Magnesium in PDB 4pqu: Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with Rna/Dna and Datp

All present enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with Rna/Dna and Datp:
2.7.7.49; 2.7.7.7; 3.1.13.2; 3.1.26.13;

The structure of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with Rna/Dna and Datp, PDB code: 4pqu was solved by K.Das, R.P.Bandwar, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.47 / 2.51
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.444, 128.288, 130.680, 90.00, 101.76, 90.00
R / Rfree (%)	20.2 / 26.6

The binding sites of Magnesium atom in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with Rna/Dna and Datp (pdb code 4pqu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with Rna/Dna and Datp, PDB code: 4pqu:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with Rna/Dna and Datp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with Rna/Dna and Datp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:30.7 occ:1.00 O3G A:DTP601 2.0 55.7 1.0 O2B A:DTP601 2.2 46.5 1.0 O A:VAL111 2.2 35.6 1.0 O1A A:DTP601 2.2 38.7 1.0 OD1 A:ASP110 2.3 51.8 1.0 OD2 A:ASP185 2.3 49.4 1.0 PG A:DTP601 3.1 53.4 1.0 PB A:DTP601 3.2 50.0 1.0 CG A:ASP110 3.3 48.3 1.0 O1G A:DTP601 3.4 46.3 1.0 C A:VAL111 3.4 43.5 1.0 PA A:DTP601 3.4 49.2 1.0 CG A:ASP185 3.5 37.9 1.0 O3B A:DTP601 3.6 52.8 1.0 O3A A:DTP601 3.6 45.1 1.0 MG A:MG603 3.6 35.8 1.0 OD2 A:ASP110 3.6 52.0 1.0 N A:VAL111 3.9 45.6 1.0 OD1 A:ASP185 4.1 41.9 1.0 CA A:VAL111 4.2 41.7 1.0 C5' A:DTP601 4.2 40.5 1.0 O5' A:DTP601 4.3 47.7 1.0 O2G A:DTP601 4.4 54.0 1.0 N A:GLY112 4.4 44.8 1.0 N A:ASP113 4.5 50.2 1.0 CA A:GLY112 4.5 43.3 1.0 CB A:ASP185 4.5 38.9 1.0 O2A A:DTP601 4.6 41.0 1.0 O1B A:DTP601 4.6 49.5 1.0 CB A:ASP110 4.6 33.6 1.0 C A:ASP110 4.6 47.7 1.0 N A:ALA114 4.7 56.0 1.0 CB A:ALA114 4.8 47.1 1.0 CB A:VAL111 4.8 43.8 1.0 O A:HOH779 4.8 39.7 1.0 C A:GLY112 4.8 46.4 1.0 NZ A:LYS219 4.9 49.4 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with Rna/Dna and Datp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with Rna/Dna and Datp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:35.8 occ:1.00 OD1 A:ASP185 2.3 41.9 1.0 OD2 A:ASP110 2.3 52.0 1.0 O A:HOH779 2.3 39.7 1.0 OD1 A:ASP186 2.4 49.7 1.0 O1A A:DTP601 2.5 38.7 1.0 CG A:ASP185 2.9 37.9 1.0 OD2 A:ASP185 2.9 49.4 1.0 C3' P:DG822 3.2 37.8 1.0 CG A:ASP110 3.2 48.3 1.0 OD1 A:ASP110 3.6 51.8 1.0 MG A:MG602 3.6 30.7 1.0 CG A:ASP186 3.6 47.9 1.0 PA A:DTP601 3.7 49.2 1.0 C4' P:DG822 3.9 38.1 1.0 O5' A:DTP601 4.0 47.7 1.0 O2A A:DTP601 4.1 41.0 1.0 C5' P:DG822 4.2 34.5 1.0 N A:ASP186 4.2 37.3 1.0 CB A:ASP185 4.2 38.9 1.0 C A:ASP185 4.2 40.0 1.0 OD2 A:ASP186 4.3 54.9 1.0 C2' P:DG822 4.3 33.7 1.0 C5' A:DTP601 4.3 40.5 1.0 O A:ASP185 4.5 41.4 1.0 CB A:ASP110 4.5 33.6 1.0 O3G A:DTP601 4.6 55.7 1.0 CA A:ASP185 4.6 39.6 1.0 O A:HOH770 4.7 40.7 1.0 CA A:ASP186 4.7 38.2 1.0 CB A:ASP186 4.7 36.4 1.0 N A:ASP185 4.8 38.5 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with Rna/Dna and Datp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with Rna/Dna and Datp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:59.2 occ:1.00 O2B C:DTP601 2.0 71.0 1.0 OD1 C:ASP110 2.1 65.3 1.0 O2G C:DTP601 2.2 82.3 1.0 O1A C:DTP601 2.2 69.0 1.0 O C:VAL111 2.2 76.9 1.0 OD2 C:ASP185 2.2 80.3 1.0 PB C:DTP601 3.0 77.7 1.0 CG C:ASP110 3.1 69.3 1.0 PA C:DTP601 3.2 80.5 1.0 PG C:DTP601 3.2 88.2 1.0 O3A C:DTP601 3.3 83.5 1.0 C C:VAL111 3.3 78.3 1.0 OD2 C:ASP110 3.4 77.2 1.0 O3B C:DTP601 3.4 85.1 1.0 CG C:ASP185 3.4 73.3 1.0 MG C:MG603 3.7 63.9 1.0 N C:VAL111 3.7 72.0 1.0 O1G C:DTP601 3.8 80.4 1.0 O5' C:DTP601 4.0 72.0 1.0 C5' C:DTP601 4.0 70.4 1.0 CA C:VAL111 4.0 72.8 1.0 OD1 C:ASP185 4.1 76.0 1.0 N C:GLY112 4.3 78.5 1.0 O1B C:DTP601 4.4 73.9 1.0 O2A C:DTP601 4.4 74.0 1.0 CB C:ASP110 4.4 71.2 1.0 CB C:ASP185 4.5 69.1 1.0 O3G C:DTP601 4.6 87.8 1.0 N C:ASP113 4.6 79.7 1.0 NZ C:LYS219 4.6 72.2 1.0 CB C:VAL111 4.6 75.5 1.0 CB C:ALA114 4.6 73.1 1.0 CA C:GLY112 4.6 77.4 1.0 N C:ALA114 4.7 84.5 1.0 C C:ASP110 4.7 73.1 1.0 O C:HOH776 4.8 69.2 1.0 C C:GLY112 4.9 76.9 1.0 CA C:ASP110 5.0 70.4 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with Rna/Dna and Datp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with Rna/Dna and Datp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg603 b:63.9 occ:1.00 OD2 C:ASP110 2.1 77.2 1.0 O C:HOH776 2.2 69.2 1.0 OD1 C:ASP185 2.4 76.0 1.0 OD1 C:ASP186 2.5 76.3 1.0 O1A C:DTP601 2.5 69.0 1.0 OD2 C:ASP185 3.0 80.3 1.0 CG C:ASP185 3.1 73.3 1.0 CG C:ASP110 3.2 69.3 1.0 C3' F:DG822 3.4 61.0 1.0 CG C:ASP186 3.6 73.0 1.0 MG C:MG602 3.7 59.2 1.0 OD1 C:ASP110 3.7 65.3 1.0 PA C:DTP601 3.7 80.5 1.0 O5' C:DTP601 3.9 72.0 1.0 N C:ASP186 4.1 69.9 1.0 O2A C:DTP601 4.1 74.0 1.0 C5' F:DG822 4.2 59.7 1.0 CB C:ASP186 4.3 67.0 1.0 C4' F:DG822 4.3 55.9 1.0 CB C:ASP110 4.4 71.2 1.0 CB C:ASP185 4.5 69.1 1.0 CA C:ASP186 4.5 69.8 1.0 OD2 C:ASP186 4.5 69.5 1.0 C2' F:DG822 4.5 57.7 1.0 C5' C:DTP601 4.6 70.4 1.0 C C:ASP185 4.6 72.1 1.0 O2G C:DTP601 4.8 82.3 1.0 O5' F:DG822 4.9 65.2 1.0 CA C:ASP185 4.9 67.5 1.0 CA C:ASP110 5.0 70.4 1.0 N C:ASP185 5.0 63.4 1.0

K.Das, S.E.Martinez, R.P.Bandwar, E.Arnold. Structures of Hiv-1 Rt-Rna/Dna Ternary Complexes with Datp and Nevirapine Reveal Conformational Flexibility of Rna/Dna: Insights Into Requirements For Rnase H Cleavage. Nucleic Acids Res. V. 42 8125 2014.
ISSN: ISSN 0305-1048
PubMed: 24880687
DOI: 10.1093/NAR/GKU487