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Magnesium in PDB 8stq: Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C) Varient 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) Varient 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) Varient 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; 3.1.26.13;

Protein crystallography data

The structure of Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C) Varient 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: 8stq was solved by K.Hollander, K.M.Frey, 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) 35.24 / 2.96
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 161.285, 73.845, 107.256, 90, 99.71, 90
R / Rfree (%) 22.6 / 27.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C) Varient 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 8stq). 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) Varient 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: 8stq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 8stq

Go back to Magnesium Binding Sites List in 8stq
Magnesium binding site 1 out of 2 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C) Varient 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) Varient 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
A:Mg602

b:72.3
occ:1.00
 OD1 A:ASP498 2.6 86.8 1.0
OD1 A:ASP443 2.7 81.8 1.0
CG A:GLU478 2.9 65.0 1.0
MG A:MG603 3.1 93.8 1.0
OE2 A:GLU478 3.2 89.1 1.0
OD2 A:ASP498 3.2 78.1 1.0
CG A:ASP498 3.3 79.6 1.0
CD A:GLU478 3.3 85.6 1.0
O A:GLY444 3.3 75.0 1.0
NZ A:LYS550 3.5 92.4 1.0
N A:GLY444 3.9 64.2 1.0
CG A:ASP443 3.9 84.1 1.0
CB A:GLU478 4.1 61.2 1.0
C A:GLY444 4.3 73.0 1.0
OE1 A:GLU478 4.4 88.1 1.0
CA A:ASP443 4.5 66.4 1.0
CB A:SER499 4.6 65.7 1.0
CA A:GLY444 4.6 64.7 1.0
N A:SER499 4.7 62.4 1.0
OD2 A:ASP443 4.7 100.1 1.0
C A:ASP443 4.7 61.0 1.0
CB A:ASP498 4.7 75.7 1.0
CA A:GLU478 4.7 64.8 1.0
CB A:ASP443 4.8 68.0 1.0
CE A:LYS550 4.8 103.0 1.0
C A:ASP498 4.9 66.7 1.0
CA A:SER499 4.9 67.7 1.0

Magnesium binding site 2 out of 2 in 8stq

Go back to Magnesium Binding Sites List in 8stq
Magnesium binding site 2 out of 2 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C) Varient 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 2 of Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C) Varient 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
A:Mg603

b:93.8
occ:1.00
 OD2 A:ASP498 2.3 78.1 1.0
OD1 A:ASP443 2.6 81.8 1.0
NZ A:LYS550 2.7 92.4 1.0
CE A:LYS550 3.1 103.0 1.0
MG A:MG602 3.1 72.3 1.0
CG A:ASP443 3.3 84.1 1.0
CG A:ASP498 3.4 79.6 1.0
OD2 A:ASP443 3.4 100.1 1.0
NE2 A:GLN547 3.6 100.4 1.0
CG A:GLN547 3.7 112.6 1.0
OD1 A:ASP498 3.8 86.8 1.0
CD A:GLN547 4.1 115.8 1.0
O A:GLY444 4.3 75.0 1.0
CB A:ALA538 4.4 77.4 1.0
CD A:LYS550 4.6 105.3 1.0
CB A:ASP498 4.7 75.7 1.0
CB A:ASP443 4.7 68.0 1.0
CB A:GLN547 4.9 111.0 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: Thu Dec 28 10:22:14 2023

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