Atomistry » Chlorine » PDB 3dn8-3dyv » 3doy
Atomistry »
  Chlorine »
    PDB 3dn8-3dyv »
      3doy »

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

Protein crystallography data

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

Resolution Low / High (Å) 15.00 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.975, 100.370, 186.622, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 23.8

Other elements in 3doy:

The structure of Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3I also contains other interesting chemical elements:

Bromine (Br) 4 atoms

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 Compound 3I (pdb code 3doy). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3I, PDB code: 3doy:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 3doy

Go back to Chlorine Binding Sites List in 3doy
Chlorine binding site 1 out of 8 in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3I


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 Compound 3I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1001

b:39.9
occ:1.00
 N A:GLY67 3.0 12.8 1.0
O B:HOH3006 3.1 15.4 1.0
O B:HOH3423 3.1 22.0 1.0
O B:HOH3367 3.6 30.4 1.0
CE1 A:HIS58 3.7 17.4 1.0
NE2 A:HIS58 3.7 16.9 1.0
CA A:PRO66 3.8 14.1 1.0
O B:HOH3070 3.8 16.6 1.0
C A:PRO66 3.9 13.5 1.0
O B:HOH3370 3.9 21.1 1.0
CA A:GLY67 3.9 12.5 1.0
O B:HOH3204 4.4 29.4 1.0
O A:PHE65 4.5 15.0 1.0
N A:PRO66 4.7 12.5 1.0
CB A:PRO66 4.7 11.8 1.0
ND1 A:HIS58 4.9 17.1 1.0
CG2 A:ILE64 5.0 14.2 1.0
C A:PHE65 5.0 13.5 1.0

Chlorine binding site 2 out of 8 in 3doy

Go back to Chlorine Binding Sites List in 3doy
Chlorine binding site 2 out of 8 in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3I


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 Compound 3I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl3001

b:44.7
occ:1.00
 CLAD A:2BE3001 0.0 44.7 1.0
CAP A:2BE3001 1.7 41.8 1.0
CAI A:2BE3001 2.7 43.1 1.0
CAH A:2BE3001 2.7 41.7 1.0
N A:ILE111 3.5 14.6 1.0
O A:PHE109 3.5 17.1 1.0
C A:ARG110 3.5 14.9 1.0
C A:PHE109 3.6 15.5 1.0
CB A:PHE109 3.7 13.2 1.0
C A:ILE111 3.7 14.6 1.0
O A:HOH3062 3.8 13.6 1.0
N A:ARG110 3.8 16.0 1.0
CA A:ILE111 3.8 14.5 1.0
N A:PRO112 3.9 13.5 1.0
O B:HOH3370 3.9 21.1 1.0
O A:ARG110 3.9 15.0 1.0
CAJ A:2BE3001 4.0 43.8 1.0
CAK A:2BE3001 4.0 43.6 1.0
CA A:ARG110 4.1 15.2 1.0
O A:ILE111 4.1 15.4 1.0
CD A:PRO112 4.2 13.1 1.0
CA A:PHE109 4.2 14.9 1.0
CA A:PRO112 4.5 14.2 1.0
CAT A:2BE3001 4.5 42.9 1.0
O B:HOH3423 4.6 22.0 1.0
CD2 B:TYR100 4.9 31.5 1.0
CE2 B:TYR100 4.9 33.0 1.0
CG A:PHE109 4.9 14.2 1.0
CB A:PRO112 5.0 13.8 1.0

Chlorine binding site 3 out of 8 in 3doy

Go back to Chlorine Binding Sites List in 3doy
Chlorine binding site 3 out of 8 in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3I


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 Compound 3I within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1002

b:57.3
occ:1.00
 O A:HOH3025 3.1 11.9 1.0
O B:HOH3026 3.1 24.3 1.0
N B:GLY67 3.1 14.6 1.0
CE1 B:HIS58 3.5 10.9 1.0
NE2 B:HIS58 3.6 12.2 1.0
O A:HOH3008 3.8 7.3 1.0
CA B:PRO66 3.9 13.3 1.0
CA B:GLY67 4.0 12.6 1.0
C B:PRO66 4.0 14.1 1.0
O B:HOH3261 4.4 15.3 1.0
O B:PHE65 4.5 14.2 1.0
CD1 A:PHE101 4.5 30.3 1.0
ND1 B:HIS58 4.8 10.7 1.0
N B:PRO66 4.9 13.8 1.0
CB B:PRO66 4.9 12.9 1.0
CD2 B:HIS58 5.0 11.1 1.0

Chlorine binding site 4 out of 8 in 3doy

Go back to Chlorine Binding Sites List in 3doy
Chlorine binding site 4 out of 8 in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3I


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 Compound 3I within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1003

b:31.5
occ:1.00
 O D:HOH3210 3.0 28.3 1.0
O D:HOH3004 3.1 13.6 1.0
N C:GLY67 3.2 15.0 1.0
CB D:PHE101 3.8 24.8 1.0
CA C:GLY67 3.9 14.6 1.0
CE1 C:HIS58 3.9 17.0 1.0
O D:HOH3014 4.1 16.0 1.0
N D:PHE101 4.1 26.8 1.0
NE2 C:HIS58 4.1 16.7 1.0
CD2 D:PHE101 4.2 23.4 1.0
C C:PRO66 4.2 14.8 1.0
CA C:PRO66 4.2 15.0 1.0
O C:HOH3044 4.3 16.9 1.0
CG D:PHE101 4.5 24.8 1.0
CA D:PHE101 4.6 25.4 1.0
O C:PHE65 4.7 15.6 1.0

Chlorine binding site 5 out of 8 in 3doy

Go back to Chlorine Binding Sites List in 3doy
Chlorine binding site 5 out of 8 in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3I


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 Compound 3I within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl3002

b:48.2
occ:1.00
 CLAD C:2BE3002 0.0 48.2 1.0
CAP C:2BE3002 1.7 45.4 1.0
CAH C:2BE3002 2.7 46.5 1.0
CAI C:2BE3002 2.7 46.1 1.0
O D:HOH3480 3.2 29.8 1.0
CD C:ARG158 3.2 29.5 1.0
NE C:ARG158 3.4 29.8 1.0
CZ C:ARG158 3.7 29.0 1.0
NH1 C:ARG158 3.8 29.1 1.0
CG C:ARG158 3.9 29.8 1.0
CAJ C:2BE3002 4.0 47.4 1.0
CAK C:2BE3002 4.0 47.6 1.0
CB D:LYS62 4.4 26.0 1.0
CB D:PHE59 4.4 14.2 1.0
NH2 C:ARG158 4.5 28.5 1.0
CAT C:2BE3002 4.5 45.9 1.0
CB C:PRO22 4.6 15.0 1.0
CG D:LYS62 4.6 28.5 1.0
CG D:PHE59 4.8 16.0 1.0
O D:PRO60 4.9 21.9 1.0

Chlorine binding site 6 out of 8 in 3doy

Go back to Chlorine Binding Sites List in 3doy
Chlorine binding site 6 out of 8 in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3I


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 Compound 3I within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1004

b:49.8
occ:1.00
 N D:GLY67 3.3 14.5 1.0
O C:HOH3003 3.4 11.5 1.0
CE1 D:HIS58 3.7 18.2 1.0
NE2 D:HIS58 3.8 17.4 1.0
CA D:PRO66 4.1 15.5 1.0
O C:HOH3006 4.1 13.9 1.0
CA D:GLY67 4.1 13.3 1.0
O D:HOH3304 4.2 29.4 1.0
C D:PRO66 4.2 15.0 1.0
O D:PHE65 4.8 16.8 1.0
CB D:PRO66 5.0 15.4 1.0
ND1 D:HIS58 5.0 17.7 1.0

Chlorine binding site 7 out of 8 in 3doy

Go back to Chlorine Binding Sites List in 3doy
Chlorine binding site 7 out of 8 in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3I


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3I within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl1005

b:30.8
occ:1.00
 O F:HOH3239 2.9 31.5 1.0
N E:GLY67 3.3 12.4 1.0
O F:HOH3018 3.5 12.5 1.0
CE1 E:HIS58 3.7 16.0 1.0
N F:PHE101 3.9 21.8 1.0
CB F:PHE101 3.9 20.4 1.0
NE2 E:HIS58 3.9 15.8 1.0
O F:HOH3087 4.0 15.0 1.0
CA E:GLY67 4.0 12.3 1.0
CA E:PRO66 4.2 12.6 1.0
CD1 F:PHE101 4.2 20.9 1.0
C E:PRO66 4.2 12.8 1.0
CA F:PHE101 4.5 21.1 1.0
O E:HOH3303 4.5 19.3 1.0
CG F:PHE101 4.6 21.0 1.0
O E:PHE65 4.6 14.2 1.0
O F:VAL99 4.7 26.2 1.0
CA F:TYR100 4.7 24.0 1.0
C F:TYR100 4.7 23.0 1.0
CG2 E:ILE64 4.8 15.5 1.0
ND1 E:HIS58 4.9 15.6 1.0

Chlorine binding site 8 out of 8 in 3doy

Go back to Chlorine Binding Sites List in 3doy
Chlorine binding site 8 out of 8 in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3I


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3I within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl1006

b:30.4
occ:1.00
 O E:HOH3262 2.8 18.8 1.0
O E:HOH3133 3.1 19.7 1.0
N F:GLY67 3.3 13.5 1.0
O E:HOH3033 3.6 8.1 1.0
CB E:PHE101 3.7 22.1 1.0
CE1 F:HIS58 3.8 16.8 1.0
N E:PHE101 3.9 21.8 1.0
CA F:GLY67 4.0 13.3 1.0
NE2 F:HIS58 4.0 15.8 1.0
O E:HOH3247 4.3 19.7 1.0
O E:HOH3092 4.3 18.3 1.0
CD2 E:PHE101 4.3 23.9 1.0
C F:PRO66 4.4 13.6 1.0
CA F:PRO66 4.4 14.2 1.0
CA E:PHE101 4.5 21.1 1.0
CG E:PHE101 4.5 22.4 1.0
O F:PHE65 4.7 16.1 1.0
O E:VAL99 4.8 27.2 1.0
CA E:TYR100 4.8 23.2 1.0
CG2 F:ILE64 4.8 16.0 1.0
C E:TYR100 4.8 23.0 1.0
O F:HOH3053 4.9 17.9 1.0

Reference:

L.He, L.Zhang, X.Liu, X.Li, M.Zheng, H.Li, K.Yu, K.Chen, X.Shen, H.Jiang, H.Liu. Discovering Potent Inhibitors Against the Beta-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) of Helicobacter Pylori: Structure-Based Design, Synthesis, Bioassay, and Crystal Structure Determination. J.Med.Chem. V. 52 2465 2009.
ISSN: ISSN 0022-2623
PubMed: 19309082
DOI: 10.1021/JM8015602
Page generated: Sat Jul 20 18:25:57 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