Magnesium in PDB 8u6k: Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with N-(2- (2-((6-Cyanonaphthalen-1-Yl)Oxy)Phenoxy)Ethyl)-N-Methylacrylamide (JLJ747), A Non-Nucleoside Inhibitor

Enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with N-(2- (2-((6-Cyanonaphthalen-1-Yl)Oxy)Phenoxy)Ethyl)-N-Methylacrylamide (JLJ747), A Non-Nucleoside Inhibitor

All present enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with N-(2- (2-((6-Cyanonaphthalen-1-Yl)Oxy)Phenoxy)Ethyl)-N-Methylacrylamide (JLJ747), 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 N-(2- (2-((6-Cyanonaphthalen-1-Yl)Oxy)Phenoxy)Ethyl)-N-Methylacrylamide (JLJ747), A Non-Nucleoside Inhibitor, PDB code: 8u6k was solved by G.Prucha, S.Henry, 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) 32.72 / 2.72
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 222.132, 68.384, 103.54, 90, 107.54, 90
R / Rfree (%) 22 / 27.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with N-(2- (2-((6-Cyanonaphthalen-1-Yl)Oxy)Phenoxy)Ethyl)-N-Methylacrylamide (JLJ747), A Non-Nucleoside Inhibitor (pdb code 8u6k). 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 N-(2- (2-((6-Cyanonaphthalen-1-Yl)Oxy)Phenoxy)Ethyl)-N-Methylacrylamide (JLJ747), A Non-Nucleoside Inhibitor, PDB code: 8u6k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 8u6k

Go back to Magnesium Binding Sites List in 8u6k
Magnesium binding site 1 out of 2 in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with N-(2- (2-((6-Cyanonaphthalen-1-Yl)Oxy)Phenoxy)Ethyl)-N-Methylacrylamide (JLJ747), 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 N-(2- (2-((6-Cyanonaphthalen-1-Yl)Oxy)Phenoxy)Ethyl)-N-Methylacrylamide (JLJ747), A Non-Nucleoside Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:91.4
occ:1.00
 OD2 A:ASP498 2.4 85.8 1.0
OD2 A:ASP443 2.7 82.8 1.0
OD1 A:ASP549 3.0 100.4 1.0
OD1 A:ASP443 3.1 90.1 1.0
CG A:ASP443 3.3 83.3 1.0
CG A:ASP498 3.4 75.6 1.0
OD1 A:ASP498 3.7 74.2 1.0
CG A:ASP549 4.2 97.9 1.0
OE2 A:GLU478 4.3 82.3 1.0
NE2 A:HIS539 4.4 97.5 1.0
CE1 A:HIS539 4.5 94.2 1.0
O A:GLY444 4.5 80.7 1.0
CB A:ASP498 4.8 67.2 1.0
CB A:ALA538 4.8 73.1 1.0
CB A:ASP443 4.8 76.0 1.0

Magnesium binding site 2 out of 2 in 8u6k

Go back to Magnesium Binding Sites List in 8u6k
Magnesium binding site 2 out of 2 in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with N-(2- (2-((6-Cyanonaphthalen-1-Yl)Oxy)Phenoxy)Ethyl)-N-Methylacrylamide (JLJ747), 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 N-(2- (2-((6-Cyanonaphthalen-1-Yl)Oxy)Phenoxy)Ethyl)-N-Methylacrylamide (JLJ747), A Non-Nucleoside Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:62.2
occ:1.00
 OD1 B:ASN57 2.6 59.1 1.0
OE1 B:GLN23 2.7 64.9 1.0
O B:THR58 2.7 60.4 1.0
N B:THR131 3.1 53.1 1.0
CB B:GLN23 3.2 56.4 1.0
O B:THR131 3.3 59.7 1.0
CG B:ASN57 3.3 52.4 1.0
ND2 B:ASN57 3.3 56.7 1.0
CD B:GLN23 3.5 63.6 1.0
CB B:THR131 3.5 56.9 1.0
C B:THR58 3.6 59.9 1.0
CA B:PRO59 3.6 62.9 1.0
OG1 B:THR131 3.6 60.5 1.0
CG B:GLN23 3.6 55.6 1.0
CA B:THR131 3.7 52.5 1.0
C B:THR131 3.9 54.9 1.0
N B:PRO59 4.0 61.0 1.0
C B:PHE130 4.1 58.9 1.0
CA B:PHE130 4.2 55.2 1.0
CA B:GLN23 4.2 55.7 1.0
N B:VAL60 4.2 55.1 1.0
C B:PRO59 4.3 56.3 1.0
CB B:PHE130 4.3 55.4 1.0
N B:THR58 4.4 56.8 1.0
CA B:THR58 4.6 59.9 1.0
CB B:ASN57 4.7 58.8 1.0
CB B:PRO59 4.8 58.7 1.0
N B:GLN23 4.8 55.4 1.0
NE2 B:GLN23 4.8 56.6 1.0
CG1 B:VAL60 4.9 52.6 1.0
CG2 B:THR131 5.0 55.9 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 21:11:08 2024

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