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

All present enzymatic activity of Structure of Hiv-1 Reverse Transcriptase in Complex with Dna, (-)Ftc- Tp, 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, (-)Ftc- Tp, and Ca(2+) Ion, PDB code: 7lry 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)	91.27 / 2.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	90.256, 129.193, 131.32, 90, 100.86, 90
R / Rfree (%)	19 / 22.2

The structure of Structure of Hiv-1 Reverse Transcriptase in Complex with Dna, (-)Ftc- Tp, and Ca(2+) Ion also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Calcium atom in the Structure of Hiv-1 Reverse Transcriptase in Complex with Dna, (-)Ftc- Tp, and Ca(2+) Ion (pdb code 7lry). 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, (-)Ftc- Tp, and Ca(2+) Ion, PDB code: 7lry:
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, (-)Ftc- Tp, 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, (-)Ftc- Tp, and Ca(2+) Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca605 b:146.7 occ:1.00 OAQ A:1RY606 1.9 170.3 1.0 OD2 A:ASP110 2.2 136.1 1.0 OD2 A:ASP185 2.4 153.8 1.0 OAD A:1RY606 2.4 147.9 1.0 OD1 A:ASP110 2.5 148.0 1.0 CG A:ASP110 2.6 143.3 1.0 PAZ A:1RY606 2.8 171.9 1.0 O A:VAL111 2.8 135.9 1.0 OAC A:1RY606 2.8 150.7 1.0 OAI A:1RY606 3.0 155.7 1.0 PBB A:1RY606 3.0 175.3 1.0 OAG A:1RY606 3.1 160.0 1.0 CG A:ASP185 3.7 133.3 1.0 OAR A:1RY606 3.7 162.7 1.0 C A:VAL111 3.8 140.0 1.0 PBA A:1RY606 3.8 161.3 1.0 CB A:ASP110 4.1 140.9 1.0 OAF A:1RY606 4.1 155.2 1.0 OAE A:1RY606 4.2 170.5 1.0 N A:VAL111 4.4 115.9 1.0 CA A:GLY112 4.4 127.2 1.0 OD1 A:ASP185 4.4 131.4 1.0 CAL A:1RY606 4.5 161.6 1.0 N A:GLY112 4.5 130.3 1.0 OAO A:1RY606 4.5 174.3 1.0 C A:ASP110 4.6 129.3 1.0 CB A:ASP185 4.6 126.6 1.0 OAH A:1RY606 4.7 163.0 1.0 CA A:VAL111 4.7 130.1 1.0 N A:ASP113 4.7 148.0 1.0 CA A:ASP110 4.9 133.3 1.0

Calcium binding site 2 out of 2 in the Structure of Hiv-1 Reverse Transcriptase in Complex with Dna, (-)Ftc- Tp, 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, (-)Ftc- Tp, and Ca(2+) Ion within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca603 b:186.9 occ:1.00 OAD C:1RY604 2.1 190.4 1.0 OD1 C:ASP110 2.2 177.7 1.0 OAI C:1RY604 2.5 199.5 1.0 OD2 C:ASP110 2.6 180.8 1.0 OD2 C:ASP185 2.6 161.2 1.0 O C:VAL111 2.7 161.8 1.0 CG C:ASP110 2.7 177.0 1.0 OAC C:1RY604 3.3 202.8 1.0 PBB C:1RY604 3.4 205.2 1.0 PBA C:1RY604 3.4 214.6 1.0 OAQ C:1RY604 3.5 205.9 1.0 OAR C:1RY604 3.6 211.8 1.0 C C:VAL111 3.8 172.9 1.0 CAL C:1RY604 3.8 192.0 1.0 OAO C:1RY604 3.8 203.0 1.0 CG C:ASP185 3.8 161.0 1.0 PAZ C:1RY604 3.9 201.9 1.0 OAF C:1RY604 4.0 186.5 1.0 CB C:ASP110 4.2 166.5 1.0 O C:HOH726 4.3 166.4 1.0 N C:VAL111 4.4 173.3 1.0 CA C:GLY112 4.5 172.3 1.0 N C:GLY112 4.5 172.1 1.0 OD1 C:ASP185 4.6 172.3 1.0 OAH C:1RY604 4.6 216.4 1.0 N C:ASP113 4.6 227.6 1.0 CA C:VAL111 4.7 168.1 1.0 C C:ASP110 4.7 175.8 1.0 CB C:ASP185 4.8 163.0 1.0 OAE C:1RY604 4.8 195.2 1.0 NZ C:LYS220 4.9 190.6 1.0 CA C:ASP110 4.9 166.5 1.0 C C:GLY112 5.0 180.1 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