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Magnesium in PDB 8stv: Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) Variant in Complex with 5-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin- 1(2H)-Yl)Ethoxy)Phenoxy)-2-Naphthonitrile (JLJ600), A Non-Nucleoside Inhibitor

Enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) Variant in Complex with 5-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin- 1(2H)-Yl)Ethoxy)Phenoxy)-2-Naphthonitrile (JLJ600), A Non-Nucleoside Inhibitor

All present enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) Variant in Complex with 5-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin- 1(2H)-Yl)Ethoxy)Phenoxy)-2-Naphthonitrile (JLJ600), A Non-Nucleoside Inhibitor:
2.7.7.49; 2.7.7.7; 3.1.13.2; 3.1.26.13;

Protein crystallography data

The structure of Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) Variant in Complex with 5-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin- 1(2H)-Yl)Ethoxy)Phenoxy)-2-Naphthonitrile (JLJ600), A Non-Nucleoside Inhibitor, PDB code: 8stv 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) 37.83 / 2.78
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 111.591, 73.222, 170.655, 90, 97.73, 90
R / Rfree (%) 23.2 / 27.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) Variant in Complex with 5-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin- 1(2H)-Yl)Ethoxy)Phenoxy)-2-Naphthonitrile (JLJ600), A Non-Nucleoside Inhibitor (pdb code 8stv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) Variant in Complex with 5-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin- 1(2H)-Yl)Ethoxy)Phenoxy)-2-Naphthonitrile (JLJ600), A Non-Nucleoside Inhibitor, PDB code: 8stv:

Magnesium binding site 1 out of 1 in 8stv

Go back to Magnesium Binding Sites List in 8stv
Magnesium binding site 1 out of 1 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) Variant in Complex with 5-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin- 1(2H)-Yl)Ethoxy)Phenoxy)-2-Naphthonitrile (JLJ600), 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) Variant in Complex with 5-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin- 1(2H)-Yl)Ethoxy)Phenoxy)-2-Naphthonitrile (JLJ600), A Non-Nucleoside Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:100.0
occ:1.00
 OD2 C:ASP443 2.6 106.7 1.0
OD1 C:ASP443 2.7 113.9 1.0
OD2 C:ASP549 2.8 124.7 1.0
CG C:ASP443 3.0 92.8 1.0
OD1 C:ASP549 3.1 128.4 1.0
CG C:ASP549 3.2 125.6 1.0
OD2 C:ASP498 3.3 106.4 1.0
O C:GLY444 3.9 100.7 1.0
CE1 C:HIS539 4.0 130.1 1.0
CG C:ASP498 4.2 97.7 1.0
OD1 C:ASP498 4.4 108.2 1.0
CB C:ASP549 4.5 111.8 1.0
CB C:ASP443 4.5 85.8 1.0
NE2 C:HIS539 4.8 135.4 1.0
C C:GLY444 4.9 89.6 1.0
CA C:ASP549 4.9 103.8 1.0
ND1 C:HIS539 4.9 125.8 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 Aug 15 16:00:54 2025

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