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Chlorine in PDB 3d04: Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Sakuranetin

Protein crystallography data

The structure of Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Sakuranetin, PDB code: 3d04 was solved by L.Zhang, Y.Kong, D.Wu, X.Shen, H.Jiang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.967, 100.312, 186.570, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 21.2

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 Sakuranetin (pdb code 3d04). 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 Sakuranetin, PDB code: 3d04:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 3d04

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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 Sakuranetin


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

b:34.4
occ:1.00
 N A:GLY67 3.1 12.7 1.0
O B:HOH164 3.2 10.1 1.0
O B:HOH206 3.4 32.8 1.0
CE1 A:HIS58 3.5 14.2 1.0
OAB A:SAK163 3.6 51.7 1.0
CA A:PRO66 3.7 13.4 1.0
NE2 A:HIS58 3.8 14.6 1.0
C A:PRO66 3.9 13.2 1.0
CAK A:SAK163 3.9 52.1 1.0
CA A:GLY67 4.0 12.8 1.0
O A:HOH180 4.1 25.1 1.0
CAN A:SAK163 4.1 53.2 1.0
O A:HOH219 4.3 23.5 1.0
O A:PHE65 4.4 14.1 1.0
O B:HOH189 4.6 32.2 1.0
CB A:PRO66 4.7 13.0 1.0
ND1 A:HIS58 4.7 14.1 1.0
N A:PRO66 4.7 13.7 1.0
CG2 A:ILE64 4.9 16.3 1.0
C A:PHE65 4.9 13.9 1.0

Chlorine binding site 2 out of 6 in 3d04

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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 Sakuranetin


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

b:42.9
occ:1.00
 O A:HOH164 3.1 13.4 1.0
N B:GLY67 3.1 13.6 1.0
O A:HOH242 3.2 26.2 1.0
CE1 B:HIS58 3.5 11.2 1.0
NE2 B:HIS58 3.8 11.9 1.0
CA B:PRO66 3.8 13.5 1.0
O B:HOH163 3.9 9.8 1.0
C B:PRO66 3.9 13.7 1.0
CA B:GLY67 4.0 13.2 1.0
O B:HOH208 4.4 17.2 1.0
O B:PHE65 4.4 14.0 1.0
CD1 A:PHE101 4.6 30.7 1.0
CB B:PRO66 4.7 13.3 1.0
ND1 B:HIS58 4.7 11.4 1.0
N B:PRO66 4.8 13.6 1.0
CG2 B:ILE64 4.9 15.4 1.0
C B:PHE65 5.0 13.7 1.0

Chlorine binding site 3 out of 6 in 3d04

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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 Sakuranetin


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

b:34.5
occ:1.00
 O D:HOH196 3.1 26.1 1.0
N C:GLY67 3.1 15.5 1.0
O D:HOH161 3.3 16.4 1.0
CE1 C:HIS58 3.8 15.1 1.0
CA C:GLY67 3.9 15.1 1.0
CB D:PHE101 4.0 25.7 1.0
N D:PHE101 4.1 27.2 1.0
C C:PRO66 4.1 15.6 1.0
CA C:PRO66 4.1 15.6 1.0
CD2 D:PHE101 4.2 25.2 1.0
NE2 C:HIS58 4.2 15.2 1.0
O C:HOH169 4.2 18.4 1.0
O C:HOH207 4.3 12.1 1.0
O C:PHE65 4.5 16.0 1.0
CG D:PHE101 4.6 25.1 1.0
CA D:PHE101 4.7 25.7 1.0
CG2 C:ILE64 4.8 18.9 1.0
O C:HOH170 4.8 14.1 1.0
O D:VAL99 5.0 31.7 1.0

Chlorine binding site 4 out of 6 in 3d04

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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 Sakuranetin


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

b:37.0
occ:1.00
 O C:HOH164 3.1 11.0 1.0
N D:GLY67 3.2 13.5 1.0
O C:HOH204 3.5 27.5 1.0
CE1 D:HIS58 3.6 14.5 1.0
NE2 D:HIS58 3.7 14.1 1.0
CA D:PRO66 3.9 13.6 1.0
O C:HOH167 3.9 18.4 1.0
C D:PRO66 4.0 13.6 1.0
CA D:GLY67 4.0 13.1 1.0
O D:PHE65 4.6 14.1 1.0
CB D:PRO66 4.7 13.4 1.0
ND1 D:HIS58 4.8 15.3 1.0
N D:PRO66 4.9 13.6 1.0

Chlorine binding site 5 out of 6 in 3d04

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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 Sakuranetin


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

b:35.5
occ:1.00
 N E:GLY67 3.4 15.2 1.0
O F:HOH198 3.5 27.1 1.0
O F:HOH165 3.7 12.5 1.0
CE1 E:HIS58 3.8 12.8 1.0
N F:PHE101 3.8 25.9 1.0
CB F:PHE101 4.0 25.1 1.0
NE2 E:HIS58 4.0 13.1 1.0
O F:HOH183 4.0 16.0 1.0
CA E:GLY67 4.2 14.8 1.0
CA E:PRO66 4.2 15.4 1.0
C E:PRO66 4.3 15.4 1.0
O E:HOH296 4.4 19.7 1.0
CD1 F:PHE101 4.4 25.2 1.0
CA F:PHE101 4.5 25.1 1.0
O F:VAL99 4.6 29.1 1.0
CA F:TYR100 4.6 27.7 1.0
O E:PHE65 4.7 16.4 1.0
CG F:PHE101 4.7 25.1 1.0
C F:TYR100 4.7 27.0 1.0
CG2 E:ILE64 4.7 17.5 1.0
O E:HOH247 4.9 15.0 1.0
ND1 E:HIS58 5.0 14.0 1.0

Chlorine binding site 6 out of 6 in 3d04

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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 Sakuranetin


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

b:32.3
occ:1.00
 O E:HOH265 3.3 20.8 1.0
N F:GLY67 3.4 14.4 1.0
O E:HOH250 3.7 14.7 1.0
CE1 F:HIS58 3.8 14.7 1.0
N E:PHE101 3.8 22.7 1.0
CB E:PHE101 4.0 22.0 1.0
CA F:GLY67 4.1 14.2 1.0
NE2 F:HIS58 4.1 15.3 1.0
O F:HOH187 4.2 29.3 1.0
O E:HOH291 4.2 13.5 1.0
CD2 E:PHE101 4.3 21.9 1.0
CA F:PRO66 4.3 14.6 1.0
C F:PRO66 4.3 14.5 1.0
CA E:PHE101 4.6 21.9 1.0
CA E:TYR100 4.6 24.0 1.0
O F:PHE65 4.6 15.3 1.0
O E:VAL99 4.6 25.1 1.0
CG E:PHE101 4.7 21.9 1.0
CG2 F:ILE64 4.7 16.2 1.0
C E:TYR100 4.8 23.5 1.0
O F:HOH166 5.0 11.8 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 04:18:12 2025

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