Magnesium in PDB 8vbi: 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 8vbi). 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: 8vbi:
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:Mg702 b:44.0 occ:1.00 OD2 A:ASP185 2.0 69.9 1.0 OD1 A:ASP110 2.0 79.6 1.0 O A:VAL111 2.1 67.3 1.0 O2G A:DTP701 2.4 71.4 1.0 O2A A:DTP701 2.5 64.7 1.0 O2B A:DTP701 2.7 69.2 1.0 CG A:ASP110 3.0 80.7 1.0 CG A:ASP185 3.1 67.8 1.0 C A:VAL111 3.3 65.9 1.0 OD2 A:ASP110 3.5 81.8 1.0 PB A:DTP701 3.6 67.8 1.0 PG A:DTP701 3.6 74.7 1.0 PA A:DTP701 3.7 65.0 1.0 OD1 A:ASP185 3.7 68.8 1.0 O3B A:DTP701 3.8 68.6 1.0 O3A A:DTP701 3.8 56.1 1.0 N A:VAL111 3.9 61.1 1.0 MG A:MG703 4.0 106.0 1.0 CA A:VAL111 4.2 62.1 1.0 N A:GLY112 4.2 68.5 1.0 NZ A:LYS220 4.2 80.2 1.0 CB A:ASP185 4.2 63.3 1.0 CA A:GLY112 4.3 66.3 1.0 C5' A:DTP701 4.3 52.3 1.0 CB A:ASP110 4.3 74.4 1.0 O5' A:DTP701 4.4 61.6 1.0 O1G A:DTP701 4.4 65.8 1.0 CB A:ALA114 4.5 56.0 1.0 C A:ASP110 4.5 71.2 1.0 N A:ASP113 4.6 65.6 1.0 O3G A:DTP701 4.7 71.9 1.0 CE A:LYS220 4.7 78.4 1.0 N A:ALA114 4.7 57.5 1.0 CG2 A:VAL111 4.7 60.9 1.0 C A:GLY112 4.7 70.1 1.0 CA A:ASP110 4.9 68.6 1.0 O1A A:DTP701 4.9 69.7 1.0 CB A:VAL111 5.0 58.0 1.0 O1B A:DTP701 5.0 70.2 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:Mg703 b:106.0 occ:1.00 OD2 A:ASP110 1.9 81.8 1.0 OD1 A:ASP185 2.2 68.8 1.0 CG A:ASP110 3.0 80.7 1.0 O2A A:DTP701 3.1 64.7 1.0 CG A:ASP185 3.1 67.8 1.0 C3' F:DOC33 3.3 49.7 1.0 OD2 A:ASP185 3.4 69.9 1.0 OD1 A:ASP110 3.6 79.6 1.0 OD1 A:ASP186 3.8 85.3 1.0 CB A:ASP186 4.0 58.1 1.0 MG A:MG702 4.0 44.0 1.0 C4' F:DOC33 4.0 51.4 1.0 CG A:ASP186 4.1 80.0 1.0 C5' F:DOC33 4.1 52.6 1.0 N A:ASP186 4.2 66.8 1.0 PA A:DTP701 4.3 65.0 1.0 CB A:ASP110 4.3 74.4 1.0 CA A:ASP186 4.3 57.5 1.0 C A:ASP185 4.3 69.5 1.0 O5' A:DTP701 4.4 61.6 1.0 C2' F:DOC33 4.5 55.2 1.0 CB A:ASP185 4.5 63.3 1.0 O5' F:DOC33 4.6 59.5 1.0 O A:ASP185 4.6 71.1 1.0 NZ A:LYS220 4.7 80.2 1.0 C5' A:DTP701 4.7 52.3 1.0 O1A A:DTP701 4.8 69.7 1.0 CA A:ASP185 4.8 63.5 1.0 N A:ASP185 4.9 68.3 1.0 OD2 A:ASP186 5.0 87.2 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