Atomistry » Magnesium » PDB 4w5o-4wfm » 4we1
Atomistry »
  Magnesium »
    PDB 4w5o-4wfm »
      4we1 »

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: Tue Aug 20 13:11:43 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy