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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

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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

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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

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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

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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

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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

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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

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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

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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: Sun Jul 21 03:33:46 2024

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