Magnesium in PDB 5j2m: Hiv-1 Reverse Transcriptase in Complex with Dna and Efda-Triphosphate, A Translocation-Defective Rt Inhibitor

The structure of Hiv-1 Reverse Transcriptase in Complex with Dna and Efda-Triphosphate, A Translocation-Defective Rt Inhibitor, PDB code: 5j2m 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)	65.23 / 2.43
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	167.468, 169.758, 101.951, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 23.3

The structure of Hiv-1 Reverse Transcriptase in Complex with Dna and Efda-Triphosphate, A Translocation-Defective Rt Inhibitor 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 and Efda-Triphosphate, A Translocation-Defective Rt Inhibitor (pdb code 5j2m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Hiv-1 Reverse Transcriptase in Complex with Dna and Efda-Triphosphate, A Translocation-Defective Rt Inhibitor, PDB code: 5j2m:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Hiv-1 Reverse Transcriptase in Complex with Dna and Efda-Triphosphate, A Translocation-Defective Rt Inhibitor


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 and Efda-Triphosphate, A Translocation-Defective Rt Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:22.3 occ:1.00 OD2 A:ASP110 2.0 39.6 1.0 O A:VAL111 2.1 33.7 1.0 OD1 A:ASP185 2.1 30.6 1.0 O1A A:6FN604 2.1 29.0 1.0 O2B A:6FN604 2.3 34.9 1.0 O1G A:6FN604 2.4 39.0 1.0 CG A:ASP110 2.7 43.2 1.0 OD1 A:ASP110 2.8 50.3 1.0 CG A:ASP185 3.2 34.7 1.0 C A:VAL111 3.3 34.3 1.0 PB A:6FN604 3.4 32.2 1.0 PA A:6FN604 3.4 36.4 1.0 PG A:6FN604 3.7 40.3 1.0 OD2 A:ASP185 3.7 29.8 1.0 N A:VAL111 3.8 34.3 1.0 O3A A:6FN604 3.8 42.2 1.0 O3B A:6FN604 4.0 43.0 1.0 C5' A:6FN604 4.0 30.9 1.0 CA A:VAL111 4.1 31.6 1.0 CB A:ASP110 4.1 36.5 1.0 MG A:MG603 4.2 74.3 1.0 NZ A:LYS220 4.2 53.3 1.0 O5' A:6FN604 4.3 35.9 1.0 N A:GLY112 4.3 31.9 1.0 O2A A:6FN604 4.3 40.9 1.0 C A:ASP110 4.4 34.7 1.0 CA A:GLY112 4.5 33.2 1.0 CB A:ASP185 4.5 33.1 1.0 O1B A:6FN604 4.5 39.1 1.0 O2G A:6FN604 4.5 34.7 1.0 O3G A:6FN604 4.6 45.0 1.0 CB A:ALA114 4.7 36.4 1.0 CB A:VAL111 4.7 29.1 1.0 N A:ASP113 4.7 38.1 1.0 CA A:ASP110 4.8 32.2 1.0 N A:ALA114 4.9 39.2 1.0 C A:GLY112 4.9 33.0 1.0 CD A:LYS220 5.0 69.2 1.0

Magnesium binding site 2 out of 3 in the Hiv-1 Reverse Transcriptase in Complex with Dna and Efda-Triphosphate, A Translocation-Defective Rt Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hiv-1 Reverse Transcriptase in Complex with Dna and Efda-Triphosphate, A Translocation-Defective Rt Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:57.0 occ:1.00 OD1 A:ASP498 2.0 54.3 1.0 O A:HOH729 2.1 58.1 1.0 O A:HOH738 2.1 58.2 1.0 O A:HOH723 2.1 49.4 1.0 OD1 A:ASP443 2.1 40.6 1.0 OE2 A:GLU478 2.2 46.1 1.0 OD2 A:ASP498 2.2 43.2 1.0 CG A:ASP498 2.4 48.2 1.0 CG A:ASP443 3.1 44.4 1.0 CD A:GLU478 3.3 45.7 1.0 O A:HOH787 3.6 52.1 1.0 OD2 A:ASP443 3.6 52.5 1.0 OE1 A:GLU478 3.7 51.3 1.0 O A:HOH801 3.8 56.1 1.0 O A:GLY444 3.9 42.0 1.0 CB A:ASP498 3.9 37.1 1.0 CB A:ASP443 4.3 37.5 1.0 N A:GLY444 4.4 39.7 1.0 CB A:ALA538 4.6 42.7 1.0 CG A:GLU478 4.6 43.8 1.0 CA A:ASP443 4.6 34.1 1.0 OP1 T:DC723 4.7 71.6 1.0 CA A:ASP498 4.8 41.0 1.0 C A:ASP498 4.8 41.7 1.0 C A:GLY444 4.9 38.4 1.0 N A:ASP498 5.0 32.7 1.0

Magnesium binding site 3 out of 3 in the Hiv-1 Reverse Transcriptase in Complex with Dna and Efda-Triphosphate, A Translocation-Defective Rt Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Hiv-1 Reverse Transcriptase in Complex with Dna and Efda-Triphosphate, A Translocation-Defective Rt Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:74.3 occ:1.00 O A:HOH816 2.1 55.8 1.0 C3' P:DG822 2.1 38.9 1.0 OD2 A:ASP185 2.3 29.8 1.0 OD1 A:ASP110 2.4 50.3 1.0 C4' P:DG822 3.1 37.6 1.0 C2' P:DG822 3.3 41.5 1.0 O1A A:6FN604 3.4 29.0 1.0 CG A:ASP185 3.4 34.7 1.0 C5' P:DG822 3.7 36.2 1.0 CG A:ASP110 3.7 43.2 1.0 CB A:ASP186 3.7 33.4 1.0 OD1 A:ASP185 3.8 30.6 1.0 O5' A:6FN604 4.0 35.9 1.0 C5' A:6FN604 4.0 30.9 1.0 N A:ASP186 4.0 23.6 1.0 PA A:6FN604 4.1 36.4 1.0 CA A:ASP186 4.2 26.2 1.0 MG A:MG601 4.2 22.3 1.0 O2A A:6FN604 4.3 40.9 1.0 O4' P:DG822 4.4 27.6 1.0 CG A:ASP186 4.4 30.1 1.0 C A:ASP185 4.4 35.5 1.0 O5' P:DG822 4.4 37.6 1.0 C1' P:DG822 4.5 37.6 1.0 OD2 A:ASP110 4.5 39.6 1.0 CB A:ASP110 4.6 36.5 1.0 CB A:ASP185 4.7 33.1 1.0 N A:ASP185 4.7 33.3 1.0 OD2 A:ASP186 4.8 44.0 1.0 CA A:ASP185 4.8 29.2 1.0 O A:HOH867 4.9 59.0 1.0 O A:ASP185 5.0 36.3 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