Atomistry » Chlorine » PDB 3dna-3dzc » 3dp3
Atomistry »
  Chlorine »
    PDB 3dna-3dzc »
      3dp3 »

Chlorine in PDB 3dp3: Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3Q

Protein crystallography data

The structure of Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3Q, PDB code: 3dp3 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 (°) 73.897, 100.226, 186.630, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 23.1

Other elements in 3dp3:

The structure of Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3Q 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 3Q (pdb code 3dp3). 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 3Q, PDB code: 3dp3:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 3dp3

Go back to Chlorine Binding Sites List in 3dp3
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 3Q


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

b:41.9
occ:1.00
N A:GLY67 3.0 12.9 1.0
O B:HOH166 3.1 15.4 1.0
O B:HOH231 3.4 28.1 1.0
CE1 A:HIS58 3.5 15.0 1.0
NE2 A:HIS58 3.5 13.9 1.0
CA A:PRO66 3.6 14.4 1.0
O B:HOH167 3.8 21.8 1.0
C A:PRO66 3.8 13.9 1.0
CA A:GLY67 3.9 12.9 1.0
O A:HOH222 4.3 26.7 1.0
O A:HOH232 4.5 37.7 1.0
O A:PHE65 4.5 15.0 1.0
CB A:PRO66 4.5 12.8 1.0
N A:PRO66 4.6 12.2 1.0
ND1 A:HIS58 4.8 13.3 1.0
CD2 A:HIS58 4.8 14.4 1.0
CG2 A:ILE64 4.9 15.9 1.0
C A:PHE65 4.9 13.6 1.0

Chlorine binding site 2 out of 6 in 3dp3

Go back to Chlorine Binding Sites List in 3dp3
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 3Q


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

b:58.3
occ:1.00
O B:HOH200 2.9 26.3 1.0
O A:HOH166 3.1 15.4 1.0
N B:GLY67 3.1 14.9 1.0
CE1 B:HIS58 3.5 12.2 1.0
NE2 B:HIS58 3.7 13.9 1.0
O A:HOH164 3.8 15.6 1.0
CA B:PRO66 3.9 14.6 1.0
CA B:GLY67 3.9 12.8 1.0
C B:PRO66 4.0 15.2 1.0
O B:HOH204 4.3 23.4 1.0
O B:PHE65 4.4 15.3 1.0
ND1 B:HIS58 4.7 11.9 1.0
CD1 A:PHE101 4.8 35.9 1.0
CG2 B:ILE64 4.8 15.9 1.0
N B:PRO66 4.8 13.4 1.0
CB B:PRO66 4.9 13.9 1.0

Chlorine binding site 3 out of 6 in 3dp3

Go back to Chlorine Binding Sites List in 3dp3
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 3Q


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

b:34.3
occ:1.00
O D:HOH162 2.9 17.4 1.0
N C:GLY67 3.2 15.7 1.0
CD1 D:PHE101 3.8 29.1 1.0
CA C:GLY67 3.9 15.2 1.0
CE1 C:HIS58 3.9 18.7 1.0
CB D:PHE101 4.0 28.3 1.0
NE2 C:HIS58 4.0 18.6 1.0
O D:HOH164 4.0 18.3 1.0
N D:PHE101 4.1 29.9 1.0
C C:PRO66 4.2 15.6 1.0
CA C:PRO66 4.2 15.4 1.0
CG D:PHE101 4.4 29.2 1.0
O C:HOH201 4.5 17.6 1.0
CA D:PHE101 4.7 28.4 1.0
O C:PHE65 4.8 16.4 1.0
CE1 D:PHE101 4.9 29.6 1.0
CA D:TYR100 4.9 33.9 1.0

Chlorine binding site 4 out of 6 in 3dp3

Go back to Chlorine Binding Sites List in 3dp3
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 3Q


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

b:60.5
occ:1.00
O C:HOH204 3.0 35.9 1.0
O C:HOH168 3.1 14.2 1.0
N D:GLY67 3.1 13.6 1.0
CE1 D:HIS58 3.6 17.2 1.0
NE2 D:HIS58 3.8 17.3 1.0
CA D:PRO66 3.9 13.6 1.0
CA D:GLY67 4.0 13.1 1.0
C D:PRO66 4.0 14.6 1.0
O C:HOH166 4.1 20.1 1.0
O D:HOH205 4.2 24.0 1.0
O C:HOH213 4.4 34.7 1.0
O D:PHE65 4.6 15.7 1.0
CB D:PRO66 4.8 13.6 1.0
ND1 D:HIS58 4.8 18.2 1.0
N D:PRO66 4.9 13.3 1.0

Chlorine binding site 5 out of 6 in 3dp3

Go back to Chlorine Binding Sites List in 3dp3
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 3Q


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

b:41.0
occ:1.00
O F:HOH236 2.8 30.6 1.0
N E:GLY67 3.2 16.4 1.0
O F:HOH192 3.4 16.9 1.0
NE2 E:HIS58 3.6 16.2 1.0
CE1 E:HIS58 3.7 17.4 1.0
CA E:GLY67 3.9 15.8 1.0
O F:HOH200 4.0 19.3 1.0
N F:PHE101 4.0 24.6 1.0
CB F:PHE101 4.0 23.7 1.0
CA E:PRO66 4.2 16.1 1.0
C E:PRO66 4.2 16.7 1.0
CD2 F:PHE101 4.2 25.4 1.0
O E:HOH203 4.5 18.6 1.0
CG F:PHE101 4.6 25.3 1.0
O E:PHE65 4.7 16.9 1.0
CA F:PHE101 4.7 23.8 1.0
O F:VAL99 4.7 30.0 1.0
CG2 E:ILE64 4.8 15.9 1.0
CA F:TYR100 4.8 28.1 1.0
C F:TYR100 4.9 26.4 1.0
O E:HOH165 4.9 15.8 1.0
ND1 E:HIS58 4.9 16.0 1.0
CD2 E:HIS58 5.0 16.2 1.0

Chlorine binding site 6 out of 6 in 3dp3

Go back to Chlorine Binding Sites List in 3dp3
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 3Q


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

b:37.7
occ:1.00
O E:HOH216 2.8 20.5 1.0
N F:GLY67 3.1 16.4 1.0
O E:HOH164 3.4 10.8 1.0
O E:HOH222 3.6 21.5 1.0
CE1 F:HIS58 3.8 17.9 1.0
CA F:GLY67 3.8 15.7 1.0
CB E:PHE101 3.9 23.7 1.0
NE2 F:HIS58 4.0 17.1 1.0
N E:PHE101 4.0 24.0 1.0
O E:HOH204 4.1 21.7 1.0
C F:PRO66 4.1 16.0 1.0
CA F:PRO66 4.2 17.3 1.0
CD2 E:PHE101 4.2 23.7 1.0
O F:HOH228 4.3 17.6 1.0
CG E:PHE101 4.6 22.8 1.0
CA E:PHE101 4.6 22.9 1.0
O F:PHE65 4.8 18.2 1.0
O E:VAL99 4.9 29.6 1.0
CA E:TYR100 5.0 25.7 1.0
C E:TYR100 5.0 25.4 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 04:36:26 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy