Magnesium in PDB 8u6g: Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 3-(2- (2-(3-Acryloyl-2-Oxo-2,3-Dihydro-1H-Benzo[D]Imidazol-1-Yl)Ethoxy)-4- Chlorophenoxy)-5-Chlorobenzonitrile (JLJ744), A Non-Nucleoside Inhibitor

Enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 3-(2- (2-(3-Acryloyl-2-Oxo-2,3-Dihydro-1H-Benzo[D]Imidazol-1-Yl)Ethoxy)-4- Chlorophenoxy)-5-Chlorobenzonitrile (JLJ744), A Non-Nucleoside Inhibitor

All present enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 3-(2- (2-(3-Acryloyl-2-Oxo-2,3-Dihydro-1H-Benzo[D]Imidazol-1-Yl)Ethoxy)-4- Chlorophenoxy)-5-Chlorobenzonitrile (JLJ744), 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 in Complex with 3-(2- (2-(3-Acryloyl-2-Oxo-2,3-Dihydro-1H-Benzo[D]Imidazol-1-Yl)Ethoxy)-4- Chlorophenoxy)-5-Chlorobenzonitrile (JLJ744), A Non-Nucleoside Inhibitor, PDB code: 8u6g was solved by G.Prucha, Z.Carter, 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) 99.30 / 2.77
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 224.206, 68.746, 104.123, 90, 107.42, 90
R / Rfree (%) 21.3 / 27

Other elements in 8u6g:

The structure of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 3-(2- (2-(3-Acryloyl-2-Oxo-2,3-Dihydro-1H-Benzo[D]Imidazol-1-Yl)Ethoxy)-4- Chlorophenoxy)-5-Chlorobenzonitrile (JLJ744), A Non-Nucleoside Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 3-(2- (2-(3-Acryloyl-2-Oxo-2,3-Dihydro-1H-Benzo[D]Imidazol-1-Yl)Ethoxy)-4- Chlorophenoxy)-5-Chlorobenzonitrile (JLJ744), A Non-Nucleoside Inhibitor (pdb code 8u6g). 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 3-(2- (2-(3-Acryloyl-2-Oxo-2,3-Dihydro-1H-Benzo[D]Imidazol-1-Yl)Ethoxy)-4- Chlorophenoxy)-5-Chlorobenzonitrile (JLJ744), A Non-Nucleoside Inhibitor, PDB code: 8u6g:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 8u6g

Go back to Magnesium Binding Sites List in 8u6g
Magnesium binding site 1 out of 2 in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 3-(2- (2-(3-Acryloyl-2-Oxo-2,3-Dihydro-1H-Benzo[D]Imidazol-1-Yl)Ethoxy)-4- Chlorophenoxy)-5-Chlorobenzonitrile (JLJ744), 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 in Complex with 3-(2- (2-(3-Acryloyl-2-Oxo-2,3-Dihydro-1H-Benzo[D]Imidazol-1-Yl)Ethoxy)-4- Chlorophenoxy)-5-Chlorobenzonitrile (JLJ744), A Non-Nucleoside Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:85.0
occ:1.00
 OD2 A:ASP186 3.4 85.1 1.0
CE A:MET230 3.6 119.5 1.0
OH A:TYR188 4.1 84.7 1.0
CE1 A:TYR183 4.2 103.2 1.0
CD1 A:TYR183 4.2 117.3 1.0
CG A:ASP186 4.3 95.5 1.0
CE A:MET184 4.6 121.5 1.0
CD1 A:TRP229 4.7 97.1 1.0
OD1 A:ASP186 4.7 108.8 1.0
NE1 A:TRP229 4.8 97.0 1.0

Magnesium binding site 2 out of 2 in 8u6g

Go back to Magnesium Binding Sites List in 8u6g
Magnesium binding site 2 out of 2 in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 3-(2- (2-(3-Acryloyl-2-Oxo-2,3-Dihydro-1H-Benzo[D]Imidazol-1-Yl)Ethoxy)-4- Chlorophenoxy)-5-Chlorobenzonitrile (JLJ744), 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 in Complex with 3-(2- (2-(3-Acryloyl-2-Oxo-2,3-Dihydro-1H-Benzo[D]Imidazol-1-Yl)Ethoxy)-4- Chlorophenoxy)-5-Chlorobenzonitrile (JLJ744), A Non-Nucleoside Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:108.2
occ:1.00
 CB A:LYS512 3.0 106.7 1.0
OD1 A:ASP364 3.1 108.2 1.0
CG2 A:THR362 3.3 120.0 1.0
OE1 A:GLN367 3.5 82.3 1.0
OD1 A:ASP511 3.6 118.2 1.0
CD A:GLN367 4.0 88.8 1.0
NE2 A:GLN367 4.2 107.5 1.0
CA A:LYS512 4.3 121.3 1.0
CG A:ASP364 4.3 117.1 1.0
CA A:GLY335 4.3 120.7 1.0
O A:THR362 4.4 111.6 1.0
OG1 A:THR362 4.5 109.3 1.0
CB A:THR362 4.5 108.1 1.0
N A:GLY335 4.5 130.5 1.0
O A:LYS512 4.5 118.1 1.0
C A:THR362 4.6 97.5 1.0
C A:LYS512 4.7 125.6 1.0
N A:LYS512 4.7 109.6 1.0
CG A:ASP511 4.8 115.3 1.0
CA A:ASN363 4.9 99.1 1.0
N A:ASP364 4.9 108.1 1.0
SD A:MET357 4.9 159.1 1.0
C A:ASN363 4.9 84.0 1.0
N A:ASN363 4.9 97.1 1.0
OD2 A:ASP364 4.9 130.8 1.0

Reference:

G.R.Prucha, S.Henry, K.Hollander, Z.J.Carter, K.A.Spasov, W.L.Jorgensen, K.S.Anderson. Covalent and Noncovalent Strategies For Targeting LYS102 in Hiv-1 Reverse Transcriptase. Eur.J.Med.Chem. V. 262 15894 2023.
ISSN: ISSN 0223-5234
PubMed: 37883896
DOI: 10.1016/J.EJMECH.2023.115894
Page generated: Fri Oct 4 21:10:56 2024

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