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Chlorine in PDB 3cf9: Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Apigenin

Protein crystallography data

The structure of Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Apigenin, PDB code: 3cf9 was solved by L.Zhang, D.Wu, W.Liu, X.Shen, H.Jiang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.925, 100.331, 187.166, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 20.1

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 Apigenin (pdb code 3cf9). 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 Apigenin, PDB code: 3cf9:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 3cf9

Go back to Chlorine Binding Sites List in 3cf9
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 Apigenin


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

b:45.2
occ:1.00
 N A:GLY67 3.1 14.5 1.0
O B:HOH168 3.2 19.1 1.0
CE1 A:HIS58 3.4 17.7 1.0
NE2 A:HIS58 3.6 18.5 1.0
O A:HOH180 3.6 20.8 1.0
O A:HOH219 3.6 38.0 1.0
CA A:PRO66 3.7 15.1 1.0
C A:PRO66 3.9 14.4 1.0
CA A:GLY67 4.0 14.0 1.0
OAA A:AGI161 4.5 46.8 1.0
O A:PHE65 4.5 17.0 1.0
CB A:PRO66 4.6 15.1 1.0
ND1 A:HIS58 4.7 19.0 1.0
N A:PRO66 4.7 16.4 1.0
CG2 A:ILE64 4.9 13.1 1.0
CD2 A:HIS58 4.9 19.0 1.0
CAJ A:AGI161 4.9 46.6 1.0
C A:PHE65 5.0 16.4 1.0

Chlorine binding site 2 out of 6 in 3cf9

Go back to Chlorine Binding Sites List in 3cf9
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 Apigenin


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

b:66.1
occ:1.00
 O A:HOH165 3.2 16.3 1.0
N B:GLY67 3.3 12.1 1.0
CE1 B:HIS58 3.4 12.2 1.0
NE2 B:HIS58 3.6 11.9 1.0
CA B:PRO66 3.9 12.1 1.0
O A:HOH162 3.9 10.2 1.0
C B:PRO66 4.1 12.4 1.0
CA B:GLY67 4.2 12.3 1.0
O B:PHE65 4.5 14.4 1.0
ND1 B:HIS58 4.6 11.9 1.0
CG2 B:ILE64 4.6 17.9 1.0
CB B:PRO66 4.8 11.6 1.0
N B:PRO66 4.8 13.2 1.0
CD2 B:HIS58 4.9 12.7 1.0

Chlorine binding site 3 out of 6 in 3cf9

Go back to Chlorine Binding Sites List in 3cf9
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 Apigenin


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

b:41.6
occ:1.00
 N C:GLY67 3.1 18.0 1.0
O D:HOH161 3.2 12.9 1.0
CA C:GLY67 3.9 17.0 1.0
CE1 C:HIS58 3.9 19.2 1.0
CB D:PHE101 4.0 30.0 1.0
CA C:PRO66 4.0 17.8 1.0
C C:PRO66 4.1 18.2 1.0
CD2 D:PHE101 4.1 29.1 1.0
NE2 C:HIS58 4.1 20.2 1.0
O D:HOH162 4.1 23.4 1.0
O C:HOH212 4.4 18.4 1.0
N D:PHE101 4.5 31.6 1.0
CG D:PHE101 4.6 29.8 1.0
O C:PHE65 4.6 18.3 1.0
CA D:PHE101 4.9 30.1 1.0
CB C:PRO66 4.9 17.6 1.0
CG2 C:ILE64 5.0 17.7 1.0

Chlorine binding site 4 out of 6 in 3cf9

Go back to Chlorine Binding Sites List in 3cf9
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 Apigenin


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

b:57.5
occ:1.00
 N D:GLY67 3.0 14.4 1.0
O C:HOH163 3.1 8.0 1.0
CE1 D:HIS58 3.8 17.9 1.0
CA D:GLY67 3.8 13.3 1.0
CA D:PRO66 3.9 14.9 1.0
C D:PRO66 3.9 15.2 1.0
O C:HOH164 4.0 17.1 1.0
NE2 D:HIS58 4.0 17.4 1.0
O D:PHE65 4.6 17.4 1.0
CB D:PRO66 4.7 15.2 1.0
N D:PRO66 4.9 15.4 1.0
ND1 D:HIS58 5.0 18.2 1.0
N D:VAL68 5.0 13.8 1.0
C D:GLY67 5.0 14.4 1.0

Chlorine binding site 5 out of 6 in 3cf9

Go back to Chlorine Binding Sites List in 3cf9
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 Apigenin


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

b:37.5
occ:1.00
 N E:GLY67 3.5 16.1 1.0
O F:HOH161 3.5 22.4 1.0
CE1 E:HIS58 3.7 15.5 1.0
NE2 E:HIS58 3.9 15.8 1.0
N F:PHE101 3.9 29.2 1.0
CB F:PHE101 3.9 28.8 1.0
O F:HOH166 4.0 22.3 1.0
CD1 F:PHE101 4.2 28.8 1.0
CA E:PRO66 4.2 15.1 1.0
CA E:GLY67 4.2 15.9 1.0
C E:PRO66 4.3 15.5 1.0
O E:HOH196 4.5 19.5 1.0
CG F:PHE101 4.6 29.7 1.0
CA F:PHE101 4.6 28.5 1.0
O F:VAL99 4.6 33.2 1.0
CG2 E:ILE64 4.8 19.9 1.0
CA F:TYR100 4.8 31.8 1.0
O E:PHE65 4.8 17.1 1.0
C F:TYR100 4.9 30.7 1.0
O E:HOH162 4.9 7.6 1.0
ND1 E:HIS58 5.0 17.6 1.0

Chlorine binding site 6 out of 6 in 3cf9

Go back to Chlorine Binding Sites List in 3cf9
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 Apigenin


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

b:37.2
occ:1.00
 O E:HOH207 3.2 30.9 1.0
N F:GLY67 3.3 16.4 1.0
O E:HOH165 3.4 16.2 1.0
CE1 F:HIS58 3.7 19.1 1.0
NE2 F:HIS58 3.9 19.5 1.0
O F:HOH171 4.0 21.9 1.0
N E:PHE101 4.0 24.4 1.0
CA F:GLY67 4.0 16.1 1.0
CB E:PHE101 4.1 24.0 1.0
CA F:PRO66 4.2 16.4 1.0
CD2 E:PHE101 4.2 22.9 1.0
C F:PRO66 4.2 16.9 1.0
O E:HOH193 4.3 21.8 1.0
O F:PHE65 4.6 17.4 1.0
CG E:PHE101 4.7 23.7 1.0
CA E:PHE101 4.7 22.8 1.0
CG2 F:ILE64 4.8 17.2 1.0
CA E:TYR100 4.8 26.4 1.0
C E:TYR100 4.9 25.5 1.0
O E:VAL99 5.0 29.8 1.0
ND1 F:HIS58 5.0 18.7 1.0
O F:HOH173 5.0 13.2 1.0

Reference:

L.Zhang, Y.Kong, D.Wu, H.Zhang, J.Wu, J.Chen, J.Ding, L.Hu, H.Jiang, X.Shen. Three Flavonoids Targeting the Beta-Hydroxyacyl-Acyl Carrier Protein Dehydratase From Helicobacter Pylori: Crystal Structure Characterization with Enzymatic Inhibition Assay Protein Sci. V. 17 1971 2008.
ISSN: ISSN 0961-8368
PubMed: 18780820
DOI: 10.1110/PS.036186.108
Page generated: Fri Jul 11 04:00:48 2025

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