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Magnesium in PDB 5hro: Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and An Alpha-Carboxy Nucleoside Phosphonate Inhibitor (Alpha-Cnp)

Enzymatic activity of Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and An Alpha-Carboxy Nucleoside Phosphonate Inhibitor (Alpha-Cnp)

All present enzymatic activity of Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and An Alpha-Carboxy Nucleoside Phosphonate Inhibitor (Alpha-Cnp):
2.7.7.49;

Protein crystallography data

The structure of Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and An Alpha-Carboxy Nucleoside Phosphonate Inhibitor (Alpha-Cnp), PDB code: 5hro 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) 38.52 / 2.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.245, 128.959, 131.049, 90.00, 101.47, 90.00
R / Rfree (%) 23.5 / 26.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and An Alpha-Carboxy Nucleoside Phosphonate Inhibitor (Alpha-Cnp) (pdb code 5hro). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and An Alpha-Carboxy Nucleoside Phosphonate Inhibitor (Alpha-Cnp), PDB code: 5hro:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5hro

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Magnesium binding site 1 out of 6 in the Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and An Alpha-Carboxy Nucleoside Phosphonate Inhibitor (Alpha-Cnp)


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 Dna Aptamer and An Alpha-Carboxy Nucleoside Phosphonate Inhibitor (Alpha-Cnp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:0.4
occ:1.00
 OD1 A:ASP110 2.2 0.6 1.0
OD2 A:ASP185 2.3 0.0 1.0
O19 A:3JY603 2.4 0.1 1.0
O17 A:3JY603 2.5 0.2 1.0
O A:VAL111 2.5 0.3 1.0
O14 A:3JY603 2.6 0.8 1.0
P16 A:3JY603 2.8 0.3 1.0
CG A:ASP110 3.1 1.0 1.0
OD2 A:ASP110 3.4 0.6 1.0
C13 A:3JY603 3.4 1.0 1.0
CG A:ASP185 3.5 0.2 1.0
MG A:MG602 3.5 0.7 1.0
C12 A:3JY603 3.6 0.7 1.0
C A:VAL111 3.7 0.8 1.0
OD1 A:ASP185 4.0 0.7 1.0
O11 A:3JY603 4.0 0.8 1.0
O18 A:3JY603 4.2 0.6 1.0
N A:VAL111 4.4 0.9 1.0
O15 A:3JY603 4.5 0.4 1.0
CB A:ASP110 4.5 0.2 1.0
CA A:GLY112 4.6 0.2 1.0
N A:GLY112 4.6 0.2 1.0
CA A:VAL111 4.6 0.7 1.0
CB A:ASP185 4.6 0.8 1.0
N A:ASP113 4.7 0.5 1.0
CB A:ALA114 4.8 0.8 1.0
CE A:LYS220 4.8 0.6 1.0
N A:ALA114 4.9 1.0 1.0
C A:ASP110 5.0 0.1 1.0

Magnesium binding site 2 out of 6 in 5hro

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Magnesium binding site 2 out of 6 in the Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and An Alpha-Carboxy Nucleoside Phosphonate Inhibitor (Alpha-Cnp)


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 Dna Aptamer and An Alpha-Carboxy Nucleoside Phosphonate Inhibitor (Alpha-Cnp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:0.7
occ:1.00
 O3' E:DG37 1.9 0.8 1.0
O14 A:3JY603 2.0 0.8 1.0
OD2 A:ASP110 2.0 0.6 1.0
OD1 A:ASP186 2.1 0.4 1.0
OD1 A:ASP185 2.1 0.7 1.0
CG A:ASP185 2.9 0.2 1.0
OD2 A:ASP185 3.0 0.0 1.0
C13 A:3JY603 3.0 1.0 1.0
CG A:ASP110 3.1 1.0 1.0
CG A:ASP186 3.1 0.6 1.0
C3' E:DG37 3.2 0.4 1.0
O15 A:3JY603 3.3 0.4 1.0
MG A:MG601 3.5 0.4 1.0
OD1 A:ASP110 3.5 0.6 1.0
OD2 A:ASP186 3.5 0.9 1.0
C2' E:DG37 4.0 0.6 1.0
N A:ASP186 4.2 99.5 1.0
C12 A:3JY603 4.2 0.7 1.0
C4' E:DG37 4.3 97.8 1.0
O17 A:3JY603 4.3 0.2 1.0
CB A:ASP185 4.3 0.8 1.0
CB A:ASP110 4.4 0.2 1.0
CB A:ASP186 4.4 97.5 1.0
C A:ASP185 4.5 0.4 1.0
O11 A:3JY603 4.6 0.8 1.0
CA A:ASP186 4.7 99.2 1.0
CA A:ASP185 4.8 0.2 1.0
C5' E:DG37 4.8 96.6 1.0
P16 A:3JY603 4.8 0.3 1.0
N A:ASP185 4.9 0.8 1.0

Magnesium binding site 3 out of 6 in 5hro

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Magnesium binding site 3 out of 6 in the Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and An Alpha-Carboxy Nucleoside Phosphonate Inhibitor (Alpha-Cnp)


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 Dna Aptamer and An Alpha-Carboxy Nucleoside Phosphonate Inhibitor (Alpha-Cnp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:70.4
occ:1.00
 O A:HOH701 1.9 0.4 1.0
OD2 A:ASP443 2.2 67.4 1.0
OD2 A:ASP549 2.4 74.7 1.0
CG A:ASP443 2.9 58.4 1.0
OD1 A:ASP443 3.0 59.3 1.0
CG A:ASP549 3.6 68.8 1.0
OD1 A:ASP498 3.9 57.2 1.0
O A:GLY444 4.0 71.7 1.0
OD2 A:ASP498 4.1 64.7 1.0
CB A:ASP549 4.4 64.4 1.0
CB A:ASP443 4.4 52.7 1.0
CG A:ASP498 4.4 61.9 1.0
OD1 A:ASP549 4.6 75.7 1.0
NE2 A:HIS539 4.7 70.4 1.0
CA A:ASP549 4.9 64.2 1.0

Magnesium binding site 4 out of 6 in 5hro

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Magnesium binding site 4 out of 6 in the Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and An Alpha-Carboxy Nucleoside Phosphonate Inhibitor (Alpha-Cnp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and An Alpha-Carboxy Nucleoside Phosphonate Inhibitor (Alpha-Cnp) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:0.1
occ:1.00
 O17 C:3JY605 2.2 0.5 1.0
OD2 C:ASP185 2.4 0.2 1.0
O18 C:3JY605 2.5 0.4 1.0
O14 C:3JY605 2.5 0.7 1.0
O C:VAL111 2.5 0.6 1.0
P16 C:3JY605 2.6 0.0 1.0
OD1 C:ASP110 2.7 0.1 1.0
C12 C:3JY605 3.1 0.8 1.0
C13 C:3JY605 3.1 0.1 1.0
O11 C:3JY605 3.2 0.8 1.0
MG C:MG603 3.5 0.0 1.0
CG C:ASP185 3.6 0.2 1.0
CG C:ASP110 3.7 0.4 1.0
C C:VAL111 3.8 0.3 1.0
OD2 C:ASP110 4.0 0.1 1.0
O19 C:3JY605 4.1 0.9 1.0
OD1 C:ASP185 4.1 0.9 1.0
N C:ASP113 4.1 0.2 1.0
O15 C:3JY605 4.2 0.1 1.0
N C:ALA114 4.3 0.3 1.0
C10 C:3JY605 4.3 0.1 1.0
CB C:ALA114 4.4 0.3 1.0
CA C:GLY112 4.5 0.9 1.0
N C:GLY112 4.6 0.1 1.0
C C:GLY112 4.6 0.6 1.0
N C:VAL111 4.7 0.1 1.0
CB C:ASP185 4.7 0.3 1.0
O3' F:DG37 4.8 0.9 1.0
CA C:VAL111 4.8 0.1 1.0
CA C:ASP113 4.8 0.1 1.0
CA C:ALA114 5.0 0.1 1.0

Magnesium binding site 5 out of 6 in 5hro

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Magnesium binding site 5 out of 6 in the Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and An Alpha-Carboxy Nucleoside Phosphonate Inhibitor (Alpha-Cnp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and An Alpha-Carboxy Nucleoside Phosphonate Inhibitor (Alpha-Cnp) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:71.0
occ:1.00
 O C:HOH702 1.9 82.1 1.0
O C:HOH701 2.1 65.8 1.0
OD2 C:ASP549 2.1 69.3 1.0
OD2 C:ASP443 2.3 61.4 1.0
OD1 C:ASP443 3.0 54.7 1.0
CG C:ASP443 3.0 52.1 1.0
CG C:ASP549 3.4 63.9 1.0
O C:GLY444 3.7 71.6 1.0
CB C:ASP549 4.2 58.4 1.0
OD2 C:ASP498 4.2 51.9 1.0
OD1 C:ASP549 4.3 62.0 1.0
OD1 C:ASP498 4.3 65.1 1.0
CB C:ASP443 4.5 44.9 1.0
CG C:ASP498 4.7 64.0 1.0
CA C:ASP549 4.7 65.2 1.0
C C:GLY444 4.8 64.9 1.0
NE2 C:HIS539 4.9 71.2 1.0

Magnesium binding site 6 out of 6 in 5hro

Go back to Magnesium Binding Sites List in 5hro
Magnesium binding site 6 out of 6 in the Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and An Alpha-Carboxy Nucleoside Phosphonate Inhibitor (Alpha-Cnp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and An Alpha-Carboxy Nucleoside Phosphonate Inhibitor (Alpha-Cnp) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg603

b:0.0
occ:1.00
 OD2 C:ASP110 1.8 0.1 1.0
O3' F:DG37 1.9 0.9 1.0
O14 C:3JY605 2.1 0.7 1.0
OD1 C:ASP185 2.2 0.9 1.0
OD1 C:ASP186 2.2 0.8 1.0
OD2 C:ASP185 2.7 0.2 1.0
CG C:ASP185 2.7 0.2 1.0
CG C:ASP110 2.8 0.4 1.0
OD1 C:ASP110 3.1 0.1 1.0
C13 C:3JY605 3.2 0.1 1.0
CG C:ASP186 3.2 0.7 1.0
C3' F:DG37 3.3 0.3 1.0
MG C:MG601 3.5 0.1 1.0
OD2 C:ASP186 3.6 0.8 1.0
O15 C:3JY605 3.8 0.1 1.0
CB C:ASP110 4.1 0.6 1.0
CB C:ASP185 4.2 0.3 1.0
C2' F:DG37 4.2 0.3 1.0
C4' F:DG37 4.2 0.7 1.0
C12 C:3JY605 4.2 0.8 1.0
N C:ASP186 4.2 0.1 1.0
O11 C:3JY605 4.3 0.8 1.0
O17 C:3JY605 4.4 0.5 1.0
C C:ASP185 4.5 0.5 1.0
CB C:ASP186 4.5 0.2 1.0
C5' F:DG37 4.6 0.4 1.0
CA C:ASP186 4.7 0.1 1.0
CA C:ASP185 4.7 0.9 1.0
O C:VAL111 4.7 0.6 1.0
CA C:ASP110 4.7 0.7 1.0
N C:ASP185 4.8 0.3 1.0
N C:VAL111 4.9 0.1 1.0
O5' F:DG37 4.9 0.4 1.0
P16 C:3JY605 5.0 0.0 1.0

Reference:

K.Das, J.Balzarini, M.T.Miller, A.R.Maguire, J.J.Destefano, E.Arnold. Conformational States of Hiv-1 Reverse Transcriptase For Nucleotide Incorporation Vs Pyrophosphorolysis-Binding of Foscarnet. Acs Chem.Biol. V. 11 2158 2016.
ISSN: ESSN 1554-8937
PubMed: 27192549
DOI: 10.1021/ACSCHEMBIO.6B00187
Page generated: Sun Sep 29 16:33:40 2024

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