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Chlorine in PDB 3dp0: Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3M

Protein crystallography data

The structure of Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3M, PDB code: 3dp0 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 (°) 74.070, 100.550, 186.487, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 23.7

Other elements in 3dp0:

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

Bromine (Br) 2 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 3M (pdb code 3dp0). 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 3M, PDB code: 3dp0:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 3dp0

Go back to Chlorine Binding Sites List in 3dp0
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 3M


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

b:37.3
occ:1.00
 N A:GLY67 3.1 18.4 1.0
O B:HOH172 3.1 15.5 1.0
O B:HOH224 3.3 23.5 1.0
NE2 A:HIS58 3.6 19.7 1.0
O B:HOH182 3.7 25.0 1.0
CE1 A:HIS58 3.7 20.4 1.0
CA A:PRO66 3.9 18.8 1.0
CA A:GLY67 3.9 18.3 1.0
O B:HOH202 3.9 26.1 1.0
C A:PRO66 3.9 19.7 1.0
O B:HOH226 4.2 31.1 1.0
O B:HOH217 4.2 28.4 1.0
O A:PHE65 4.5 21.2 1.0
CAL B:2BC162 4.5 40.6 1.0
CAI B:2BC162 4.6 39.6 1.0
N A:PRO66 4.8 18.1 1.0
CB A:PRO66 4.8 18.2 1.0
O A:HOH164 4.9 10.2 1.0
CD2 A:HIS58 4.9 19.3 1.0
ND1 A:HIS58 5.0 20.1 1.0

Chlorine binding site 2 out of 6 in 3dp0

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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 3M


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

b:50.6
occ:1.00
 O A:HOH169 2.9 17.9 1.0
O A:HOH175 3.0 30.5 1.0
N B:GLY67 3.0 15.8 1.0
CE1 B:HIS58 3.8 16.9 1.0
CA B:GLY67 3.8 14.8 1.0
O B:HOH201 3.9 19.3 1.0
C B:PRO66 3.9 16.2 1.0
CA B:PRO66 3.9 15.0 1.0
NE2 B:HIS58 4.0 17.9 1.0
O A:HOH163 4.1 10.2 1.0
O B:PHE65 4.3 17.6 1.0
CD1 A:PHE101 4.5 58.1 1.0
CG2 B:ILE64 4.8 19.0 1.0
N B:PRO66 4.9 15.8 1.0
CB B:PRO66 4.9 14.2 1.0
C B:PHE65 5.0 16.6 1.0

Chlorine binding site 3 out of 6 in 3dp0

Go back to Chlorine Binding Sites List in 3dp0
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 3M


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

b:35.8
occ:1.00
 O D:HOH197 3.1 25.3 1.0
N C:GLY67 3.2 21.8 1.0
O D:HOH161 3.3 18.5 1.0
CB D:PHE101 3.8 35.5 1.0
CA C:GLY67 3.9 18.5 1.0
CE1 C:HIS58 3.9 18.6 1.0
O C:HOH202 4.0 20.4 1.0
NE2 C:HIS58 4.1 20.0 1.0
N D:PHE101 4.2 39.8 1.0
C C:PRO66 4.2 20.8 1.0
O C:HOH168 4.2 18.1 1.0
CD2 D:PHE101 4.2 37.0 1.0
CA C:PRO66 4.2 21.1 1.0
O C:PHE65 4.5 22.6 1.0
CG D:PHE101 4.5 36.1 1.0
CA D:PHE101 4.7 36.0 1.0
O C:HOH163 5.0 9.0 1.0

Chlorine binding site 4 out of 6 in 3dp0

Go back to Chlorine Binding Sites List in 3dp0
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 3M


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

b:41.8
occ:1.00
 N D:GLY67 2.9 16.9 1.0
O D:HOH168 3.0 20.8 1.0
CE1 D:HIS58 3.7 20.5 1.0
CA D:GLY67 3.7 15.7 1.0
NE2 D:HIS58 3.8 18.9 1.0
CA D:PRO66 3.9 17.7 1.0
C D:PRO66 3.9 17.3 1.0
O C:HOH167 4.2 21.0 1.0
O D:PHE65 4.5 19.6 1.0
CB D:PRO66 4.8 17.2 1.0
N D:PRO66 4.9 17.7 1.0
C D:GLY67 4.9 16.4 1.0
N D:VAL68 4.9 16.1 1.0
ND1 D:HIS58 5.0 21.1 1.0

Chlorine binding site 5 out of 6 in 3dp0

Go back to Chlorine Binding Sites List in 3dp0
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 3M


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

b:45.1
occ:1.00
 O F:HOH195 3.1 27.1 1.0
N E:GLY67 3.4 18.9 1.0
CE1 E:HIS58 3.7 19.4 1.0
N F:PHE101 3.8 29.0 1.0
CB F:PHE101 3.9 27.8 1.0
O F:HOH162 3.9 11.3 1.0
NE2 E:HIS58 3.9 20.0 1.0
O E:HOH266 4.1 23.1 1.0
CA E:GLY67 4.1 17.1 1.0
O F:HOH164 4.2 18.1 1.0
C E:PRO66 4.3 20.2 1.0
CA E:PRO66 4.3 19.3 1.0
CA F:PHE101 4.5 28.9 1.0
O E:PHE65 4.5 21.9 1.0
O F:VAL99 4.5 32.5 1.0
CG2 E:ILE64 4.6 20.2 1.0
CA F:TYR100 4.6 31.2 1.0
O E:HOH232 4.6 14.5 1.0
CD1 F:PHE101 4.6 26.5 1.0
C F:TYR100 4.7 30.1 1.0
CG F:PHE101 4.8 26.9 1.0
CD2 F:TYR100 5.0 35.2 1.0
ND1 E:HIS58 5.0 20.1 1.0

Chlorine binding site 6 out of 6 in 3dp0

Go back to Chlorine Binding Sites List in 3dp0
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 3M


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

b:38.5
occ:1.00
 O E:HOH254 3.1 31.0 1.0
N F:GLY67 3.2 18.3 1.0
O E:HOH235 3.4 20.4 1.0
CE1 F:HIS58 3.8 24.0 1.0
O E:HOH243 3.9 30.2 1.0
NE2 F:HIS58 3.9 24.2 1.0
CA F:GLY67 3.9 16.9 1.0
CB E:PHE101 4.0 24.9 1.0
N E:PHE101 4.0 28.2 1.0
CA F:PRO66 4.1 18.2 1.0
C F:PRO66 4.1 17.6 1.0
O F:HOH197 4.2 23.2 1.0
CD2 E:PHE101 4.3 24.7 1.0
O F:PHE65 4.6 22.0 1.0
CG E:PHE101 4.7 25.5 1.0
CA E:PHE101 4.7 25.0 1.0
O E:VAL99 4.7 33.5 1.0
CA E:TYR100 4.8 29.8 1.0
C E:TYR100 4.9 28.6 1.0
O F:HOH172 5.0 22.2 1.0
CG2 F:ILE64 5.0 19.6 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 18:26:50 2024

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