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

All present enzymatic activity of Structure of Hiv-1 Reverse Transcriptase in Complex with Dna, L-Dttp, 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, L-Dttp, and Ca(2+) Ion, PDB code: 7lsk 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)	70.76 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.942, 132.467, 139.342, 90, 97.6, 90
R / Rfree (%)	21.6 / 25.3

The binding sites of Calcium atom in the Structure of Hiv-1 Reverse Transcriptase in Complex with Dna, L-Dttp, and Ca(2+) Ion (pdb code 7lsk). 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, L-Dttp, and Ca(2+) Ion, PDB code: 7lsk:
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, L-Dttp, 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, L-Dttp, and Ca(2+) Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:115.5 occ:1.00 O A:VAL111 2.4 118.7 1.0 OD2 A:ASP110 2.6 122.9 1.0 O6 A:XRF605 2.6 145.2 1.0 O5 A:XRF605 2.6 124.4 1.0 O10 A:XRF605 2.6 124.4 1.0 OD2 A:ASP185 2.7 122.4 1.0 CG A:ASP110 3.1 119.2 1.0 O7 A:XRF605 3.1 166.0 1.0 OD1 A:ASP110 3.2 139.3 1.0 C A:VAL111 3.2 121.2 1.0 P A:XRF605 3.2 136.2 1.0 P1 A:XRF605 3.3 173.4 1.0 O9 A:XRF605 3.6 159.9 1.0 P2 A:XRF605 3.6 151.1 1.0 N A:VAL111 3.7 107.0 1.0 CG A:ASP185 3.8 103.0 1.0 O3 A:XRF605 3.9 137.5 1.0 N A:GLY112 3.9 120.9 1.0 CA A:VAL111 4.0 105.9 1.0 CA A:GLY112 4.1 122.3 1.0 O4 A:XRF605 4.4 131.3 1.0 CB A:ASP110 4.4 116.4 1.0 O11 A:XRF605 4.4 138.8 1.0 C A:ASP110 4.5 115.7 1.0 N A:ASP113 4.5 138.4 1.0 C A:GLY112 4.5 124.5 1.0 OD1 A:ASP185 4.6 102.6 1.0 O8 A:XRF605 4.7 154.6 1.0 CB A:ALA114 4.7 123.0 1.0 N A:ALA114 4.7 128.3 1.0 O12 A:XRF605 4.7 152.2 1.0 CB A:ASP185 4.8 97.2 1.0 CB A:VAL111 4.8 101.7 1.0 CA A:ASP110 4.9 104.1 1.0

Calcium binding site 2 out of 2 in the Structure of Hiv-1 Reverse Transcriptase in Complex with Dna, L-Dttp, 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, L-Dttp, and Ca(2+) Ion within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca601 b:149.9 occ:1.00 OD2 C:ASP110 2.2 154.0 1.0 O5 C:XRF603 2.2 116.8 1.0 O12 C:XRF603 2.2 143.2 1.0 O C:VAL111 2.3 113.0 1.0 O7 C:XRF603 2.3 169.0 1.0 OD2 C:ASP185 2.3 134.2 1.0 OD1 C:ASP110 2.3 132.0 1.0 CG C:ASP110 2.5 132.4 1.0 C C:VAL111 3.2 124.2 1.0 P1 C:XRF603 3.4 184.8 1.0 CG C:ASP185 3.4 111.4 1.0 P C:XRF603 3.5 134.2 1.0 P2 C:XRF603 3.6 147.6 1.0 O6 C:XRF603 3.7 143.2 1.0 N C:VAL111 3.7 108.6 1.0 O9 C:XRF603 3.8 175.8 1.0 O3 C:XRF603 3.9 162.1 1.0 CB C:ASP110 4.0 114.6 1.0 NZ C:LYS220 4.0 131.6 1.0 N C:GLY112 4.1 122.8 1.0 CA C:VAL111 4.1 113.0 1.0 C9 C:XRF603 4.1 134.8 1.0 OD1 C:ASP185 4.2 110.1 1.0 CA C:GLY112 4.2 120.6 1.0 O11 C:XRF603 4.4 141.3 1.0 C C:ASP110 4.4 115.0 1.0 CB C:ASP185 4.4 104.5 1.0 O10 C:XRF603 4.7 146.6 1.0 CA C:ASP110 4.7 109.5 1.0 O4 C:XRF603 4.7 123.8 1.0 O8 C:XRF603 4.7 164.2 1.0 N C:ASP113 4.8 148.5 1.0 C C:GLY112 4.8 130.2 1.0 O3' F:DG34 4.9 133.3 1.0 CB C:VAL111 4.9 109.8 1.0 OD1 C:ASP186 5.0 156.1 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