Magnesium in PDB 5j2n: Hiv-1 Reverse Transcriptase in Complex with Dna That Has Incorporated Efda-Mp at the P-(Post-Translocation) Site and Dtmp at the N-(Pre- Translocation) Site

The structure of Hiv-1 Reverse Transcriptase in Complex with Dna That Has Incorporated Efda-Mp at the P-(Post-Translocation) Site and Dtmp at the N-(Pre- Translocation) Site, PDB code: 5j2n was solved by Z.L.Salie, K.A.Kirby, S.G.Sarafianos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.62 / 2.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	166.827, 169.885, 102.656, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 24.2

The structure of Hiv-1 Reverse Transcriptase in Complex with Dna That Has Incorporated Efda-Mp at the P-(Post-Translocation) Site and Dtmp at the N-(Pre- Translocation) Site also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Magnesium atom in the Hiv-1 Reverse Transcriptase in Complex with Dna That Has Incorporated Efda-Mp at the P-(Post-Translocation) Site and Dtmp at the N-(Pre- Translocation) Site (pdb code 5j2n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Hiv-1 Reverse Transcriptase in Complex with Dna That Has Incorporated Efda-Mp at the P-(Post-Translocation) Site and Dtmp at the N-(Pre- Translocation) Site, PDB code: 5j2n:

Magnesium binding site 1 out of 1 in the Hiv-1 Reverse Transcriptase in Complex with Dna That Has Incorporated Efda-Mp at the P-(Post-Translocation) Site and Dtmp at the N-(Pre- Translocation) Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hiv-1 Reverse Transcriptase in Complex with Dna That Has Incorporated Efda-Mp at the P-(Post-Translocation) Site and Dtmp at the N-(Pre- Translocation) Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:29.2 occ:1.00 OD2 A:ASP443 2.0 54.1 1.0 OD2 A:ASP498 2.0 56.2 1.0 O A:HOH703 2.1 84.5 1.0 O A:HOH701 2.1 63.4 1.0 OE2 A:GLU478 2.1 32.4 1.0 O A:HOH702 2.1 72.2 1.0 OD1 A:ASP498 2.1 53.2 1.0 CG A:ASP498 2.3 54.1 1.0 CG A:ASP443 3.0 44.0 1.0 CD A:GLU478 3.0 41.8 1.0 OE1 A:GLU478 3.3 50.0 1.0 OD1 A:ASP443 3.6 52.1 1.0 O A:GLY444 3.8 48.2 1.0 CB A:ASP498 3.8 31.1 1.0 CB A:ASP443 4.2 42.7 1.0 N A:GLY444 4.2 32.8 1.0 CG A:GLU478 4.4 43.3 1.0 CA A:ASP443 4.4 41.7 1.0 CB A:ALA538 4.5 36.0 1.0 CA A:ASP498 4.7 41.3 1.0 C A:ASP498 4.7 39.5 1.0 C A:GLY444 4.8 39.9 1.0 C A:ASP443 4.9 32.5 1.0 N A:ASP498 4.9 36.7 1.0 N A:SER499 5.0 41.6 1.0 O A:ASP498 5.0 38.4 1.0

Z.L.Salie, K.A.Kirby, E.Michailidis, B.Marchand, K.Singh, L.C.Rohan, E.N.Kodama, H.Mitsuya, M.A.Parniak, S.G.Sarafianos. Structural Basis of Hiv Inhibition By Translocation-Defective Rt Inhibitor 4'-Ethynyl-2-Fluoro-2'-Deoxyadenosine (Efda). Proc.Natl.Acad.Sci.Usa V. 113 9274 2016.
ISSN: ESSN 1091-6490
PubMed: 27489345
DOI: 10.1073/PNAS.1605223113