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Chlorine in PDB 3b7j: Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(Fabz) From Helicobacter Pylori Complexed with Juglone

Protein crystallography data

The structure of Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(Fabz) From Helicobacter Pylori Complexed with Juglone, PDB code: 3b7j was solved by L.Zhang, Y.H.Kong, D.Wu, X.Shen, H.L.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 (°) 73.983, 100.369, 186.236, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 22.8

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(Fabz) From Helicobacter Pylori Complexed with Juglone (pdb code 3b7j). 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 Complexed with Juglone, PDB code: 3b7j:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 3b7j

Go back to Chlorine Binding Sites List in 3b7j
Chlorine binding site 1 out of 6 in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(Fabz) From Helicobacter Pylori Complexed with Juglone


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 Complexed with Juglone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl160

b:32.4
occ:1.00
 N A:GLY67 3.0 12.3 1.0
O B:HOH165 3.2 14.6 1.0
O B:HOH195 3.4 22.2 1.0
CE1 A:HIS58 3.6 20.7 1.0
NE2 A:HIS58 3.6 18.1 1.0
CA A:PRO66 3.7 14.2 1.0
O B:HOH184 3.9 17.8 1.0
C A:PRO66 3.9 14.6 1.0
CA A:GLY67 4.0 12.3 1.0
CAD B:JUG163 4.1 52.6 1.0
O A:HOH162 4.2 25.7 1.0
O B:HOH232 4.3 34.8 1.0
O A:PHE65 4.4 15.0 1.0
CB A:PRO66 4.7 14.6 1.0
CAE B:JUG163 4.7 52.2 1.0
N A:PRO66 4.7 13.6 1.0
ND1 A:HIS58 4.8 18.9 1.0
CG2 A:ILE64 4.8 18.5 1.0
C A:PHE65 4.9 13.6 1.0
CD2 A:HIS58 4.9 18.2 1.0
O A:HOH168 4.9 14.5 1.0
CAH B:JUG163 5.0 52.2 1.0

Chlorine binding site 2 out of 6 in 3b7j

Go back to Chlorine Binding Sites List in 3b7j
Chlorine binding site 2 out of 6 in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(Fabz) From Helicobacter Pylori Complexed with Juglone


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 Complexed with Juglone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl160

b:54.5
occ:1.00
 O B:HOH211 2.8 23.3 1.0
N B:GLY67 3.1 13.0 1.0
O A:HOH164 3.5 18.8 1.0
CE1 B:HIS58 3.5 12.1 1.0
NE2 B:HIS58 3.8 13.9 1.0
CA B:PRO66 3.9 12.8 1.0
CA B:GLY67 4.0 12.4 1.0
C B:PRO66 4.0 14.6 1.0
O B:HOH213 4.0 16.8 1.0
O A:HOH163 4.2 11.7 1.0
O B:PHE65 4.3 14.7 1.0
CG2 B:ILE64 4.6 16.0 1.0
CD1 A:PHE101 4.7 36.0 1.0
ND1 B:HIS58 4.8 10.9 1.0
N B:PRO66 4.8 13.7 1.0
CB B:PRO66 4.9 13.5 1.0
O B:HOH169 4.9 19.0 1.0
C B:PHE65 5.0 13.7 1.0

Chlorine binding site 3 out of 6 in 3b7j

Go back to Chlorine Binding Sites List in 3b7j
Chlorine binding site 3 out of 6 in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(Fabz) From Helicobacter Pylori Complexed with Juglone


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 Complexed with Juglone within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl160

b:29.9
occ:1.00
 O D:HOH221 3.0 27.4 1.0
O D:HOH190 3.1 15.1 1.0
N C:GLY67 3.1 14.8 1.0
CA C:GLY67 3.8 14.2 1.0
CE1 C:HIS58 3.9 14.1 1.0
CB D:PHE101 3.9 27.1 1.0
CD2 D:PHE101 4.0 28.5 1.0
NE2 C:HIS58 4.0 14.3 1.0
O D:HOH193 4.1 20.2 1.0
N D:PHE101 4.1 29.0 1.0
C C:PRO66 4.1 15.4 1.0
CA C:PRO66 4.1 14.2 1.0
O C:HOH202 4.4 15.0 1.0
CG D:PHE101 4.5 28.3 1.0
O C:PHE65 4.6 14.8 1.0
CA D:PHE101 4.7 26.4 1.0
O D:VAL99 4.9 37.4 1.0
O C:HOH165 5.0 11.7 1.0
C C:GLY67 5.0 15.3 1.0

Chlorine binding site 4 out of 6 in 3b7j

Go back to Chlorine Binding Sites List in 3b7j
Chlorine binding site 4 out of 6 in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(Fabz) From Helicobacter Pylori Complexed with Juglone


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 Complexed with Juglone within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl160

b:39.4
occ:1.00
 O D:HOH217 3.1 25.2 1.0
N D:GLY67 3.2 16.1 1.0
O D:HOH189 3.2 15.0 1.0
CE1 D:HIS58 3.6 18.6 1.0
NE2 D:HIS58 3.7 17.5 1.0
CA D:PRO66 3.9 14.3 1.0
C D:PRO66 4.1 15.6 1.0
O C:HOH164 4.1 17.3 1.0
CA D:GLY67 4.1 14.9 1.0
O D:HOH249 4.5 30.9 1.0
O D:PHE65 4.7 14.3 1.0
CB D:PRO66 4.8 14.9 1.0
ND1 D:HIS58 4.9 18.4 1.0
N D:PRO66 4.9 14.2 1.0

Chlorine binding site 5 out of 6 in 3b7j

Go back to Chlorine Binding Sites List in 3b7j
Chlorine binding site 5 out of 6 in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(Fabz) From Helicobacter Pylori Complexed with Juglone


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 Complexed with Juglone within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl160

b:37.8
occ:1.00
 N E:GLY67 3.1 14.7 1.0
O F:HOH165 3.3 15.2 1.0
O F:HOH196 3.6 28.1 1.0
CE1 E:HIS58 3.7 14.7 1.0
CA E:GLY67 3.9 12.7 1.0
NE2 E:HIS58 3.9 14.0 1.0
CB F:PHE101 3.9 21.9 1.0
CA E:PRO66 3.9 13.8 1.0
N F:PHE101 4.0 23.1 1.0
C E:PRO66 4.0 14.8 1.0
O F:HOH185 4.0 17.9 1.0
CD1 F:PHE101 4.2 23.5 1.0
O E:HOH207 4.4 14.3 1.0
O E:PHE65 4.5 16.0 1.0
CG F:PHE101 4.6 22.5 1.0
CA F:PHE101 4.6 22.0 1.0
CG2 E:ILE64 4.9 16.5 1.0
CB E:PRO66 4.9 14.0 1.0
CA F:TYR100 4.9 26.4 1.0
O F:VAL99 4.9 29.1 1.0
C F:TYR100 4.9 25.2 1.0
ND1 E:HIS58 4.9 15.3 1.0
N E:PRO66 4.9 14.3 1.0

Chlorine binding site 6 out of 6 in 3b7j

Go back to Chlorine Binding Sites List in 3b7j
Chlorine binding site 6 out of 6 in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(Fabz) From Helicobacter Pylori Complexed with Juglone


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 Complexed with Juglone within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl160

b:35.3
occ:1.00
 O E:HOH194 3.1 24.5 1.0
N F:GLY67 3.3 13.3 1.0
N E:PHE101 3.7 24.2 1.0
CB E:PHE101 3.8 22.2 1.0
O E:HOH170 3.8 14.5 1.0
CE1 F:HIS58 4.0 16.4 1.0
CA F:GLY67 4.0 12.8 1.0
O F:HOH182 4.1 29.6 1.0
NE2 F:HIS58 4.2 15.5 1.0
O F:HOH203 4.2 13.2 1.0
CD2 E:PHE101 4.3 20.6 1.0
C F:PRO66 4.3 14.7 1.0
CA E:PHE101 4.4 22.8 1.0
CA F:PRO66 4.4 15.1 1.0
CA E:TYR100 4.5 25.0 1.0
CG E:PHE101 4.6 21.7 1.0
O F:PHE65 4.6 17.1 1.0
C E:TYR100 4.6 25.0 1.0
O E:VAL99 4.7 28.5 1.0
CG2 F:ILE64 4.9 14.5 1.0
O F:HOH171 5.0 19.2 1.0

Reference:

Y.H.Kong, L.Zhang, Z.Y.Yang, C.Han, L.H.Hu, H.L.Jiang, X.Shen. Natural Product Juglone Targets Three Key Enzymes From Helicobacter Pylori: Inhibition Assay with Crystal Structure Characterization Acta Pharmacol.Sin. V. 29 870 2008.
ISSN: ISSN 1671-4083
PubMed: 18565285
DOI: 10.1111/J.1745-7254.2008.00808.X
Page generated: Fri Jul 11 03:23:20 2025

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