Magnesium in PDB 8vbg: Kinetic Intermediate States of Hiv-1 Rt Dna Synthesis Captured By Cryo-Em

The binding sites of Magnesium atom in the Kinetic Intermediate States of Hiv-1 Rt Dna Synthesis Captured By Cryo-Em (pdb code 8vbg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Kinetic Intermediate States of Hiv-1 Rt Dna Synthesis Captured By Cryo-Em, PDB code: 8vbg:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Kinetic Intermediate States of Hiv-1 Rt Dna Synthesis Captured By Cryo-Em


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Kinetic Intermediate States of Hiv-1 Rt Dna Synthesis Captured By Cryo-Em within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:32.4 occ:1.00 OD2 A:ASP185 2.1 46.3 1.0 OD2 A:ASP110 2.3 56.0 1.0 O A:VAL111 2.4 59.3 1.0 O2B A:F2A601 2.5 54.5 1.0 O3G A:F2A601 2.9 58.4 1.0 O1A A:F2A601 3.1 60.4 1.0 CG A:ASP185 3.3 42.3 1.0 C A:VAL111 3.4 49.6 1.0 CG A:ASP110 3.5 56.0 1.0 PB A:F2A601 3.6 66.2 1.0 O3B A:F2A601 3.8 54.7 1.0 C5' A:F2A601 3.9 44.8 1.0 PA A:F2A601 4.0 49.6 1.0 PG A:F2A601 4.0 68.9 1.0 C3A A:F2A601 4.0 44.7 1.0 MG A:MG603 4.1 56.7 1.0 CA A:GLY112 4.1 52.3 1.0 N A:GLY112 4.1 55.0 1.0 N A:VAL111 4.2 49.7 1.0 CB A:ASP185 4.2 45.9 1.0 OD1 A:ASP185 4.2 44.3 1.0 O5' A:F2A601 4.3 49.8 1.0 OD1 A:ASP110 4.3 59.2 1.0 C A:ASP110 4.3 52.7 1.0 CB A:ALA114 4.3 36.6 1.0 CA A:VAL111 4.4 47.1 1.0 N A:ASP113 4.4 55.3 1.0 C A:GLY112 4.5 59.5 1.0 CB A:ASP110 4.5 53.9 1.0 N A:ALA114 4.6 45.7 1.0 NZ A:LYS220 4.8 65.9 1.0 O3' F:DG33 4.8 36.0 1.0 O A:ASP110 4.8 60.0 1.0 CA A:ASP110 4.9 50.2 1.0 O2G A:F2A601 4.9 64.2 1.0 O1B A:F2A601 4.9 54.9 1.0 O1G A:F2A601 5.0 58.3 1.0

Magnesium binding site 2 out of 2 in the Kinetic Intermediate States of Hiv-1 Rt Dna Synthesis Captured By Cryo-Em


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Kinetic Intermediate States of Hiv-1 Rt Dna Synthesis Captured By Cryo-Em within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:56.7 occ:1.00 O1A A:F2A601 2.4 60.4 1.0 O3' F:DG33 2.4 36.0 1.0 OD1 A:ASP110 2.5 59.2 1.0 OD2 A:ASP110 3.0 56.0 1.0 CG A:ASP110 3.0 56.0 1.0 C3' F:DG33 3.6 27.6 1.0 PA A:F2A601 3.7 49.6 1.0 NZ A:LYS220 4.0 65.9 1.0 OD2 A:ASP185 4.1 46.3 1.0 MG A:MG602 4.1 32.4 1.0 O2A A:F2A601 4.1 56.6 1.0 O5' A:F2A601 4.2 49.8 1.0 CB A:ASP110 4.5 53.9 1.0 OD1 A:ASP185 4.6 44.3 1.0 C4' F:DG33 4.6 23.3 1.0 C5' F:DG33 4.7 26.2 1.0 CG A:ASP185 4.7 42.3 1.0 C2' F:DG33 4.7 25.4 1.0 CE A:LYS220 4.9 64.0 1.0 O5' F:DG33 4.9 34.4 1.0 C5' A:F2A601 5.0 44.8 1.0

S.Vergara, X.Zhou, U.Santiago, M.Alaoui-El-Azher, J.F.Conway, N.Sluis-Cremer, G.Calero. Structural Basis of Deoxynucleotide Addition By Hiv-1 Rt During Reverse Transcription Nat Commun V. 15 10553 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-54618-Y