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Chlorine in PDB 3cf8: Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Quercetin

Protein crystallography data

The structure of Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Quercetin, PDB code: 3cf8 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 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.987, 100.438, 186.009, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 22.6

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 Quercetin (pdb code 3cf8). 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 Quercetin, PDB code: 3cf8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 3cf8

Go back to Chlorine Binding Sites List in 3cf8
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 Quercetin


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

b:55.5
occ:1.00
 N A:GLY67 3.2 15.8 1.0
O B:HOH165 3.2 15.4 1.0
CE1 A:HIS58 3.3 20.9 1.0
O B:HOH203 3.5 28.7 1.0
NE2 A:HIS58 3.6 18.8 1.0
CA A:PRO66 3.7 16.7 1.0
O B:HOH176 3.9 20.9 1.0
O27 A:QUE164 3.9 49.6 1.0
C A:PRO66 3.9 16.7 1.0
CA A:GLY67 4.1 15.9 1.0
O A:HOH227 4.2 30.0 1.0
O A:PHE65 4.3 17.4 1.0
O B:HOH191 4.4 37.1 1.0
C15 A:QUE164 4.6 47.0 1.0
ND1 A:HIS58 4.6 20.5 1.0
N A:PRO66 4.6 17.4 1.0
CB A:PRO66 4.7 16.8 1.0
CG2 A:ILE64 4.8 18.3 1.0
C A:PHE65 4.9 17.2 1.0
CD2 A:HIS58 4.9 20.0 1.0
C10 A:QUE164 4.9 48.8 1.0
C16 A:QUE164 5.0 46.4 1.0

Chlorine binding site 2 out of 6 in 3cf8

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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 Quercetin


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

b:69.3
occ:1.00
 N B:GLY67 3.1 17.1 1.0
O A:HOH217 3.1 29.3 1.0
O A:HOH165 3.2 18.4 1.0
CE1 B:HIS58 3.4 13.6 1.0
CA B:PRO66 3.7 16.4 1.0
NE2 B:HIS58 3.7 14.7 1.0
C B:PRO66 3.9 17.5 1.0
CA B:GLY67 4.0 16.1 1.0
O A:HOH169 4.1 14.8 1.0
O B:HOH216 4.2 29.0 1.0
O B:PHE65 4.3 18.9 1.0
CG2 B:ILE64 4.5 19.7 1.0
ND1 B:HIS58 4.6 12.7 1.0
CB B:PRO66 4.7 16.2 1.0
N B:PRO66 4.7 16.7 1.0
C B:PHE65 4.8 17.0 1.0
O B:HOH169 4.9 19.9 1.0

Chlorine binding site 3 out of 6 in 3cf8

Go back to Chlorine Binding Sites List in 3cf8
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 Quercetin


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

b:32.2
occ:1.00
 N C:GLY67 3.2 20.3 1.0
O D:HOH161 3.4 20.3 1.0
O D:HOH215 3.5 27.8 1.0
CE1 C:HIS58 3.8 20.1 1.0
CB D:PHE101 3.9 27.1 1.0
N D:PHE101 4.0 28.8 1.0
CA C:GLY67 4.0 20.4 1.0
CA C:PRO66 4.1 20.0 1.0
C C:PRO66 4.2 21.0 1.0
O C:HOH169 4.2 21.7 1.0
NE2 C:HIS58 4.2 19.5 1.0
O D:HOH195 4.2 24.1 1.0
CD2 D:PHE101 4.2 27.0 1.0
O C:PHE65 4.5 21.1 1.0
CG D:PHE101 4.6 27.1 1.0
CA D:PHE101 4.6 27.0 1.0
CG2 C:ILE64 4.8 20.9 1.0
CA D:TYR100 4.9 32.4 1.0
O D:VAL99 4.9 33.9 1.0
C D:TYR100 4.9 30.3 1.0
O C:HOH163 4.9 18.2 1.0

Chlorine binding site 4 out of 6 in 3cf8

Go back to Chlorine Binding Sites List in 3cf8
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 Quercetin


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

b:45.3
occ:1.00
 O C:HOH164 3.3 16.0 1.0
N D:GLY67 3.3 15.7 1.0
CE1 D:HIS58 3.4 20.4 1.0
NE2 D:HIS58 3.7 20.6 1.0
CA D:PRO66 3.9 15.9 1.0
C D:PRO66 4.1 16.0 1.0
O C:HOH168 4.1 23.1 1.0
CA D:GLY67 4.2 15.7 1.0
O D:PHE65 4.4 17.9 1.0
O C:HOH218 4.7 35.6 1.0
ND1 D:HIS58 4.7 21.1 1.0
CB D:PRO66 4.8 16.1 1.0
CG2 D:ILE64 4.8 16.6 1.0
N D:PRO66 4.8 16.3 1.0

Chlorine binding site 5 out of 6 in 3cf8

Go back to Chlorine Binding Sites List in 3cf8
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 Quercetin


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

b:44.8
occ:1.00
 N E:GLY67 3.3 19.5 1.0
O F:HOH163 3.5 16.0 1.0
CE1 E:HIS58 3.7 19.7 1.0
N F:PHE101 3.8 29.7 1.0
O F:HOH170 3.9 25.9 1.0
NE2 E:HIS58 3.9 18.8 1.0
CB F:PHE101 4.0 29.0 1.0
CA E:PRO66 4.1 18.4 1.0
CA E:GLY67 4.1 19.2 1.0
C E:PRO66 4.2 19.0 1.0
CD1 F:PHE101 4.3 30.2 1.0
CA F:PHE101 4.6 29.2 1.0
O E:HOH224 4.6 27.2 1.0
O F:VAL99 4.6 33.9 1.0
CG F:PHE101 4.7 30.2 1.0
CA F:TYR100 4.7 33.0 1.0
O E:PHE65 4.7 20.2 1.0
C F:TYR100 4.8 31.1 1.0
CG2 E:ILE64 4.8 22.0 1.0
ND1 E:HIS58 4.9 19.6 1.0
CB E:PRO66 5.0 17.3 1.0

Chlorine binding site 6 out of 6 in 3cf8

Go back to Chlorine Binding Sites List in 3cf8
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 Quercetin


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

b:41.5
occ:1.00
 N F:GLY67 3.2 17.4 1.0
O E:HOH167 3.5 16.0 1.0
O E:HOH216 3.5 32.0 1.0
O F:HOH191 3.8 33.0 1.0
CE1 F:HIS58 3.8 20.7 1.0
CA F:GLY67 3.9 17.1 1.0
N E:PHE101 3.9 27.9 1.0
CB E:PHE101 4.0 25.8 1.0
CD2 E:PHE101 4.0 24.2 1.0
NE2 F:HIS58 4.0 20.6 1.0
C F:PRO66 4.2 18.6 1.0
CA F:PRO66 4.2 18.5 1.0
O E:HOH208 4.4 21.1 1.0
CG E:PHE101 4.5 24.7 1.0
CA E:PHE101 4.6 26.1 1.0
O F:PHE65 4.7 20.8 1.0
CA E:TYR100 4.8 29.9 1.0
O E:VAL99 4.9 32.1 1.0
CG2 F:ILE64 4.9 20.6 1.0
C E:TYR100 4.9 29.2 1.0
ND1 F:HIS58 5.0 19.8 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: Sat Dec 12 09:36:11 2020

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