Atomistry » Chlorine » PDB 3csw-3d37 » 3d04
Atomistry »
  Chlorine »
    PDB 3csw-3d37 »
      3d04 »

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

Go back to Chlorine Binding Sites List in 3d04
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

Go back to Chlorine Binding Sites List in 3d04
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

Go back to Chlorine Binding Sites List in 3d04
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

Go back to Chlorine Binding Sites List in 3d04
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

Go back to Chlorine Binding Sites List in 3d04
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

Go back to Chlorine Binding Sites List in 3d04
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: Sat Jul 20 17:56:22 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy