2 1.0
O F:VAL99 4.6 25.6 1.0
O E:PHE65 4.7 13.9 1.0
CG F:PHE101 4.7 21.2 1.0
C F:TYR100 4.7 23.0 1.0
CG2 E:ILE64 4.7 15.6 1.0
ND1 E:HIS58 4.9 12.8 1.0

Chlorine binding site 6 out of 6 in 3dp1

Go back to Chlorine Binding Sites List in 3dp1
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 3N


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 3N within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl160

b:34.2
occ:1.00
 O E:HOH212 2.7 18.6 1.0
N F:GLY67 3.3 14.1 1.0
O E:HOH204 3.4 26.4 1.0
O E:HOH175 3.6 12.3 1.0
CE1 F:HIS58 3.8 15.8 1.0
N E:PHE101 3.9 21.5 1.0
CA F:GLY67 4.0 12.7 1.0
CB E:PHE101 4.0 20.6 1.0
NE2 F:HIS58 4.0 14.7 1.0
O E:HOH188 4.1 20.5 1.0
CD2 E:PHE101 4.2 20.7 1.0
C F:PRO66 4.3 14.1 1.0
O E:HOH205 4.3 14.3 1.0
CA F:PRO66 4.3 14.6 1.0
CA E:PHE101 4.6 19.6 1.0
CG E:PHE101 4.6 20.7 1.0
O F:PHE65 4.7 15.0 1.0
CA E:TYR100 4.7 22.9 1.0
O E:VAL99 4.8 26.3 1.0
CG2 F:ILE64 4.8 12.8 1.0
C E:TYR100 4.8 22.4 1.0
O F:HOH169 5.0 14.0 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 18:26:56 2024

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