Atomistry » Magnesium » PDB 5hia-5hqw » 5hp1
Atomistry »
  Magnesium »
    PDB 5hia-5hqw »
      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: Sun Sep 29 16:04:00 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy