Magnesium in PDB 8sts: Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) Varient in Complex with 5-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin- 1(2H)-Yl)Ethoxy)-4-Fluorophenoxy)-7-Fluoro-2-Naphthonitrile (JLJ636), A Non-Nucleoside Inhibitor

Enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) Varient in Complex with 5-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin- 1(2H)-Yl)Ethoxy)-4-Fluorophenoxy)-7-Fluoro-2-Naphthonitrile (JLJ636), A Non-Nucleoside Inhibitor

All present enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) Varient in Complex with 5-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin- 1(2H)-Yl)Ethoxy)-4-Fluorophenoxy)-7-Fluoro-2-Naphthonitrile (JLJ636), A Non-Nucleoside Inhibitor:
2.7.7.49; 2.7.7.7; 3.1.26.13;

Protein crystallography data

The structure of Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) Varient in Complex with 5-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin- 1(2H)-Yl)Ethoxy)-4-Fluorophenoxy)-7-Fluoro-2-Naphthonitrile (JLJ636), A Non-Nucleoside Inhibitor, PDB code: 8sts was solved by K.Hollander, W.L.Jorgensen, K.S.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.11 / 3.02
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.86, 128.26, 133.042, 90, 105.32, 90
R / Rfree (%) 24 / 28.5

Other elements in 8sts:

The structure of Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) Varient in Complex with 5-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin- 1(2H)-Yl)Ethoxy)-4-Fluorophenoxy)-7-Fluoro-2-Naphthonitrile (JLJ636), A Non-Nucleoside Inhibitor also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) Varient in Complex with 5-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin- 1(2H)-Yl)Ethoxy)-4-Fluorophenoxy)-7-Fluoro-2-Naphthonitrile (JLJ636), A Non-Nucleoside Inhibitor (pdb code 8sts). 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 (Y181C, V106A) Varient in Complex with 5-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin- 1(2H)-Yl)Ethoxy)-4-Fluorophenoxy)-7-Fluoro-2-Naphthonitrile (JLJ636), A Non-Nucleoside Inhibitor, PDB code: 8sts:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 8sts

Go back to Magnesium Binding Sites List in 8sts
Magnesium binding site 1 out of 2 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) Varient in Complex with 5-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin- 1(2H)-Yl)Ethoxy)-4-Fluorophenoxy)-7-Fluoro-2-Naphthonitrile (JLJ636), A Non-Nucleoside Inhibitor


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 (Y181C, V106A) Varient in Complex with 5-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin- 1(2H)-Yl)Ethoxy)-4-Fluorophenoxy)-7-Fluoro-2-Naphthonitrile (JLJ636), A Non-Nucleoside Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:87.7
occ:1.00
 OD1 C:ASP549 2.4 137.7 1.0
OD2 C:ASP443 2.8 114.2 1.0
OD1 C:ASP443 3.2 101.4 1.0
OD2 C:ASP498 3.3 115.4 1.0
CG C:ASP443 3.4 115.8 1.0
CG C:ASP549 3.5 145.8 1.0
OD2 C:ASP549 4.2 137.9 1.0
NE2 C:HIS539 4.3 130.2 1.0
CG C:ASP498 4.4 115.3 1.0
CB C:ASP549 4.5 144.1 1.0
O C:GLY444 4.7 112.7 1.0
CE1 C:HIS539 4.7 136.8 1.0
OD1 C:ASP498 4.9 108.8 1.0
CB C:ASP443 4.9 98.1 1.0
CB C:ALA538 5.0 119.6 1.0

Magnesium binding site 2 out of 2 in 8sts

Go back to Magnesium Binding Sites List in 8sts
Magnesium binding site 2 out of 2 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) Varient in Complex with 5-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin- 1(2H)-Yl)Ethoxy)-4-Fluorophenoxy)-7-Fluoro-2-Naphthonitrile (JLJ636), A Non-Nucleoside Inhibitor


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 (Y181C, V106A) Varient in Complex with 5-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin- 1(2H)-Yl)Ethoxy)-4-Fluorophenoxy)-7-Fluoro-2-Naphthonitrile (JLJ636), A Non-Nucleoside Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:86.4
occ:1.00
 OD2 A:ASP549 2.3 112.9 1.0
OD2 A:ASP443 2.7 92.1 1.0
OD1 A:ASP443 3.3 83.9 1.0
CG A:ASP549 3.4 103.0 1.0
CG A:ASP443 3.4 94.0 1.0
OD2 A:ASP498 3.6 115.2 1.0
O A:GLY444 4.1 117.8 1.0
OD1 A:ASP549 4.2 109.3 1.0
CB A:ASP549 4.3 84.0 1.0
CE1 A:HIS539 4.4 120.0 1.0
NE2 A:HIS539 4.6 129.6 1.0
CG A:ASP498 4.7 105.5 1.0
CB A:ALA538 4.9 110.2 1.0
CB A:ASP443 4.9 82.7 1.0
OD1 A:ASP498 4.9 101.8 1.0

Reference:

K.Hollander, A.H.Chan, K.M.Frey, O.Hunker, J.A.Ippolito, K.A.Spasov, Y.J.Yeh, W.L.Jorgensen, Y.C.Ho, K.S.Anderson. Exploring Novel Hiv-1 Reverse Transcriptase Inhibitors with Drug Resistant Mutants: A Double Mutant Surprise. Protein Sci. E4814 2023.
ISSN: ESSN 1469-896X
PubMed: 37861472
DOI: 10.1002/PRO.4814
Page generated: Fri Oct 4 20:11:42 2024

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