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Chlorine in PDB 3ed0: Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Emodin

Protein crystallography data

The structure of Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Emodin, PDB code: 3ed0 was solved by L.Zhang, H.Zhang, W.Liu, Y.Guo, X.Shen, H.Jiang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.204, 100.397, 186.431, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 26.5

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 Emodin (pdb code 3ed0). 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 Emodin, PDB code: 3ed0:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 3ed0

Go back to Chlorine Binding Sites List in 3ed0
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 Emodin


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 Emodin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl162

b:33.5
occ:1.00
 N A:GLY67 3.0 15.6 1.0
O A:HOH165 3.1 35.1 1.0
O B:HOH163 3.3 14.5 1.0
O19 A:EMO163 3.5 45.5 0.8
O A:HOH257 3.5 44.0 1.0
NE2 A:HIS58 3.6 21.9 1.0
O1 A:EMO163 3.6 43.1 0.8
CA A:PRO66 3.8 17.1 1.0
C A:PRO66 3.9 17.1 1.0
CA A:GLY67 3.9 15.5 1.0
CE1 A:HIS58 4.0 20.3 1.0
O B:HOH178 4.0 22.2 1.0
O A:HOH226 4.1 28.1 1.0
O A:PHE65 4.4 19.3 1.0
O B:HOH213 4.6 42.6 1.0
O17 A:EMO163 4.7 46.7 0.8
CB A:PRO66 4.7 16.0 1.0
C19 A:EMO163 4.7 44.5 0.8
N A:PRO66 4.7 17.2 1.0
CD2 A:HIS58 4.8 20.2 1.0
C1 A:EMO163 4.9 44.5 0.8
C A:PHE65 5.0 17.2 1.0
N A:VAL68 5.0 15.7 1.0

Chlorine binding site 2 out of 6 in 3ed0

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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 Emodin


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 Emodin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl162

b:47.0
occ:1.00
 O A:HOH175 3.0 29.0 1.0
N B:GLY67 3.1 17.7 1.0
O A:HOH172 3.1 17.4 1.0
CE1 B:HIS58 3.6 14.1 1.0
NE2 B:HIS58 3.8 15.4 1.0
O A:HOH166 3.9 14.0 1.0
CA B:GLY67 3.9 16.1 1.0
CA B:PRO66 3.9 17.0 1.0
C B:PRO66 4.0 18.6 1.0
O B:HOH208 4.2 25.6 1.0
O B:PHE65 4.4 17.8 1.0
CD1 A:PHE101 4.5 42.1 1.0
ND1 B:HIS58 4.8 12.8 1.0
CB B:PRO66 4.8 16.4 1.0
N B:PRO66 4.9 16.6 1.0

Chlorine binding site 3 out of 6 in 3ed0

Go back to Chlorine Binding Sites List in 3ed0
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 Emodin


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

b:39.8
occ:1.00
 O D:HOH231 3.0 32.8 1.0
N C:GLY67 3.2 18.6 1.0
O D:HOH162 3.4 15.2 1.0
CA C:GLY67 3.9 18.2 1.0
CB D:PHE101 3.9 31.5 1.0
CE1 C:HIS58 4.0 17.6 1.0
N D:PHE101 4.1 34.2 1.0
NE2 C:HIS58 4.2 18.9 1.0
C C:PRO66 4.2 19.1 1.0
O D:HOH163 4.2 23.2 1.0
CD2 D:PHE101 4.2 31.4 1.0
CA C:PRO66 4.3 17.8 1.0
O D:HOH198 4.3 20.0 1.0
O C:PHE65 4.5 19.0 1.0
CG D:PHE101 4.6 31.2 1.0
CA D:PHE101 4.7 31.3 1.0
CG2 C:ILE64 5.0 22.8 1.0

Chlorine binding site 4 out of 6 in 3ed0

Go back to Chlorine Binding Sites List in 3ed0
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 Emodin


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 Emodin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl161

b:47.5
occ:1.00
 O C:HOH165 3.1 17.3 1.0
N D:GLY67 3.1 17.6 1.0
O C:HOH199 3.5 31.2 1.0
CE1 D:HIS58 3.8 21.1 1.0
NE2 D:HIS58 3.8 19.7 1.0
CA D:PRO66 3.9 18.2 1.0
CA D:GLY67 4.0 15.8 1.0
C D:PRO66 4.0 18.4 1.0
O C:HOH164 4.1 22.1 1.0
O C:HOH226 4.4 43.2 1.0
O D:HOH232 4.4 31.8 1.0
O D:PHE65 4.7 21.1 1.0
CB D:PRO66 4.8 18.3 1.0
N D:PRO66 4.9 18.0 1.0

Chlorine binding site 5 out of 6 in 3ed0

Go back to Chlorine Binding Sites List in 3ed0
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 Emodin


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 Emodin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl162

b:38.9
occ:1.00
 O F:HOH244 2.9 34.7 1.0
N E:GLY67 3.2 15.2 1.0
O F:HOH187 3.7 15.9 1.0
CE1 E:HIS58 3.8 16.1 1.0
N F:PHE101 3.9 29.3 1.0
O F:HOH223 4.0 38.9 1.0
CB F:PHE101 4.0 27.9 1.0
CA E:GLY67 4.0 15.6 1.0
NE2 E:HIS58 4.0 15.5 1.0
CA E:PRO66 4.1 15.6 1.0
C E:PRO66 4.1 16.8 1.0
O F:HOH196 4.2 21.5 1.0
O E:HOH205 4.3 19.1 1.0
O E:PHE65 4.4 18.1 1.0
CD1 F:PHE101 4.5 27.2 1.0
CA F:PHE101 4.6 27.9 1.0
CA F:TYR100 4.7 32.8 1.0
O F:VAL99 4.7 34.1 1.0
CG2 E:ILE64 4.8 19.8 1.0
CG F:PHE101 4.8 27.9 1.0
C F:TYR100 4.8 31.4 1.0
O E:HOH169 4.8 22.4 1.0

Chlorine binding site 6 out of 6 in 3ed0

Go back to Chlorine Binding Sites List in 3ed0
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 Emodin


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

b:39.6
occ:1.00
 O E:HOH209 2.7 26.2 1.0
N F:GLY67 3.2 16.3 1.0
O E:HOH177 3.2 17.6 1.0
CE1 F:HIS58 3.7 18.9 1.0
NE2 F:HIS58 3.7 16.2 1.0
O E:HOH181 3.9 25.2 1.0
CB E:PHE101 4.0 24.5 1.0
CA F:GLY67 4.0 15.7 1.0
O E:HOH183 4.0 24.9 1.0
N E:PHE101 4.0 25.5 1.0
CA F:PRO66 4.1 18.0 1.0
C F:PRO66 4.2 16.7 1.0
CD2 E:PHE101 4.3 24.8 1.0
O F:HOH225 4.5 20.6 1.0
CA E:PHE101 4.7 24.0 1.0
CG E:PHE101 4.7 24.5 1.0
O F:PHE65 4.7 18.8 1.0
O E:VAL99 4.7 33.4 1.0
CA E:TYR100 4.9 28.9 1.0
ND1 F:HIS58 4.9 18.0 1.0
C E:TYR100 4.9 28.0 1.0
CB F:PRO66 5.0 18.2 1.0

Reference:

J.Chen, L.Zhang, Y.Zhang, H.Zhang, J.Du, J.Ding, Y.Guo, H.Jiang, X.Shen. Emodin Targets the Beta-Hydroxyacyl-Acyl Carrier Protein Dehydratase From Helicobacter Pylori: Enzymatic Inhibition Assay with Crystal Structural and Thermodynamic Characterization Bmc Microbiol. V. 9 91 2009.
ISSN: ESSN 1471-2180
PubMed: 19433000
DOI: 10.1186/1471-2180-9-91
Page generated: Fri Jul 11 04:47:06 2025

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