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Magnesium in PDB 5hlf: Structure of Hiv-1 Reverse Transcriptase in Complex with A 38-Mer Hairpin Template-Primer Dna Aptamer and An Alpha-Carboxyphosphonate Inhibitor

Enzymatic activity of Structure of Hiv-1 Reverse Transcriptase in Complex with A 38-Mer Hairpin Template-Primer Dna Aptamer and An Alpha-Carboxyphosphonate Inhibitor

All present enzymatic activity of Structure of Hiv-1 Reverse Transcriptase in Complex with A 38-Mer Hairpin Template-Primer Dna Aptamer and An Alpha-Carboxyphosphonate Inhibitor:
2.7.7.49;

Protein crystallography data

The structure of Structure of Hiv-1 Reverse Transcriptase in Complex with A 38-Mer Hairpin Template-Primer Dna Aptamer and An Alpha-Carboxyphosphonate Inhibitor, PDB code: 5hlf was solved by K.Das, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.00 / 2.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.060, 128.560, 132.410, 90.00, 101.46, 90.00
R / Rfree (%) 20.8 / 25.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Hiv-1 Reverse Transcriptase in Complex with A 38-Mer Hairpin Template-Primer Dna Aptamer and An Alpha-Carboxyphosphonate Inhibitor (pdb code 5hlf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of Hiv-1 Reverse Transcriptase in Complex with A 38-Mer Hairpin Template-Primer Dna Aptamer and An Alpha-Carboxyphosphonate Inhibitor, PDB code: 5hlf:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5hlf

Go back to Magnesium Binding Sites List in 5hlf
Magnesium binding site 1 out of 3 in the Structure of Hiv-1 Reverse Transcriptase in Complex with A 38-Mer Hairpin Template-Primer Dna Aptamer and An Alpha-Carboxyphosphonate Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Hiv-1 Reverse Transcriptase in Complex with A 38-Mer Hairpin Template-Primer Dna Aptamer and An Alpha-Carboxyphosphonate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:0.1
occ:1.00
 O15 A:64A602 2.2 0.1 1.0
O A:VAL111 2.3 0.3 1.0
O17 A:64A602 2.4 0.8 1.0
OD2 A:ASP185 2.5 0.9 1.0
C13 A:64A602 3.2 0.2 1.0
C A:VAL111 3.4 0.2 1.0
C16 A:64A602 3.4 0.7 1.0
CB A:ASP110 3.5 0.7 1.0
CG A:ASP185 3.6 0.3 1.0
C12 A:64A602 3.8 1.0 1.0
N A:VAL111 4.0 0.1 1.0
C A:ASP110 4.1 0.3 1.0
O14 A:64A602 4.1 0.8 1.0
CA A:GLY112 4.2 0.9 1.0
OD1 A:ASP185 4.2 0.9 1.0
N A:GLY112 4.2 0.7 1.0
CA A:ASP110 4.3 0.5 1.0
CA A:VAL111 4.4 0.3 1.0
CG A:ASP110 4.4 0.2 1.0
O11 A:64A602 4.4 0.7 1.0
O18 A:64A602 4.5 0.9 1.0
O A:ASP110 4.5 0.3 1.0
OD2 A:ASP110 4.6 0.4 1.0
CB A:ASP185 4.7 0.9 1.0
N A:ASP113 4.7 0.6 1.0
C A:GLY112 4.9 0.9 1.0

Magnesium binding site 2 out of 3 in 5hlf

Go back to Magnesium Binding Sites List in 5hlf
Magnesium binding site 2 out of 3 in the Structure of Hiv-1 Reverse Transcriptase in Complex with A 38-Mer Hairpin Template-Primer Dna Aptamer and An Alpha-Carboxyphosphonate Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Hiv-1 Reverse Transcriptase in Complex with A 38-Mer Hairpin Template-Primer Dna Aptamer and An Alpha-Carboxyphosphonate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:82.4
occ:1.00
 OD2 A:ASP443 1.9 86.8 1.0
O A:HOH701 2.1 83.9 1.0
OD1 A:ASP549 2.6 97.5 1.0
CG A:ASP443 2.7 77.6 1.0
OD1 A:ASP443 2.7 81.0 1.0
CG A:ASP549 3.6 95.9 1.0
OD2 A:ASP498 4.0 80.6 1.0
OD1 A:ASP498 4.1 80.6 1.0
CB A:ASP443 4.1 64.6 1.0
CB A:ASP549 4.3 88.1 1.0
O A:GLY444 4.3 75.9 1.0
CG A:ASP498 4.4 73.0 1.0
OD2 A:ASP549 4.5 0.8 1.0
CA A:ASP549 4.7 86.6 1.0
N A:GLY444 5.0 58.3 1.0
CB A:ALA538 5.0 77.3 1.0

Magnesium binding site 3 out of 3 in 5hlf

Go back to Magnesium Binding Sites List in 5hlf
Magnesium binding site 3 out of 3 in the Structure of Hiv-1 Reverse Transcriptase in Complex with A 38-Mer Hairpin Template-Primer Dna Aptamer and An Alpha-Carboxyphosphonate Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Hiv-1 Reverse Transcriptase in Complex with A 38-Mer Hairpin Template-Primer Dna Aptamer and An Alpha-Carboxyphosphonate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:81.3
occ:1.00
 O C:HOH701 2.1 80.8 1.0
O C:HOH703 2.1 76.8 1.0
O C:HOH702 2.1 67.3 1.0
OD2 C:ASP443 2.2 77.2 1.0
OD1 C:ASP549 2.5 75.1 1.0
OD1 C:ASP443 2.6 69.7 1.0
CG C:ASP443 2.8 64.8 1.0
CG C:ASP549 3.7 79.5 1.0
OD1 C:ASP498 4.0 75.2 1.0
O C:GLY444 4.1 78.8 1.0
CB C:ASP549 4.3 71.1 1.0
CB C:ASP443 4.3 53.0 1.0
CA C:ASP549 4.6 72.0 1.0
OD2 C:ASP549 4.7 69.2 1.0
N C:GLY444 4.9 56.5 1.0
CB C:ALA538 5.0 78.9 1.0
C C:GLY444 5.0 68.3 1.0

Reference:

N.D.Mullins, N.M.Maguire, A.Ford, K.Das, E.Arnold, J.Balzarini, A.R.Maguire. Exploring the Role of the Alpha-Carboxyphosphonate Moiety in the Hiv-Rt Activity of Alpha-Carboxy Nucleoside Phosphonates. Org.Biomol.Chem. V. 14 2454 2016.
ISSN: ESSN 1477-0539
PubMed: 26813581
DOI: 10.1039/C5OB02507A
Page generated: Mon Dec 14 20:27:30 2020

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