Atomistry » Chlorine » PDB 3dna-3dzc » 3dp2
Atomistry »
  Chlorine »
    PDB 3dna-3dzc »
      3dp2 »

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

Go back to Chlorine Binding Sites List in 3dp2
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: Fri Jul 11 04:36:11 2025

Last articles

Na in 8AD5
Na in 8AD0
Na in 8ACY
Na in 8ACR
Na in 8A9S
Na in 8A8O
Na in 8A9O
Na in 8A9D
Na in 8A5B
Na in 8A66
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy