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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

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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

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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

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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

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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

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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

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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

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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 Dec 12 09:38:55 2020

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