Magnesium in PDB 6eli: Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Rilpivirine and An Rnase H Inhibitor XZ462

The structure of Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Rilpivirine and An Rnase H Inhibitor XZ462, PDB code: 6eli was solved by K.Das, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.56 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	163.120, 72.920, 109.250, 90.00, 101.36, 90.00
R / Rfree (%)	18.4 / 22.1

The binding sites of Magnesium atom in the Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Rilpivirine and An Rnase H Inhibitor XZ462 (pdb code 6eli). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Rilpivirine and An Rnase H Inhibitor XZ462, PDB code: 6eli:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Rilpivirine and An Rnase H Inhibitor XZ462


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Rilpivirine and An Rnase H Inhibitor XZ462 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:31.1 occ:1.00 O16 A:BA5702 1.9 38.6 1.0 OD1 A:ASP549 2.0 31.8 1.0 OD2 A:ASP443 2.1 33.1 1.0 O A:HOH888 2.1 34.9 1.0 O A:HOH852 2.1 31.6 1.0 O17 A:BA5702 2.2 36.1 1.0 N15 A:BA5702 2.7 36.0 1.0 C14 A:BA5702 2.9 32.6 1.0 CG A:ASP443 3.1 30.2 1.0 CG A:ASP549 3.1 33.8 1.0 OD1 A:ASP443 3.4 30.6 1.0 CB A:ASP549 3.6 27.3 1.0 MG A:MG704 3.6 36.5 1.0 O A:HOH923 3.9 53.2 1.0 C4 A:BA5702 4.0 34.2 1.0 NE2 A:HIS539 4.1 43.3 1.0 CA A:ASP549 4.1 34.7 1.0 OG A:SER553 4.2 61.7 1.0 OD2 A:ASP549 4.2 35.4 1.0 OD2 A:ASP498 4.2 34.0 1.0 O A:GLY444 4.2 34.2 1.0 C9 A:BA5702 4.3 44.6 1.0 CB A:ASP443 4.4 25.5 1.0 N5 A:BA5702 4.5 35.0 1.0 O A:HOH826 4.6 29.0 1.0 CE1 A:HIS539 4.6 30.3 1.0 O11 A:BA5702 4.8 50.3 1.0 O A:ASP549 4.8 35.4 1.0 CD2 A:HIS539 4.9 39.2 1.0 C A:ASP549 4.9 34.2 1.0

Magnesium binding site 2 out of 2 in the Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Rilpivirine and An Rnase H Inhibitor XZ462


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Rilpivirine and An Rnase H Inhibitor XZ462 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:36.5 occ:1.00 N5 A:BA5702 1.9 35.0 1.0 OE2 A:GLU478 2.0 31.6 1.0 O16 A:BA5702 2.0 38.6 1.0 OD1 A:ASP498 2.1 34.7 1.0 OD1 A:ASP443 2.2 30.6 1.0 C4 A:BA5702 2.7 34.2 1.0 N15 A:BA5702 2.8 36.0 1.0 C6 A:BA5702 2.9 45.5 1.0 CG A:ASP498 2.9 33.6 1.0 CD A:GLU478 3.1 33.4 1.0 OD2 A:ASP498 3.1 34.0 1.0 CG A:ASP443 3.2 30.2 1.0 OD2 A:ASP443 3.6 33.1 1.0 OE1 A:GLU478 3.6 28.8 1.0 MG A:MG703 3.6 31.1 1.0 O A:HOH852 4.0 31.6 1.0 C3 A:BA5702 4.0 41.7 1.0 C14 A:BA5702 4.0 32.6 1.0 O A:HOH877 4.1 30.6 1.0 C7 A:BA5702 4.2 50.8 1.0 O A:GLY444 4.2 34.2 1.0 CG A:GLU478 4.3 31.1 1.0 CB A:ASP498 4.3 31.1 1.0 O A:HOH888 4.3 34.9 1.0 CB A:ASP443 4.5 25.5 1.0 N A:GLY444 4.6 32.1 1.0 O17 A:BA5702 4.7 36.1 1.0 C8 A:BA5702 4.7 44.0 1.0 C A:ASP498 4.7 28.5 1.0 CA A:ASP443 4.8 26.4 1.0 N A:SER499 4.8 28.2 1.0 O A:ASP498 4.9 29.0 1.0 CA A:ASP498 5.0 31.9 1.0 CB A:ALA538 5.0 27.5 1.0

P.L.Boyer, S.J.Smith, X.Z.Zhao, K.Das, K.Gruber, E.Arnold, T.R.Burke, S.H.Hughes. Developing and Evaluating Inhibitors Against the Rnase H Active Site of Hiv-1 Reverse Transcriptase. J. Virol. V. 92 2018.
ISSN: ESSN 1098-5514
PubMed: 29643235
DOI: 10.1128/JVI.02203-17