Atomistry » Magnesium » PDB 5hif-5hr6 » 5hp1
Atomistry »
  Magnesium »
    PDB 5hif-5hr6 »
      5hp1 »

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

Go back to Magnesium Binding Sites List in 5hp1
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

Go back to Magnesium Binding Sites List in 5hp1
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

Go back to Magnesium Binding Sites List in 5hp1
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

Go back to Magnesium Binding Sites List in 5hp1
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

Go back to Magnesium Binding Sites List in 5hp1
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

Go back to Magnesium Binding Sites List in 5hp1
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

Go back to Magnesium Binding Sites List in 5hp1
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

Go back to Magnesium Binding Sites List in 5hp1
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: Tue Aug 12 10:57:36 2025

Last articles

Mg in 5KDL
Mg in 5KAP
Mg in 5KB5
Mg in 5KB3
Mg in 5KAL
Mg in 5KAM
Mg in 5K9B
Mg in 5K9R
Mg in 5K9T
Mg in 5K8F
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy