Atomistry » Chlorine » PDB 3r41-3rcg » 3ras
Atomistry »
  Chlorine »
    PDB 3r41-3rcg »
      3ras »

Chlorine in PDB 3ras: Crystal Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) Complexed with A Lipophilic Phosphonate Inhibitor

Enzymatic activity of Crystal Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) Complexed with A Lipophilic Phosphonate Inhibitor

All present enzymatic activity of Crystal Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) Complexed with A Lipophilic Phosphonate Inhibitor:
1.1.1.267;

Protein crystallography data

The structure of Crystal Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) Complexed with A Lipophilic Phosphonate Inhibitor, PDB code: 3ras was solved by J.Diao, L.Deng, B.V.V.Prasad, Y.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.45 / 2.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.250, 65.179, 85.408, 90.00, 101.28, 90.00
R / Rfree (%) 20.8 / 27.8

Other elements in 3ras:

The structure of Crystal Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) Complexed with A Lipophilic Phosphonate Inhibitor also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) Complexed with A Lipophilic Phosphonate Inhibitor (pdb code 3ras). 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 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) Complexed with A Lipophilic Phosphonate Inhibitor, PDB code: 3ras:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 3ras

Go back to Chlorine Binding Sites List in 3ras
Chlorine binding site 1 out of 8 in the Crystal Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) Complexed with A Lipophilic Phosphonate Inhibitor


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 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) Complexed with A Lipophilic Phosphonate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl390

b:46.9
occ:0.50
 CL2 A:FM5390 0.0 46.9 0.5
CL2 A:DCV391 0.1 45.1 0.5
C9 A:FM5390 1.7 49.6 0.5
CAH A:DCV391 1.8 48.8 0.5
CAF A:DCV391 2.7 47.8 0.5
C10 A:FM5390 2.7 48.8 0.5
C8 A:FM5390 2.8 49.2 0.5
CAG A:DCV391 2.8 48.3 0.5
NE1 A:TRP203 2.9 0.5 1.0
CL1 A:FM5390 3.3 51.4 0.5
CD1 A:TRP203 3.4 0.3 1.0
CL1 A:DCV391 3.4 50.4 0.5
CE2 A:TRP203 3.7 0.4 1.0
CB A:SER245 3.8 42.0 1.0
CB A:PRO265 3.8 40.5 1.0
CG A:PRO265 3.8 38.9 1.0
OG A:SER245 4.0 46.6 1.0
CAD A:DCV391 4.0 48.1 0.5
C11 A:FM5390 4.1 48.6 0.5
C7 A:FM5390 4.1 48.9 0.5
CAE A:DCV391 4.1 48.1 0.5
CZ2 A:TRP203 4.3 0.9 1.0
CG A:TRP203 4.3 0.7 1.0
CD2 A:TRP203 4.5 0.3 1.0
C6 A:FM5390 4.6 48.5 0.5
CAC A:DCV391 4.7 48.0 0.5
CE1 A:HIS200 4.9 0.9 1.0

Chlorine binding site 2 out of 8 in 3ras

Go back to Chlorine Binding Sites List in 3ras
Chlorine binding site 2 out of 8 in the Crystal Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) Complexed with A Lipophilic Phosphonate Inhibitor


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 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) Complexed with A Lipophilic Phosphonate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl390

b:51.4
occ:0.50
 CL1 A:FM5390 0.0 51.4 0.5
CL1 A:DCV391 0.3 50.4 0.5
C8 A:FM5390 1.7 49.2 0.5
CAG A:DCV391 1.9 48.3 0.5
C7 A:FM5390 2.7 48.9 0.5
C9 A:FM5390 2.8 49.6 0.5
CAH A:DCV391 2.9 48.8 0.5
CAE A:DCV391 3.0 48.1 0.5
CL2 A:DCV391 3.2 45.1 0.5
CL2 A:FM5390 3.3 46.9 0.5
CB A:SER245 3.6 42.0 1.0
C5 A:DCV391 3.8 51.8 0.5
CE1 A:HIS248 3.9 38.5 1.0
C5 A:FM5390 4.0 47.8 0.5
OG A:SER245 4.0 46.6 1.0
ND1 A:HIS248 4.0 38.7 1.0
C6 A:FM5390 4.0 48.5 0.5
O A:HOH413 4.1 45.4 1.0
O A:SER245 4.1 43.3 1.0
C10 A:FM5390 4.1 48.8 0.5
CAF A:DCV391 4.2 47.8 0.5
CB A:PRO265 4.3 40.5 1.0
CAC A:DCV391 4.3 48.0 0.5
CG A:PRO265 4.4 38.9 1.0
C1 A:FM5390 4.6 49.8 0.5
OG A:SER152 4.6 43.4 1.0
C11 A:FM5390 4.6 48.6 0.5
CA A:SER245 4.7 42.9 1.0
C1 A:DCV391 4.8 51.7 0.5
CAD A:DCV391 4.8 48.1 0.5
C A:SER245 4.8 42.4 1.0
CA A:PRO265 4.9 41.6 1.0
O1 A:FM5390 5.0 50.2 0.5

Chlorine binding site 3 out of 8 in 3ras

Go back to Chlorine Binding Sites List in 3ras
Chlorine binding site 3 out of 8 in the Crystal Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) Complexed with A Lipophilic Phosphonate Inhibitor


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 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) Complexed with A Lipophilic Phosphonate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl391

b:50.4
occ:0.50
 CL1 A:DCV391 0.0 50.4 0.5
CL1 A:FM5390 0.3 51.4 0.5
C8 A:FM5390 1.6 49.2 0.5
CAG A:DCV391 1.7 48.3 0.5
C7 A:FM5390 2.4 48.9 0.5
CAE A:DCV391 2.7 48.1 0.5
C9 A:FM5390 2.8 49.6 0.5
CAH A:DCV391 2.8 48.8 0.5
CL2 A:DCV391 3.3 45.1 0.5
CL2 A:FM5390 3.4 46.9 0.5
CB A:SER245 3.6 42.0 1.0
O A:HOH413 3.8 45.4 1.0
C5 A:DCV391 3.8 51.8 0.5
C6 A:FM5390 3.8 48.5 0.5
OG A:SER245 3.8 46.6 1.0
C5 A:FM5390 4.0 47.8 0.5
C10 A:FM5390 4.0 48.8 0.5
ND1 A:HIS248 4.1 38.7 1.0
CE1 A:HIS248 4.1 38.5 1.0
CAC A:DCV391 4.1 48.0 0.5
CAF A:DCV391 4.1 47.8 0.5
O A:SER245 4.2 43.3 1.0
C11 A:FM5390 4.4 48.6 0.5
C1 A:FM5390 4.5 49.8 0.5
OG A:SER152 4.6 43.4 1.0
CB A:PRO265 4.6 40.5 1.0
CA A:SER245 4.6 42.9 1.0
CAD A:DCV391 4.6 48.1 0.5
CG A:PRO265 4.7 38.9 1.0
C1 A:DCV391 4.7 51.7 0.5
C A:SER245 4.8 42.4 1.0
O1 A:FM5390 4.9 50.2 0.5
C4 A:FM5390 4.9 46.5 0.5

Chlorine binding site 4 out of 8 in 3ras

Go back to Chlorine Binding Sites List in 3ras
Chlorine binding site 4 out of 8 in the Crystal Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) Complexed with A Lipophilic Phosphonate Inhibitor


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 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) Complexed with A Lipophilic Phosphonate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl391

b:45.1
occ:0.50
 CL2 A:DCV391 0.0 45.1 0.5
CL2 A:FM5390 0.1 46.9 0.5
C9 A:FM5390 1.7 49.6 0.5
CAH A:DCV391 1.7 48.8 0.5
C8 A:FM5390 2.7 49.2 0.5
CAF A:DCV391 2.7 47.8 0.5
C10 A:FM5390 2.7 48.8 0.5
CAG A:DCV391 2.8 48.3 0.5
NE1 A:TRP203 3.0 0.5 1.0
CL1 A:FM5390 3.2 51.4 0.5
CL1 A:DCV391 3.3 50.4 0.5
CD1 A:TRP203 3.5 0.3 1.0
CB A:SER245 3.7 42.0 1.0
CE2 A:TRP203 3.8 0.4 1.0
CB A:PRO265 3.8 40.5 1.0
CG A:PRO265 3.8 38.9 1.0
OG A:SER245 3.9 46.6 1.0
C7 A:FM5390 4.0 48.9 0.5
CAD A:DCV391 4.1 48.1 0.5
C11 A:FM5390 4.1 48.6 0.5
CAE A:DCV391 4.1 48.1 0.5
CZ2 A:TRP203 4.3 0.9 1.0
CG A:TRP203 4.4 0.7 1.0
CD2 A:TRP203 4.5 0.3 1.0
C6 A:FM5390 4.6 48.5 0.5
CAC A:DCV391 4.6 48.0 0.5
O A:SER245 5.0 43.3 1.0
CE1 A:HIS200 5.0 0.9 1.0

Chlorine binding site 5 out of 8 in 3ras

Go back to Chlorine Binding Sites List in 3ras
Chlorine binding site 5 out of 8 in the Crystal Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) Complexed with A Lipophilic Phosphonate Inhibitor


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 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) Complexed with A Lipophilic Phosphonate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl390

b:60.6
occ:0.50
 CL2 B:FM5390 0.0 60.6 0.5
CL2 B:DCV391 0.2 61.2 0.5
CAH B:DCV391 1.7 65.1 0.5
C9 B:FM5390 1.7 65.0 0.5
CAF B:DCV391 2.6 66.2 0.5
C10 B:FM5390 2.7 65.8 0.5
C8 B:FM5390 2.8 65.3 0.5
CAG B:DCV391 2.9 65.5 0.5
CL1 B:FM5390 3.4 63.5 0.5
CL1 B:DCV391 3.5 62.9 0.5
CZ3 B:TRP203 3.7 72.4 1.0
O B:TRP203 3.8 84.4 1.0
CE1 B:HIS50 3.9 53.2 1.0
CE3 B:TRP203 3.9 73.1 1.0
CAD B:DCV391 3.9 68.6 0.5
C11 B:FM5390 4.0 68.2 0.5
NE2 B:HIS50 4.1 54.3 1.0
C7 B:FM5390 4.1 67.4 0.5
CA B:SER204 4.1 88.0 1.0
CAE B:DCV391 4.1 67.4 0.5
ND1 B:HIS50 4.3 53.1 1.0
CB B:SER204 4.5 88.1 1.0
O B:THR21 4.5 45.4 1.0
CAC B:DCV391 4.6 70.0 0.5
C6 B:FM5390 4.6 69.6 0.5
CH2 B:TRP203 4.6 72.5 1.0
C B:TRP203 4.7 85.0 1.0
CD2 B:HIS50 4.7 52.5 1.0
O B:SER204 4.7 89.2 1.0
CG B:HIS50 4.8 50.6 1.0
N B:SER204 4.8 86.4 1.0
CD2 B:TRP203 4.9 74.9 1.0
C B:SER204 4.9 89.0 1.0

Chlorine binding site 6 out of 8 in 3ras

Go back to Chlorine Binding Sites List in 3ras
Chlorine binding site 6 out of 8 in the Crystal Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) Complexed with A Lipophilic Phosphonate Inhibitor


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 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) Complexed with A Lipophilic Phosphonate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl390

b:63.5
occ:0.50
 CL1 B:FM5390 0.0 63.5 0.5
CL1 B:DCV391 0.3 62.9 0.5
C8 B:FM5390 1.7 65.3 0.5
CAG B:DCV391 1.9 65.5 0.5
C7 B:FM5390 2.7 67.4 0.5
CAH B:DCV391 2.8 65.1 0.5
C9 B:FM5390 2.8 65.0 0.5
CAE B:DCV391 3.0 67.4 0.5
CL2 B:DCV391 3.2 61.2 0.5
CL2 B:FM5390 3.4 60.6 0.5
O B:THR21 3.4 45.4 1.0
OG1 B:THR53 3.5 44.8 1.0
CG2 B:THR53 3.9 36.8 1.0
CG B:HIS50 4.0 50.6 1.0
CB B:THR53 4.0 40.6 1.0
C6 B:FM5390 4.1 69.6 0.5
C10 B:FM5390 4.1 65.8 0.5
CAF B:DCV391 4.1 66.2 0.5
CB B:HIS50 4.2 47.2 1.0
CAC B:DCV391 4.3 70.0 0.5
ND1 B:HIS50 4.3 53.1 1.0
CB B:THR21 4.4 41.5 1.0
CD2 B:HIS50 4.4 52.5 1.0
C B:THR21 4.4 43.9 1.0
C11 B:FM5390 4.6 68.2 0.5
CAD B:DCV391 4.7 68.6 0.5
CA B:THR21 4.8 42.1 1.0
CE1 B:HIS50 4.8 53.2 1.0
NE2 B:HIS50 4.8 54.3 1.0
O B:HOH395 4.9 37.4 1.0

Chlorine binding site 7 out of 8 in 3ras

Go back to Chlorine Binding Sites List in 3ras
Chlorine binding site 7 out of 8 in the Crystal Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) Complexed with A Lipophilic Phosphonate Inhibitor


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 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) Complexed with A Lipophilic Phosphonate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl391

b:62.9
occ:0.50
 CL1 B:DCV391 0.0 62.9 0.5
CL1 B:FM5390 0.3 63.5 0.5
C8 B:FM5390 1.6 65.3 0.5
CAG B:DCV391 1.7 65.5 0.5
C7 B:FM5390 2.5 67.4 0.5
CAE B:DCV391 2.7 67.4 0.5
C9 B:FM5390 2.8 65.0 0.5
CAH B:DCV391 2.8 65.1 0.5
OG1 B:THR53 3.3 44.8 1.0
CL2 B:DCV391 3.3 61.2 0.5
CL2 B:FM5390 3.5 60.6 0.5
O B:THR21 3.7 45.4 1.0
C6 B:FM5390 3.8 69.6 0.5
CG2 B:THR53 3.8 36.8 1.0
CB B:THR53 3.9 40.6 1.0
CG B:HIS50 3.9 50.6 1.0
C10 B:FM5390 4.0 65.8 0.5
CB B:HIS50 4.1 47.2 1.0
CAC B:DCV391 4.1 70.0 0.5
CAF B:DCV391 4.1 66.2 0.5
CD2 B:HIS50 4.3 52.5 1.0
ND1 B:HIS50 4.3 53.1 1.0
C11 B:FM5390 4.4 68.2 0.5
CB B:THR21 4.5 41.5 1.0
CAD B:DCV391 4.6 68.6 0.5
O B:HOH395 4.6 37.4 1.0
C B:THR21 4.7 43.9 1.0
NE2 B:HIS50 4.8 54.3 1.0
CE1 B:HIS50 4.8 53.2 1.0
CA B:THR21 4.9 42.1 1.0
C4 B:FM5390 5.0 72.6 0.5

Chlorine binding site 8 out of 8 in 3ras

Go back to Chlorine Binding Sites List in 3ras
Chlorine binding site 8 out of 8 in the Crystal Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) Complexed with A Lipophilic Phosphonate Inhibitor


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 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) Complexed with A Lipophilic Phosphonate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl391

b:61.2
occ:0.50
 CL2 B:DCV391 0.0 61.2 0.5
CL2 B:FM5390 0.2 60.6 0.5
CAH B:DCV391 1.7 65.1 0.5
C9 B:FM5390 1.8 65.0 0.5
CAF B:DCV391 2.7 66.2 0.5
C8 B:FM5390 2.7 65.3 0.5
CAG B:DCV391 2.8 65.5 0.5
C10 B:FM5390 2.8 65.8 0.5
CL1 B:FM5390 3.2 63.5 0.5
CL1 B:DCV391 3.3 62.9 0.5
CE1 B:HIS50 3.8 53.2 1.0
CZ3 B:TRP203 3.8 72.4 1.0
CAD B:DCV391 4.0 68.6 0.5
O B:TRP203 4.0 84.4 1.0
CE3 B:TRP203 4.1 73.1 1.0
C7 B:FM5390 4.1 67.4 0.5
NE2 B:HIS50 4.1 54.3 1.0
CAE B:DCV391 4.1 67.4 0.5
C11 B:FM5390 4.1 68.2 0.5
ND1 B:HIS50 4.2 53.1 1.0
CA B:SER204 4.3 88.0 1.0
O B:THR21 4.3 45.4 1.0
CB B:SER204 4.6 88.1 1.0
CAC B:DCV391 4.6 70.0 0.5
CD2 B:HIS50 4.6 52.5 1.0
C6 B:FM5390 4.6 69.6 0.5
CG B:HIS50 4.7 50.6 1.0
CH2 B:TRP203 4.7 72.5 1.0
O B:SER204 4.7 89.2 1.0
C B:TRP203 4.9 85.0 1.0

Reference:

L.Deng, J.Diao, P.Chen, V.Pujari, Y.Yao, G.Cheng, D.C.Crick, B.V.Prasad, Y.Song. Inhibition of 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase By Lipophilic Phosphonates: Sar, Qsar, and Crystallographic Studies. J.Med.Chem. V. 54 4721 2011.
ISSN: ISSN 0022-2623
PubMed: 21561155
DOI: 10.1021/JM200363D
Page generated: Fri Jul 11 09:46:33 2025

Last articles

Mg in 2A6E
Mg in 2A5Z
Mg in 2A5L
Mg in 2A5Y
Mg in 2A5J
Mg in 2A43
Mg in 2A5G
Mg in 2A5D
Mg in 2A5F
Mg in 2A42
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy