Magnesium in PDB 5j2p: Hiv-1 Reverse Transcriptase in Complex with Dna That Has Incorporated Efda-Mp at the P-(Post-Translocation) Site and A Second Efda-Mp 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 A Second Efda-Mp at the N-(Pre-Translocation) Site, PDB code: 5j2p 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)	63.78 / 2.53
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	165.977, 170.183, 99.695, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 24.6

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

Fluorine

(F)

2 atoms

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 A Second Efda-Mp at the N-(Pre-Translocation) Site (pdb code 5j2p). 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 A Second Efda-Mp at the N-(Pre-Translocation) Site, PDB code: 5j2p:

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 A Second Efda-Mp 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 A Second Efda-Mp at the N-(Pre-Translocation) Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:31.9 occ:1.00 OD2 A:ASP443 2.0 35.1 1.0 OE2 A:GLU478 2.0 31.9 1.0 O A:HOH848 2.0 32.5 1.0 O A:HOH748 2.0 88.2 1.0 OD1 A:ASP498 2.1 67.3 1.0 OD2 A:ASP498 2.1 41.6 1.0 CG A:ASP498 2.3 37.5 1.0 CD A:GLU478 2.9 46.9 1.0 CG A:ASP443 3.1 45.4 1.0 OE1 A:GLU478 3.1 51.7 1.0 O A:HOH701 3.5 31.1 1.0 OD1 A:ASP443 3.6 51.8 1.0 O A:HOH820 3.7 32.8 1.0 O A:GLY444 3.8 33.8 1.0 CB A:ASP498 3.8 30.6 1.0 O A:HOH842 3.9 46.3 1.0 O A:HOH716 4.1 68.1 1.0 N A:GLY444 4.1 39.9 1.0 CB A:ASP443 4.2 48.5 1.0 CG A:GLU478 4.3 47.4 1.0 CA A:ASP443 4.4 32.7 1.0 C A:ASP498 4.6 38.9 1.0 O A:HOH736 4.6 51.5 1.0 CA A:ASP498 4.6 36.0 1.0 CB A:ALA538 4.8 31.5 1.0 N A:SER499 4.8 29.9 1.0 C A:GLY444 4.8 43.5 1.0 C A:ASP443 4.8 42.0 1.0 N A:ASP498 4.8 34.7 1.0 O A:ASP498 4.9 35.5 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