Calcium in PDB 7lrm: Structure of Hiv-1 Reverse Transcriptase in Complex with Dna, Dctp, and Ca(2+) Ion

All present enzymatic activity of Structure of Hiv-1 Reverse Transcriptase in Complex with Dna, Dctp, and Ca(2+) Ion:
2.7.7.49; 2.7.7.7; 3.1.26.13;

The structure of Structure of Hiv-1 Reverse Transcriptase in Complex with Dna, Dctp, and Ca(2+) Ion, PDB code: 7lrm was solved by A.Hoang, F.X.Ruiz, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.13 / 3.14
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.663, 131.247, 137.491, 90, 97.72, 90
R / Rfree (%)	19.4 / 24.4

The binding sites of Calcium atom in the Structure of Hiv-1 Reverse Transcriptase in Complex with Dna, Dctp, and Ca(2+) Ion (pdb code 7lrm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Hiv-1 Reverse Transcriptase in Complex with Dna, Dctp, and Ca(2+) Ion, PDB code: 7lrm:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Hiv-1 Reverse Transcriptase in Complex with Dna, Dctp, and Ca(2+) Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Hiv-1 Reverse Transcriptase in Complex with Dna, Dctp, and Ca(2+) Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca605 b:100.3 occ:1.00 O2G A:DCP603 2.0 101.8 1.0 O2B A:DCP603 2.2 95.3 1.0 O2A A:DCP603 2.2 82.5 1.0 OD2 A:ASP185 2.3 85.8 1.0 O A:VAL111 2.3 84.9 1.0 OD2 A:ASP110 2.3 113.1 1.0 OD1 A:ASP110 2.4 113.9 1.0 CG A:ASP110 2.6 102.8 1.0 C A:VAL111 3.4 86.7 1.0 PG A:DCP603 3.4 102.4 1.0 CG A:ASP185 3.5 79.9 1.0 PB A:DCP603 3.5 109.5 1.0 PA A:DCP603 3.6 69.8 1.0 O3B A:DCP603 3.7 101.7 1.0 O3A A:DCP603 3.8 99.4 1.0 CB A:ASP110 4.1 99.2 1.0 N A:VAL111 4.1 72.2 1.0 C A:ASP110 4.1 87.1 1.0 CA A:GLY112 4.2 88.0 1.0 N A:GLY112 4.2 83.9 1.0 OD1 A:ASP185 4.3 68.2 1.0 O1G A:DCP603 4.3 94.8 1.0 O3G A:DCP603 4.3 118.4 1.0 CA A:VAL111 4.4 74.8 1.0 C5' A:DCP603 4.4 82.7 1.0 CB A:ASP185 4.4 75.7 1.0 O A:ASP110 4.4 95.1 1.0 O5' A:DCP603 4.4 80.2 1.0 O1A A:DCP603 4.6 78.5 1.0 CA A:ASP110 4.6 95.0 1.0 N A:ASP113 4.7 87.4 1.0 O1B A:DCP603 4.9 94.5 1.0 C A:GLY112 4.9 83.5 1.0

Calcium binding site 2 out of 2 in the Structure of Hiv-1 Reverse Transcriptase in Complex with Dna, Dctp, and Ca(2+) Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Hiv-1 Reverse Transcriptase in Complex with Dna, Dctp, and Ca(2+) Ion within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca606 b:132.8 occ:1.00 O C:VAL111 1.8 134.1 1.0 N C:VAL111 2.3 132.2 1.0 OD2 C:ASP110 2.3 148.2 1.0 OD2 C:ASP185 2.3 116.1 1.0 OD1 C:ASP110 2.4 135.1 1.0 C C:VAL111 2.4 135.1 1.0 CG C:ASP110 2.4 138.6 1.0 O1A C:DCP604 2.6 121.4 1.0 CA C:VAL111 2.8 128.2 1.0 O2G C:DCP604 3.0 120.9 1.0 O2B C:DCP604 3.2 107.5 1.0 C C:ASP110 3.3 135.2 1.0 CG C:ASP185 3.5 117.3 1.0 N C:GLY112 3.5 130.2 1.0 CB C:ASP110 3.6 120.9 1.0 CB C:VAL111 3.6 114.5 1.0 CA C:ASP110 3.8 115.6 1.0 PA C:DCP604 4.1 128.3 1.0 CA C:GLY112 4.2 127.1 1.0 O C:ASP110 4.2 139.1 1.0 C5' C:DCP604 4.3 101.5 1.0 OD1 C:ASP185 4.4 118.2 1.0 CB C:ASP185 4.4 103.7 1.0 PG C:DCP604 4.5 138.7 1.0 PB C:DCP604 4.6 131.8 1.0 CG1 C:VAL111 4.6 127.7 1.0 O3A C:DCP604 4.6 136.6 1.0 CG2 C:VAL111 4.7 108.4 1.0 O5' C:DCP604 4.7 102.0 1.0 C C:GLY112 4.7 133.0 1.0 CB C:ALA114 4.8 127.3 1.0 N C:ASP113 4.8 153.5 1.0 O3B C:DCP604 4.9 151.9 1.0 N C:ALA114 4.9 117.7 1.0

F.X.Ruiz, A.Hoang, C.R.Dilmore, J.J.Destefano, E.Arnold. Structural Basis of Hiv Inhibition By L-Nucleosides: Opportunities For Drug Development and Repurposing. Drug Discov Today V. 27 1832 2022.
ISSN: ESSN 1878-5832
PubMed: 35218925
DOI: 10.1016/J.DRUDIS.2022.02.016