Calcium in PDB 4pwd: Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with Bulge-Rna/Dna and Nevirapine

All present enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with Bulge-Rna/Dna and Nevirapine:
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 Bulge-Rna/Dna and Nevirapine, PDB code: 4pwd was solved by K.Das, S.E.Martinez, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.68 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.684, 130.765, 141.866, 90.00, 100.75, 90.00
R / Rfree (%)	22.1 / 29.1

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

Calcium binding site 1 out of 2 in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with Bulge-Rna/Dna and Nevirapine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with Bulge-Rna/Dna and Nevirapine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:73.8 occ:1.00 OD2 A:ASP443 2.5 52.5 1.0 OD1 A:ASP549 2.8 79.1 1.0 CG A:ASP443 3.4 35.4 1.0 OD1 A:ASP443 3.4 36.6 1.0 OD1 A:ASN498 4.0 45.2 1.0 CG A:ASP549 4.0 76.8 1.0 NE2 A:HIS539 4.1 80.4 1.0 O A:GLY444 4.2 47.4 1.0 ND2 A:ASN498 4.4 43.2 1.0 CG A:ASN498 4.5 41.6 1.0 OG A:SER553 4.6 81.8 1.0 CE1 A:HIS539 4.8 81.2 1.0 OD2 A:ASP549 4.8 80.2 1.0 CB A:ASP443 4.8 27.5 1.0 CB A:ASP549 4.9 64.1 1.0 CD2 A:HIS539 5.0 73.4 1.0 CB A:ALA538 5.0 53.2 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with Bulge-Rna/Dna and Nevirapine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with Bulge-Rna/Dna and Nevirapine within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca902 b:73.4 occ:1.00 OD2 C:ASP443 2.5 45.3 1.0 OD1 C:ASP549 2.5 62.2 1.0 OD1 C:ASP443 3.2 32.9 1.0 CG C:ASP443 3.2 33.9 1.0 O C:GLY444 3.5 42.0 1.0 CG C:ASP549 3.7 60.6 1.0 OP1 E:C723 4.0 0.8 1.0 ND2 C:ASN498 4.4 35.9 1.0 CB C:ASP549 4.5 53.5 1.0 OD2 C:ASP549 4.6 54.4 1.0 C C:GLY444 4.6 36.5 1.0 CB C:ASP443 4.7 23.0 1.0 OD1 C:ASN498 4.7 43.1 1.0 CB C:ALA445 4.8 36.7 1.0 CA C:ASP549 4.9 47.4 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