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Chlorine in PDB 3dp2: Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3J

Protein crystallography data

The structure of Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3J, PDB code: 3dp2 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 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.970, 100.323, 186.417, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 23

Other elements in 3dp2:

The structure of Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3J 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 3J (pdb code 3dp2). 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 3J, PDB code: 3dp2:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 3dp2

Go back to Chlorine Binding Sites List in 3dp2
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 3J


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

b:31.4
occ:1.00
 N A:GLY67 3.2 10.5 1.0
O B:HOH204 3.2 32.8 1.0
O B:HOH167 3.3 9.4 1.0
O B:HOH188 3.4 21.6 1.0
CE1 A:HIS58 3.5 13.6 1.0
NE2 A:HIS58 3.6 12.5 1.0
CA A:PRO66 3.9 12.9 1.0
O B:HOH187 4.0 17.7 1.0
C A:PRO66 4.0 13.9 1.0
CA A:GLY67 4.0 11.2 1.0
O A:HOH216 4.2 20.9 1.0
O B:HOH211 4.3 31.2 1.0
O A:PHE65 4.5 13.8 1.0
N A:PRO66 4.8 13.3 1.0
ND1 A:HIS58 4.8 12.3 1.0
CB A:PRO66 4.9 12.9 1.0
CG2 A:ILE64 4.9 16.3 1.0
CD2 A:HIS58 5.0 12.3 1.0

Chlorine binding site 2 out of 6 in 3dp2

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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 3J


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

b:53.9
occ:1.00
 O B:HOH213 2.9 16.2 1.0
O A:HOH168 2.9 11.7 1.0
N B:GLY67 3.0 9.4 1.0
CE1 B:HIS58 3.7 9.9 1.0
CA B:GLY67 3.8 7.9 1.0
NE2 B:HIS58 3.8 9.9 1.0
CA B:PRO66 3.9 9.8 1.0
C B:PRO66 3.9 11.1 1.0
O B:HOH212 4.2 10.7 1.0
O A:HOH167 4.2 9.8 1.0
O B:PHE65 4.4 13.0 1.0
CD1 A:PHE101 4.5 30.7 1.0
CB B:PRO66 4.9 10.0 1.0
N B:PRO66 4.9 10.5 1.0
ND1 B:HIS58 4.9 9.9 1.0
CB A:PHE101 4.9 28.1 1.0
O B:HOH169 5.0 12.0 1.0
CG2 B:ILE64 5.0 15.3 1.0
C B:GLY67 5.0 8.1 1.0

Chlorine binding site 3 out of 6 in 3dp2

Go back to Chlorine Binding Sites List in 3dp2
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 3J


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

b:33.6
occ:1.00
 N C:GLY67 3.1 14.8 1.0
O D:HOH188 3.1 27.2 1.0
O D:HOH163 3.2 9.3 1.0
CA C:GLY67 3.8 12.4 1.0
CE1 C:HIS58 3.8 12.6 1.0
CB D:PHE101 3.9 20.9 1.0
CD2 D:PHE101 4.1 21.4 1.0
C C:PRO66 4.1 13.9 1.0
O C:HOH168 4.1 14.2 1.0
CA C:PRO66 4.1 12.8 1.0
NE2 C:HIS58 4.2 12.3 1.0
N D:PHE101 4.2 22.7 1.0
O D:HOH202 4.3 13.2 1.0
CG D:PHE101 4.5 21.4 1.0
O C:PHE65 4.5 14.4 1.0
CA D:PHE101 4.7 20.8 1.0
CG2 C:ILE64 4.9 17.6 1.0

Chlorine binding site 4 out of 6 in 3dp2

Go back to Chlorine Binding Sites List in 3dp2
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 3J


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

b:47.6
occ:1.00
 N D:GLY67 3.0 10.5 1.0
O D:HOH162 3.0 5.8 1.0
CE1 D:HIS58 3.7 14.4 1.0
NE2 D:HIS58 3.8 13.8 1.0
CA D:GLY67 3.9 8.7 1.0
CA D:PRO66 3.9 11.7 1.0
C D:PRO66 3.9 11.6 1.0
O C:HOH173 4.1 16.8 1.0
O C:HOH226 4.6 30.1 1.0
O D:PHE65 4.7 14.4 1.0
O D:HOH215 4.8 25.6 1.0
CB D:PRO66 4.8 11.8 1.0
N D:PRO66 4.9 11.8 1.0
ND1 D:HIS58 4.9 14.8 1.0

Chlorine binding site 5 out of 6 in 3dp2

Go back to Chlorine Binding Sites List in 3dp2
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 3J


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

b:43.8
occ:1.00
 N E:GLY67 3.2 13.5 1.0
O F:HOH189 3.5 21.6 1.0
O F:HOH163 3.6 9.1 1.0
CE1 E:HIS58 3.7 12.0 1.0
N F:PHE101 3.9 18.8 1.0
CA E:GLY67 3.9 11.0 1.0
CB F:PHE101 4.0 18.8 1.0
NE2 E:HIS58 4.0 11.0 1.0
CA E:PRO66 4.1 13.3 1.0
C E:PRO66 4.1 14.2 1.0
O F:HOH177 4.2 13.8 1.0
O E:HOH210 4.3 15.4 1.0
CD1 F:PHE101 4.4 19.4 1.0
O E:PHE65 4.5 16.0 1.0
CA F:PHE101 4.6 18.4 1.0
CG F:PHE101 4.7 20.0 1.0
CA F:TYR100 4.7 21.1 1.0
CG2 E:ILE64 4.7 14.1 1.0
O F:VAL99 4.8 23.5 1.0
C F:TYR100 4.8 20.7 1.0
O E:HOH170 4.9 16.9 1.0
ND1 E:HIS58 5.0 12.1 1.0

Chlorine binding site 6 out of 6 in 3dp2

Go back to Chlorine Binding Sites List in 3dp2
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 3J


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

b:44.4
occ:1.00
 O E:HOH217 2.8 18.0 1.0
N F:GLY67 3.2 11.2 1.0
O E:HOH194 3.3 17.7 1.0
O E:HOH164 3.7 8.5 1.0
CA F:GLY67 3.8 9.0 1.0
CB E:PHE101 3.8 20.4 1.0
CE1 F:HIS58 3.9 15.0 1.0
N E:PHE101 4.0 20.4 1.0
NE2 F:HIS58 4.1 14.7 1.0
C F:PRO66 4.2 10.8 1.0
CD2 E:PHE101 4.2 19.1 1.0
CA F:PRO66 4.2 12.0 1.0
O F:HOH201 4.3 10.4 1.0
O E:HOH184 4.4 24.2 1.0
CG E:PHE101 4.5 19.6 1.0
O F:PHE65 4.6 15.3 1.0
CA E:PHE101 4.6 19.6 1.0
O F:HOH175 4.8 16.0 1.0
CG2 F:ILE64 4.9 12.1 1.0
O E:VAL99 4.9 24.4 1.0
CA E:TYR100 4.9 20.8 1.0
C E:TYR100 4.9 21.1 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 18:27:52 2024

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