Calcium in PDB 6bsg: Structure of Hiv-1 Rt Complexed with Rna/Dna Hybrid in An Rna Hydrolysis-Off Mode

The structure of Structure of Hiv-1 Rt Complexed with Rna/Dna Hybrid in An Rna Hydrolysis-Off Mode, PDB code: 6bsg was solved by L.Tian, M.Kim, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.51 / 2.44
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	162.040, 162.040, 129.180, 90.00, 90.00, 120.00
R / Rfree (%)	19.1 / 22.4

The structure of Structure of Hiv-1 Rt Complexed with Rna/Dna Hybrid in An Rna Hydrolysis-Off Mode also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the Structure of Hiv-1 Rt Complexed with Rna/Dna Hybrid in An Rna Hydrolysis-Off Mode (pdb code 6bsg). 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 Rt Complexed with Rna/Dna Hybrid in An Rna Hydrolysis-Off Mode, PDB code: 6bsg:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Hiv-1 Rt Complexed with Rna/Dna Hybrid in An Rna Hydrolysis-Off Mode


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 Rt Complexed with Rna/Dna Hybrid in An Rna Hydrolysis-Off Mode within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:92.5 occ:1.00 OD1 A:ASP498 2.3 70.8 1.0 OE1 A:GLU478 2.5 73.5 1.0 OD1 A:ASP443 2.6 74.5 1.0 CG A:ASP498 3.0 66.2 1.0 OD2 A:ASP498 3.0 69.2 1.0 O3' R:C24 3.2 80.8 0.8 CD A:GLU478 3.3 74.0 1.0 O2' R:C24 3.4 82.3 0.8 OE2 A:GLU478 3.5 72.8 1.0 CA A:CA603 3.7 0.3 1.0 CG A:ASP443 3.7 66.7 1.0 C3' R:C24 4.0 76.6 0.8 OP1 R:A25 4.0 95.2 0.8 O A:GLY444 4.0 66.1 1.0 C4' R:C24 4.1 68.9 0.8 OD2 A:ASP443 4.2 77.6 1.0 P R:A25 4.3 96.0 0.8 C2' R:C24 4.3 74.9 0.8 CB A:ASP498 4.5 58.8 1.0 N A:GLY444 4.5 62.3 1.0 CG A:GLU478 4.6 72.5 1.0 CB A:ASP443 4.9 61.4 1.0 CA A:ASP443 5.0 54.2 1.0 C A:ASP498 5.0 61.9 1.0

Calcium binding site 2 out of 2 in the Structure of Hiv-1 Rt Complexed with Rna/Dna Hybrid in An Rna Hydrolysis-Off Mode


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 Rt Complexed with Rna/Dna Hybrid in An Rna Hydrolysis-Off Mode within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:0.3 occ:1.00 OD1 A:ASP549 2.8 79.5 1.0 OD2 A:ASP443 2.8 77.6 1.0 OP1 R:A25 3.0 95.2 0.8 O A:GLY444 3.3 66.1 1.0 OD1 A:ASP443 3.4 74.5 1.0 CG A:ASP443 3.5 66.7 1.0 CA A:CA602 3.7 92.5 1.0 CG A:ASP549 3.8 69.6 1.0 NH2 A:ARG557 3.9 84.8 1.0 P R:A25 4.1 96.0 0.8 O3' R:C24 4.3 80.8 0.8 C A:GLY444 4.4 61.6 1.0 C5' R:A25 4.4 89.7 0.8 CB A:ALA445 4.6 72.7 1.0 O5' R:A25 4.6 89.6 0.8 CG2 A:VAL552 4.6 63.0 1.0 CB A:ASP549 4.6 61.4 1.0 OD2 A:ASP549 4.7 85.8 1.0 CB A:ASP443 4.9 61.4 1.0 CA A:ASP549 4.9 62.2 1.0 OD2 A:ASP498 4.9 69.2 1.0 N A:GLY444 4.9 62.3 1.0 OE1 A:GLU478 4.9 73.5 1.0

L.Tian, M.S.Kim, H.Li, J.Wang, W.Yang. Structure of Hiv-1 Reverse Transcriptase Cleaving Rna in An Rna/Dna Hybrid. Proc. Natl. Acad. Sci. V. 115 507 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29295939
DOI: 10.1073/PNAS.1719746115