Atomistry » Manganese » PDB 3q7c-3rl4 » 3ras
Atomistry »
  Manganese »
    PDB 3q7c-3rl4 »
      3ras »

Manganese 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:

Chlorine (Cl) 8 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese 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 Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 3ras

Go back to Manganese Binding Sites List in 3ras
Manganese binding site 1 out of 2 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 Manganese with other atoms in the Mn 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:Mn392

b:51.5
occ:1.00
 OE1 A:GLU153 2.0 43.0 1.0
OD1 A:ASP151 2.0 51.5 1.0
O2 A:DCV391 2.0 52.4 0.5
OE1 A:GLU222 2.1 45.0 1.0
O2 A:FM5390 2.2 51.0 0.5
O1 A:FM5390 2.3 50.2 0.5
O1 A:DCV391 2.5 52.3 0.5
N1 A:DCV391 2.8 51.3 0.5
CD A:GLU153 2.9 44.5 1.0
N1 A:FM5390 3.0 49.4 0.5
C1 A:DCV391 3.0 51.7 0.5
C1 A:FM5390 3.0 49.8 0.5
OE2 A:GLU153 3.1 44.2 1.0
CG A:ASP151 3.1 48.9 1.0
CD A:GLU222 3.1 43.0 1.0
OD2 A:ASP151 3.5 48.2 1.0
OE2 A:GLU222 3.6 44.5 1.0
OG A:SER152 3.9 43.4 1.0
NZ A:LYS128 3.9 55.3 1.0
C3 A:DCV391 4.0 48.1 0.5
C2 A:DCV391 4.1 50.2 0.5
C5N A:NDP1391 4.1 49.6 1.0
N A:SER152 4.2 43.4 1.0
ND2 A:ASN218 4.2 40.6 1.0
CG A:GLU153 4.2 43.7 1.0
N A:GLU153 4.3 40.1 1.0
CB A:ASP151 4.4 47.4 1.0
C2 A:FM5390 4.4 50.0 0.5
C5 A:DCV391 4.4 51.8 0.5
CG A:GLU222 4.4 42.0 1.0
C5 A:FM5390 4.5 47.8 0.5
NZ A:LYS219 4.6 47.4 1.0
CA A:ASP151 4.7 44.8 1.0
CB A:GLU153 4.7 41.2 1.0
C A:ASP151 4.7 45.0 1.0
C4N A:NDP1391 4.8 48.8 1.0
C4 A:FM5390 4.8 46.5 0.5
C3 A:FM5390 4.8 47.3 0.5
CA A:SER152 4.9 41.5 1.0
CB A:SER152 4.9 40.4 1.0
C6N A:NDP1391 5.0 51.4 1.0

Manganese binding site 2 out of 2 in 3ras

Go back to Manganese Binding Sites List in 3ras
Manganese binding site 2 out of 2 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 Manganese with other atoms in the Mn 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
B:Mn392

b:66.8
occ:1.00
 OE1 B:GLU222 2.0 49.4 1.0
OD1 B:ASP151 2.2 57.1 1.0
O B:HOH462 2.5 32.8 1.0
OE1 B:GLU153 2.6 47.6 1.0
OD2 B:ASP151 2.8 54.5 1.0
CG B:ASP151 2.8 53.2 1.0
CD B:GLU222 3.3 51.0 1.0
O B:HOH463 3.4 47.1 1.0
CD B:GLU153 3.8 48.9 1.0
OE2 B:GLU222 4.0 51.7 1.0
OG B:SER152 4.1 46.1 1.0
C5N B:NDP1392 4.1 63.4 1.0
ND2 B:ASN218 4.2 53.7 1.0
NZ B:LYS128 4.3 59.4 1.0
CG B:GLU222 4.3 48.5 1.0
CB B:ASP151 4.3 48.0 1.0
C4N B:NDP1392 4.4 63.8 1.0
OE2 B:GLU153 4.5 50.0 1.0
N B:SER152 4.5 43.6 1.0
N B:GLU153 4.6 38.6 1.0
CG B:GLU153 4.8 45.1 1.0
CB B:GLU153 4.9 42.5 1.0
CA B:ASP151 4.9 43.8 1.0
CB B:SER152 5.0 42.8 1.0
OD1 B:ASN218 5.0 57.4 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: Sat Oct 5 17:43:54 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy