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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: Tue Dec 15 04:14:39 2020

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