Magnesium in PDB 7snz: Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 6- ((2-((4-Cyanophenyl)Amino)Pyrimidin-4-Yl)Amino)-5,7- Dimethylindolizine-2-Carbonitrile (JLJ604)

Enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 6- ((2-((4-Cyanophenyl)Amino)Pyrimidin-4-Yl)Amino)-5,7- Dimethylindolizine-2-Carbonitrile (JLJ604)

All present enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 6- ((2-((4-Cyanophenyl)Amino)Pyrimidin-4-Yl)Amino)-5,7- Dimethylindolizine-2-Carbonitrile (JLJ604):
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 in Complex with 6- ((2-((4-Cyanophenyl)Amino)Pyrimidin-4-Yl)Amino)-5,7- Dimethylindolizine-2-Carbonitrile (JLJ604), PDB code: 7snz was solved by K.M.Frey, K.S.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.83 / 2.37
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 161.909, 72.527, 108.95, 90, 100.46, 90
R / Rfree (%) 20.5 / 24.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 6- ((2-((4-Cyanophenyl)Amino)Pyrimidin-4-Yl)Amino)-5,7- Dimethylindolizine-2-Carbonitrile (JLJ604) (pdb code 7snz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 6- ((2-((4-Cyanophenyl)Amino)Pyrimidin-4-Yl)Amino)-5,7- Dimethylindolizine-2-Carbonitrile (JLJ604), PDB code: 7snz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7snz

Go back to Magnesium Binding Sites List in 7snz
Magnesium binding site 1 out of 4 in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 6- ((2-((4-Cyanophenyl)Amino)Pyrimidin-4-Yl)Amino)-5,7- Dimethylindolizine-2-Carbonitrile (JLJ604)


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 6- ((2-((4-Cyanophenyl)Amino)Pyrimidin-4-Yl)Amino)-5,7- Dimethylindolizine-2-Carbonitrile (JLJ604) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:76.5
occ:1.00
 O A:HOH763 2.2 63.2 1.0
OH A:TYR271 2.9 54.9 1.0
N A:ILE244 3.4 63.1 1.0
O A:ILE244 3.6 60.6 1.0
CZ A:TYR271 3.7 59.2 1.0
O A:LEU310 4.0 64.4 1.0
CB A:ILE244 4.1 69.7 1.0
CA A:ILE244 4.1 68.4 1.0
C A:ILE244 4.3 65.1 1.0
CE1 A:TYR271 4.3 58.6 1.0
CA A:PRO243 4.4 67.3 1.0
C A:PRO243 4.4 66.9 1.0
CE2 A:TYR271 4.4 57.4 1.0
CG1 A:ILE244 4.6 66.6 1.0
C A:LEU310 4.9 64.4 1.0
CD2 A:LEU310 5.0 57.8 1.0

Magnesium binding site 2 out of 4 in 7snz

Go back to Magnesium Binding Sites List in 7snz
Magnesium binding site 2 out of 4 in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 6- ((2-((4-Cyanophenyl)Amino)Pyrimidin-4-Yl)Amino)-5,7- Dimethylindolizine-2-Carbonitrile (JLJ604)


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 6- ((2-((4-Cyanophenyl)Amino)Pyrimidin-4-Yl)Amino)-5,7- Dimethylindolizine-2-Carbonitrile (JLJ604) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:64.6
occ:1.00
 O A:HOH753 2.3 59.0 1.0
OD2 A:ASP498 2.3 43.1 1.0
OE2 A:GLU546 2.4 73.4 1.0
OD2 A:ASP443 2.8 63.3 1.0
CD A:GLU546 3.2 73.0 1.0
CG A:ASP498 3.5 42.6 1.0
CG A:ASP443 3.7 53.2 1.0
OE1 A:GLU546 3.8 72.6 1.0
CB A:ALA538 3.9 53.0 1.0
OD1 A:ASP443 4.0 55.0 1.0
OD1 A:ASP498 4.0 46.2 1.0
CG A:GLU546 4.0 77.9 1.0
CE1 A:HIS539 4.3 71.5 1.0
ND1 A:HIS539 4.3 68.9 1.0
N A:HIS539 4.5 67.4 1.0
CA A:ALA538 4.5 53.9 1.0
CB A:ASP498 4.6 38.2 1.0

Magnesium binding site 3 out of 4 in 7snz

Go back to Magnesium Binding Sites List in 7snz
Magnesium binding site 3 out of 4 in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 6- ((2-((4-Cyanophenyl)Amino)Pyrimidin-4-Yl)Amino)-5,7- Dimethylindolizine-2-Carbonitrile (JLJ604)


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 6- ((2-((4-Cyanophenyl)Amino)Pyrimidin-4-Yl)Amino)-5,7- Dimethylindolizine-2-Carbonitrile (JLJ604) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg606

b:63.2
occ:1.00
 O A:GLU138 3.9 50.0 1.0
CB A:GLU138 4.5 48.3 1.0
CA A:GLU138 4.8 54.8 1.0
C A:GLU138 4.8 50.8 1.0
CG A:GLU138 4.8 48.0 1.0

Magnesium binding site 4 out of 4 in 7snz

Go back to Magnesium Binding Sites List in 7snz
Magnesium binding site 4 out of 4 in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 6- ((2-((4-Cyanophenyl)Amino)Pyrimidin-4-Yl)Amino)-5,7- Dimethylindolizine-2-Carbonitrile (JLJ604)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 6- ((2-((4-Cyanophenyl)Amino)Pyrimidin-4-Yl)Amino)-5,7- Dimethylindolizine-2-Carbonitrile (JLJ604) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:70.6
occ:1.00
 OE2 B:GLU404 3.4 57.3 1.0
CG B:GLU404 3.5 51.0 1.0
CD1 A:ILE380 3.5 49.0 1.0
CZ3 B:TRP401 3.6 46.5 1.0
O B:THR400 3.7 48.0 1.0
CE3 B:TRP401 3.7 48.2 1.0
CD B:GLU404 3.7 54.7 1.0
CH2 B:TRP401 4.5 47.6 1.0
CG2 B:THR27 4.6 37.0 1.0
CD2 B:TRP401 4.7 45.3 1.0
OG1 A:THR386 4.8 44.2 1.0
OE1 B:GLU404 4.8 52.2 1.0
C B:THR400 4.8 46.0 1.0
CG1 A:ILE380 4.8 33.6 1.0
CB B:GLU404 4.9 49.3 1.0
O B:HOH607 4.9 44.5 1.0

Reference:

K.M.Frey, N.Bertoletti, A.H.Chan, J.A.Ippolito, M.Bollini, K.A.Spasov, W.L.Jorgensen, K.S.Anderson. Structural Studies and Structure Activity Relationships For Novel Computationally Designed Non-Nucleoside Inhibitors and Their Interactions with Hiv-1 Reverse Transcriptase. Front Mol Biosci V. 9 05187 2022.
ISSN: ESSN 2296-889X
PubMed: 35237658
DOI: 10.3389/FMOLB.2022.805187
Page generated: Thu Oct 3 08:49:06 2024

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