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Magnesium in PDB 5hp1: Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and Foscarnet, A Pyrophosphate Analog

Enzymatic activity of Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and Foscarnet, A Pyrophosphate Analog

All present enzymatic activity of Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and Foscarnet, A Pyrophosphate Analog:
2.7.7.49;

Protein crystallography data

The structure of Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and Foscarnet, A Pyrophosphate Analog, PDB code: 5hp1 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) 45.64 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.325, 129.069, 131.542, 90.00, 101.00, 90.00
R / Rfree (%) 24.6 / 27.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and Foscarnet, A Pyrophosphate Analog (pdb code 5hp1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and Foscarnet, A Pyrophosphate Analog, PDB code: 5hp1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5hp1

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Magnesium binding site 1 out of 8 in the Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and Foscarnet, A Pyrophosphate Analog


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 Foscarnet, A Pyrophosphate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:80.4
occ:1.00
 O A:HOH701 2.0 79.7 1.0
OD1 A:ASP549 2.2 76.9 1.0
OD2 A:ASP443 2.2 62.6 1.0
CG A:ASP443 3.2 54.1 1.0
CG A:ASP549 3.2 77.5 1.0
OD1 A:ASP443 3.5 72.5 1.0
MG A:MG605 3.7 80.3 1.0
CB A:ASP549 4.0 69.9 1.0
OD2 A:ASP549 4.1 84.5 1.0
OD2 A:ASP498 4.3 57.2 1.0
CA A:ASP549 4.3 72.8 1.0
CB A:ASP443 4.5 52.7 1.0
OD1 A:ASP498 4.6 60.5 1.0
CG A:ASP498 4.8 60.0 1.0
O A:GLY444 4.8 62.8 1.0
CE1 A:HIS539 4.9 85.4 1.0
O A:ASP549 4.9 85.0 1.0
OG A:SER553 4.9 92.5 1.0

Magnesium binding site 2 out of 8 in 5hp1

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Magnesium binding site 2 out of 8 in the Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and Foscarnet, A Pyrophosphate Analog


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 Foscarnet, A Pyrophosphate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:0.1
occ:0.80
 O3' F:DG33 2.0 0.8 1.0
OD2 A:ASP186 2.0 0.3 1.0
OD2 A:ASP110 2.1 0.7 1.0
OP2 F:ATM101 2.1 0.6 1.0
OD1 A:ASP185 2.1 0.1 1.0
OD2 A:ASP185 2.6 0.6 1.0
P F:ATM101 2.6 0.6 1.0
CG A:ASP185 2.6 0.2 1.0
CG A:ASP110 2.8 0.0 1.0
CG A:ASP186 3.0 0.3 1.0
OD1 A:ASP110 3.0 0.7 1.0
MG A:MG604 3.2 0.4 1.0
C3' F:DG33 3.3 0.7 1.0
OP1 F:ATM101 3.5 0.1 1.0
OD1 A:ASP186 3.5 0.3 1.0
O5' F:ATM101 3.8 0.6 1.0
C4' F:DG33 3.9 0.3 1.0
CB A:ASP185 4.1 0.9 1.0
N A:ASP186 4.1 0.2 1.0
C5' F:ATM101 4.1 0.6 1.0
CB A:ASP110 4.2 0.7 1.0
C2' F:DG33 4.2 0.2 1.0
CB A:ASP186 4.2 1.0 1.0
C5' F:DG33 4.3 0.2 1.0
C A:ASP185 4.3 0.1 1.0
O4 A:PPF602 4.4 0.3 1.0
CA A:ASP186 4.4 0.3 1.0
CA A:ASP185 4.6 0.1 1.0
O A:ASP185 4.8 0.6 1.0
N A:ASP185 4.9 0.7 1.0
O A:VAL111 5.0 0.7 1.0

Magnesium binding site 3 out of 8 in 5hp1

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Magnesium binding site 3 out of 8 in the Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and Foscarnet, A Pyrophosphate Analog


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 Foscarnet, A Pyrophosphate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:0.4
occ:1.00
 OD1 A:ASP110 2.0 0.7 1.0
OD2 A:ASP185 2.1 0.6 1.0
O4 A:PPF602 2.2 0.3 1.0
O2 A:PPF602 2.3 0.9 1.0
OP2 F:ATM101 2.5 0.6 1.0
O A:VAL111 2.6 0.7 1.0
C1 A:PPF602 2.8 0.4 1.0
P1 A:PPF602 2.9 0.5 1.0
CG A:ASP110 3.0 0.0 1.0
MG A:MG603 3.2 0.1 0.8
CG A:ASP185 3.3 0.2 1.0
O1 A:PPF602 3.5 0.2 1.0
OD2 A:ASP110 3.5 0.7 1.0
P F:ATM101 3.8 0.6 1.0
C A:VAL111 3.8 0.7 1.0
O5 A:PPF602 4.0 0.2 1.0
OD1 A:ASP185 4.0 0.1 1.0
C5' F:ATM101 4.1 0.6 1.0
O5' F:ATM101 4.1 0.6 1.0
CB A:ASP185 4.3 0.9 1.0
CB A:ASP110 4.3 0.7 1.0
O3 A:PPF602 4.3 1.0 1.0
O3' F:DG33 4.5 0.8 1.0
CA A:GLY112 4.5 0.3 1.0
OP1 F:ATM101 4.6 0.1 1.0
N A:VAL111 4.6 0.1 1.0
N A:GLY112 4.6 0.6 1.0
N A:ASP113 4.8 0.2 1.0
CA A:VAL111 4.8 0.6 1.0
C A:ASP110 4.9 0.9 1.0

Magnesium binding site 4 out of 8 in 5hp1

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Magnesium binding site 4 out of 8 in the Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and Foscarnet, A Pyrophosphate Analog


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 Foscarnet, A Pyrophosphate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:80.3
occ:1.00
 OD1 A:ASP443 2.1 72.5 1.0
OD1 A:ASP498 2.2 60.5 1.0
CG A:ASP498 3.1 60.0 1.0
CG A:ASP443 3.2 54.1 1.0
OD2 A:ASP498 3.4 57.2 1.0
OD2 A:ASP443 3.6 62.6 1.0
MG A:MG601 3.7 80.4 1.0
OE2 A:GLU478 3.8 60.3 1.0
CG A:GLU478 3.9 50.2 1.0
O A:GLY444 3.9 62.8 1.0
CD A:GLU478 4.1 67.1 1.0
O A:HOH701 4.3 79.7 1.0
N A:GLY444 4.4 44.2 1.0
CB A:ASP443 4.4 52.7 1.0
CB A:ASP498 4.5 53.8 1.0
C A:ASP498 4.7 46.9 1.0
CA A:ASP443 4.7 48.3 1.0
N A:SER499 4.8 46.2 1.0
O A:ASP498 4.8 57.3 1.0
OE1 A:GLU478 4.9 77.8 1.0
C A:GLY444 5.0 56.3 1.0
CA A:ASP498 5.0 44.2 1.0

Magnesium binding site 5 out of 8 in 5hp1

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Magnesium binding site 5 out of 8 in the Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and Foscarnet, A Pyrophosphate Analog


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 Foscarnet, A Pyrophosphate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:62.3
occ:1.00
 OD1 C:ASP549 2.2 69.8 1.0
OD2 C:ASP443 2.2 57.7 1.0
O C:HOH701 2.4 63.7 1.0
CG C:ASP549 3.1 69.5 1.0
CG C:ASP443 3.2 47.5 1.0
OD1 C:ASP443 3.4 63.1 1.0
MG C:MG606 3.5 63.2 1.0
CB C:ASP549 3.8 68.8 1.0
OD2 C:ASP549 4.0 70.2 1.0
OD2 C:ASP498 4.1 49.5 1.0
OD1 C:ASP498 4.3 63.2 1.0
CA C:ASP549 4.4 64.7 1.0
CB C:ASP443 4.5 41.6 1.0
CG C:ASP498 4.6 55.3 1.0
O C:GLY444 4.8 68.5 1.0
CE1 C:HIS539 4.8 84.4 1.0
NE2 C:HIS539 4.8 88.2 1.0
CB C:ALA538 4.9 71.7 1.0

Magnesium binding site 6 out of 8 in 5hp1

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Magnesium binding site 6 out of 8 in the Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and Foscarnet, A Pyrophosphate Analog


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 Foscarnet, A Pyrophosphate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg603

b:0.6
occ:1.00
 O3' E:DG33 1.9 0.3 1.0
OP2 E:ATM101 2.0 0.5 1.0
OD1 C:ASP110 2.0 0.2 1.0
OD1 C:ASP186 2.1 0.4 1.0
OD1 C:ASP185 2.1 0.9 1.0
OD2 C:ASP185 2.4 0.6 1.0
P E:ATM101 2.5 1.0 1.0
CG C:ASP185 2.5 1.0 1.0
CG C:ASP110 2.9 0.1 1.0
CG C:ASP186 3.2 0.2 1.0
OD2 C:ASP110 3.2 0.7 1.0
MG C:MG604 3.3 0.0 1.0
C3' E:DG33 3.3 0.9 1.0
OP1 E:ATM101 3.5 0.8 1.0
O5' E:ATM101 3.7 0.9 1.0
OD2 C:ASP186 3.7 0.3 1.0
C5' E:ATM101 3.9 0.2 1.0
C4' E:DG33 3.9 0.0 1.0
CB C:ASP185 4.0 0.9 1.0
O4 C:PPF601 4.0 0.6 1.0
N C:ASP186 4.2 0.7 1.0
C2' E:DG33 4.2 0.9 1.0
CB C:ASP110 4.3 0.6 1.0
C5' E:DG33 4.3 0.9 1.0
C C:ASP185 4.4 0.7 1.0
CB C:ASP186 4.4 0.1 1.0
CA C:ASP186 4.5 0.5 1.0
CA C:ASP185 4.6 0.4 1.0
O C:ASP185 4.8 1.0 1.0
N C:ASP185 4.9 0.4 1.0
O C:VAL111 4.9 0.3 1.0

Magnesium binding site 7 out of 8 in 5hp1

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Magnesium binding site 7 out of 8 in the Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and Foscarnet, A Pyrophosphate Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and Foscarnet, A Pyrophosphate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg604

b:0.0
occ:1.00
 O2 C:PPF601 2.0 0.9 1.0
OD2 C:ASP110 2.1 0.7 1.0
OD2 C:ASP185 2.1 0.6 1.0
O4 C:PPF601 2.4 0.6 1.0
O C:VAL111 2.5 0.3 1.0
OP2 E:ATM101 2.5 0.5 1.0
P1 C:PPF601 2.9 0.1 1.0
C1 C:PPF601 3.0 0.4 1.0
CG C:ASP110 3.1 0.1 1.0
MG C:MG603 3.3 0.6 1.0
CG C:ASP185 3.3 1.0 1.0
OD1 C:ASP110 3.4 0.2 1.0
O1 C:PPF601 3.7 0.8 1.0
C C:VAL111 3.7 0.8 1.0
P E:ATM101 3.8 1.0 1.0
C5' E:ATM101 3.9 0.2 1.0
O5' E:ATM101 3.9 0.9 1.0
OD1 C:ASP185 4.1 0.9 1.0
O3 C:PPF601 4.2 0.4 1.0
O5 C:PPF601 4.3 0.8 1.0
CB C:ASP185 4.3 0.9 1.0
CB C:ASP110 4.4 0.6 1.0
CA C:GLY112 4.5 0.5 1.0
OP1 E:ATM101 4.5 0.8 1.0
O3' E:DG33 4.5 0.3 1.0
N C:GLY112 4.5 0.9 1.0
N C:VAL111 4.6 0.2 1.0
N C:ASP113 4.6 0.2 1.0
CA C:VAL111 4.7 0.4 1.0
N3' E:ATM101 4.9 0.3 1.0
N C:ALA114 4.9 1.0 1.0
CB C:ALA114 4.9 0.9 1.0
C C:GLY112 4.9 0.2 1.0
C C:ASP110 4.9 0.9 1.0

Magnesium binding site 8 out of 8 in 5hp1

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Magnesium binding site 8 out of 8 in the Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and Foscarnet, A Pyrophosphate Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Hiv-1 Reverse Transcriptase in Complex with A Dna Aptamer and Foscarnet, A Pyrophosphate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg606

b:63.2
occ:1.00
 OD1 C:ASP443 2.0 63.1 1.0
OD1 C:ASP498 2.2 63.2 1.0
CG C:ASP498 3.1 55.3 1.0
CG C:ASP443 3.1 47.5 1.0
OD2 C:ASP498 3.4 49.5 1.0
MG C:MG602 3.5 62.3 1.0
OD2 C:ASP443 3.6 57.7 1.0
O C:HOH701 3.7 63.7 1.0
O C:GLY444 3.8 68.5 1.0
CG C:GLU478 3.8 51.7 1.0
OE2 C:GLU478 3.8 73.2 1.0
CD C:GLU478 4.1 66.2 1.0
N C:GLY444 4.3 50.1 1.0
CB C:ASP443 4.4 41.6 1.0
CB C:ASP498 4.5 44.1 1.0
CA C:ASP443 4.6 42.4 1.0
C C:ASP498 4.7 43.9 1.0
C C:GLY444 4.8 58.3 1.0
O C:ASP498 4.8 56.0 1.0
N C:SER499 4.9 39.4 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 16:04:00 2024

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