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Magnesium in PDB 4we1: Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 5-(2- (2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy)Phenoxy)-2- Naphthonitrile (JLJ600)

Enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 5-(2- (2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy)Phenoxy)-2- Naphthonitrile (JLJ600)

All present enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 5-(2- (2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy)Phenoxy)-2- Naphthonitrile (JLJ600):
2.7.7.49; 2.7.7.7; 3.1.13.2; 3.1.26.13; 3.4.23.16;

Protein crystallography data

The structure of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 5-(2- (2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy)Phenoxy)-2- Naphthonitrile (JLJ600), PDB code: 4we1 was solved by K.M.Frey, K.S.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.77 / 2.49
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 220.271, 67.218, 102.483, 90.00, 108.08, 90.00
R / Rfree (%) 23.8 / 28.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 5-(2- (2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy)Phenoxy)-2- Naphthonitrile (JLJ600) (pdb code 4we1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 5-(2- (2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy)Phenoxy)-2- Naphthonitrile (JLJ600), PDB code: 4we1:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4we1

Go back to Magnesium Binding Sites List in 4we1
Magnesium binding site 1 out of 2 in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 5-(2- (2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy)Phenoxy)-2- Naphthonitrile (JLJ600)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 5-(2- (2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy)Phenoxy)-2- Naphthonitrile (JLJ600) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:75.8
occ:1.00
 OD1 A:ASP185 2.5 64.2 1.0
OD1 A:ASP186 2.5 57.5 1.0
CG A:ASP185 2.9 69.5 1.0
OD2 A:ASP185 3.1 68.1 1.0
CG A:ASP186 3.3 57.7 1.0
OD2 A:ASP110 3.3 69.0 1.0
OD2 A:ASP186 3.6 60.4 1.0
CB A:ASP185 4.0 52.5 1.0
N A:ASP186 4.3 49.9 1.0
CG A:ASP110 4.4 71.3 1.0
CB A:ASP186 4.6 48.8 1.0
CB A:ASP110 4.7 58.9 1.0
CA A:ASP186 4.8 52.7 1.0
CA A:ASP185 4.8 58.0 1.0
C A:ASP185 4.9 59.1 1.0
N A:ASP185 4.9 52.6 1.0

Magnesium binding site 2 out of 2 in 4we1

Go back to Magnesium Binding Sites List in 4we1
Magnesium binding site 2 out of 2 in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 5-(2- (2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy)Phenoxy)-2- Naphthonitrile (JLJ600)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 5-(2- (2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy)Phenoxy)-2- Naphthonitrile (JLJ600) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:58.7
occ:1.00
 OD1 A:ASP498 2.2 48.8 1.0
OE2 A:GLU478 2.4 62.0 1.0
OD2 A:ASP498 2.8 63.4 1.0
CG A:ASP498 2.8 43.4 1.0
OD1 A:ASP443 3.0 69.4 1.0
OD2 A:ASP443 3.1 66.0 1.0
CG A:ASP443 3.4 65.0 1.0
O A:HOH739 3.4 46.9 1.0
CD A:GLU478 3.6 63.7 1.0
CB A:ASP498 4.2 39.6 1.0
OE1 A:GLU478 4.2 64.2 1.0
O A:GLY444 4.4 63.5 1.0
OE2 A:GLU546 4.5 90.3 1.0
CG A:GLU478 4.7 63.9 1.0
C A:ASP498 4.8 46.2 1.0
CB A:ASP443 4.8 58.4 1.0
OE1 A:GLU546 4.9 94.0 1.0
CB A:ALA538 4.9 45.6 1.0
CD A:GLU546 5.0 85.8 1.0

Reference:

W.G.Lee, K.M.Frey, R.Gallardo-Macias, K.A.Spasov, M.Bollini, K.S.Anderson, W.L.Jorgensen. Picomolar Inhibitors of Hiv-1 Reverse Transcriptase: Design and Crystallography of Naphthyl Phenyl Ethers. Acs Med.Chem.Lett. V. 5 1259 2014.
ISSN: ISSN 1948-5875
PubMed: 25408842
DOI: 10.1021/ML5003713
Page generated: Mon Dec 14 19:40:13 2020

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