Magnesium in PDB 8u6l: Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with N-(2- (5-Chloro-2-((6-Cyanonaphthalen-1-Yl)Oxy)Phenoxy)Ethyl)-N- Methylacrylamide (JLJ748), A Non-Nucleoside Inhibitor

Enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with N-(2- (5-Chloro-2-((6-Cyanonaphthalen-1-Yl)Oxy)Phenoxy)Ethyl)-N- Methylacrylamide (JLJ748), A Non-Nucleoside Inhibitor

All present enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with N-(2- (5-Chloro-2-((6-Cyanonaphthalen-1-Yl)Oxy)Phenoxy)Ethyl)-N- Methylacrylamide (JLJ748), 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- (5-Chloro-2-((6-Cyanonaphthalen-1-Yl)Oxy)Phenoxy)Ethyl)-N- Methylacrylamide (JLJ748), A Non-Nucleoside Inhibitor, PDB code: 8u6l 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) 31.61 / 2.49
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 222.881, 67.633, 103.709, 90, 107.88, 90
R / Rfree (%) 22.1 / 26.7

Other elements in 8u6l:

The structure of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with N-(2- (5-Chloro-2-((6-Cyanonaphthalen-1-Yl)Oxy)Phenoxy)Ethyl)-N- Methylacrylamide (JLJ748), A Non-Nucleoside Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with N-(2- (5-Chloro-2-((6-Cyanonaphthalen-1-Yl)Oxy)Phenoxy)Ethyl)-N- Methylacrylamide (JLJ748), A Non-Nucleoside Inhibitor (pdb code 8u6l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with N-(2- (5-Chloro-2-((6-Cyanonaphthalen-1-Yl)Oxy)Phenoxy)Ethyl)-N- Methylacrylamide (JLJ748), A Non-Nucleoside Inhibitor, PDB code: 8u6l:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 8u6l

Go back to Magnesium Binding Sites List in 8u6l
Magnesium binding site 1 out of 3 in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with N-(2- (5-Chloro-2-((6-Cyanonaphthalen-1-Yl)Oxy)Phenoxy)Ethyl)-N- Methylacrylamide (JLJ748), 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- (5-Chloro-2-((6-Cyanonaphthalen-1-Yl)Oxy)Phenoxy)Ethyl)-N- Methylacrylamide (JLJ748), A Non-Nucleoside Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:83.3
occ:1.00
 OD2 A:ASP498 2.4 79.4 1.0
OD2 A:ASP443 2.9 76.5 1.0
OD1 A:ASP498 3.0 63.5 1.0
OD1 A:ASP443 3.0 77.1 1.0
CG A:ASP498 3.0 63.5 1.0
CG A:ASP443 3.3 71.3 1.0
OD1 A:ASP549 3.4 87.5 1.0
OE2 A:GLU478 3.6 76.3 1.0
CB A:ALA538 4.4 55.5 1.0
CB A:ASP498 4.5 53.9 1.0
CG A:ASP549 4.6 79.6 1.0
CB A:ASP443 4.7 62.7 1.0
O A:GLY444 4.8 70.3 1.0
NE2 A:HIS539 4.8 80.0 1.0
CD A:GLU478 4.8 77.3 1.0
CE1 A:HIS539 4.9 85.9 1.0

Magnesium binding site 2 out of 3 in 8u6l

Go back to Magnesium Binding Sites List in 8u6l
Magnesium binding site 2 out of 3 in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with N-(2- (5-Chloro-2-((6-Cyanonaphthalen-1-Yl)Oxy)Phenoxy)Ethyl)-N- Methylacrylamide (JLJ748), 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- (5-Chloro-2-((6-Cyanonaphthalen-1-Yl)Oxy)Phenoxy)Ethyl)-N- Methylacrylamide (JLJ748), A Non-Nucleoside Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:74.7
occ:1.00
 N A:ARG358 2.9 84.8 1.0
N A:MET357 3.4 83.0 1.0
CA A:ARG358 3.6 90.0 1.0
NE A:ARG356 3.9 89.3 1.0
C A:MET357 4.0 82.9 1.0
CB A:ARG356 4.0 76.8 1.0
NH2 A:ARG356 4.0 92.1 1.0
CA A:ARG356 4.0 80.6 1.0
CA A:MET357 4.1 84.9 1.0
C A:ARG356 4.1 81.6 1.0
CB A:ARG358 4.3 91.4 1.0
CB A:MET357 4.4 88.4 1.0
CZ A:ARG356 4.4 93.8 1.0
CG A:ARG356 4.6 79.8 1.0
C A:ARG358 4.8 81.7 1.0
CD A:ARG356 4.9 85.4 1.0
NH1 A:ARG277 4.9 89.2 1.0
N A:GLY359 5.0 78.6 1.0

Magnesium binding site 3 out of 3 in 8u6l

Go back to Magnesium Binding Sites List in 8u6l
Magnesium binding site 3 out of 3 in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with N-(2- (5-Chloro-2-((6-Cyanonaphthalen-1-Yl)Oxy)Phenoxy)Ethyl)-N- Methylacrylamide (JLJ748), A Non-Nucleoside Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with N-(2- (5-Chloro-2-((6-Cyanonaphthalen-1-Yl)Oxy)Phenoxy)Ethyl)-N- Methylacrylamide (JLJ748), A Non-Nucleoside Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:61.6
occ:1.00
 N B:THR131 2.7 49.4 1.0
OE1 B:GLN23 2.7 54.7 1.0
O B:THR58 2.9 54.4 1.0
OD1 B:ASN57 2.9 53.1 1.0
O B:THR131 3.0 55.1 1.0
ND2 B:ASN57 3.2 50.2 1.0
CB B:THR131 3.2 53.8 1.0
CA B:THR131 3.3 51.8 1.0
CB B:GLN23 3.4 51.6 1.0
CG B:ASN57 3.4 50.0 1.0
OG1 B:THR131 3.6 54.8 1.0
CD B:GLN23 3.6 57.9 1.0
C B:THR131 3.6 52.5 1.0
C B:PHE130 3.7 50.3 1.0
C B:THR58 3.8 50.2 1.0
CG B:GLN23 3.8 52.7 1.0
CA B:PHE130 3.8 51.4 1.0
CA B:PRO59 3.9 52.4 1.0
CB B:PHE130 4.1 50.1 1.0
CA B:GLN23 4.2 53.3 1.0
N B:VAL60 4.2 45.4 1.0
N B:PRO59 4.3 55.3 1.0
C B:PRO59 4.4 52.3 1.0
N B:THR58 4.5 52.8 1.0
CG2 B:THR131 4.6 50.7 1.0
CG2 B:VAL60 4.6 44.4 1.0
N B:GLN23 4.7 58.2 1.0
CA B:THR58 4.8 50.9 1.0
O B:PHE130 4.8 51.8 1.0
NE2 B:GLN23 4.8 55.8 1.0
CG1 B:VAL60 4.9 57.1 1.0
CB B:ASN57 4.9 52.6 1.0
N B:ILE132 4.9 47.0 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 21:11:35 2024

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