Magnesium in PDB 8vbd: 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 8vbd). 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: 8vbd:
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:Mg601 b:94.1 occ:1.00 OD2 A:ASP110 2.1 112.3 1.0 O3G A:DTP603 2.2 113.0 0.8 O1A A:DTP603 2.2 113.3 0.8 OD2 A:ASP185 2.6 104.7 1.0 O A:VAL111 2.7 95.2 1.0 O1G A:DTP603 2.8 110.5 0.2 O2B A:DTP603 2.8 108.9 0.8 CG A:ASP110 3.2 110.5 1.0 C A:VAL111 3.4 91.2 1.0 NZ A:LYS220 3.5 111.8 1.0 PA A:DTP603 3.6 111.9 0.8 PG A:DTP603 3.6 111.5 0.8 PB A:DTP603 3.7 110.7 0.8 O3A A:DTP603 3.8 109.3 0.2 CG A:ASP185 3.8 106.1 1.0 PG A:DTP603 3.9 111.6 0.2 O3A A:DTP603 3.9 103.7 0.8 O3G A:DTP603 3.9 109.8 0.2 N A:VAL111 3.9 93.1 1.0 OD1 A:ASP110 3.9 103.3 1.0 O3B A:DTP603 4.0 111.0 0.8 O5' A:DTP603 4.0 109.7 0.2 N A:GLY112 4.0 102.3 1.0 CA A:GLY112 4.1 104.5 1.0 O2B A:DTP603 4.2 109.4 0.2 OD1 A:ASP185 4.2 104.2 1.0 C A:ASP110 4.3 104.9 1.0 CA A:VAL111 4.3 87.8 1.0 CB A:ASP110 4.3 106.7 1.0 PA A:DTP603 4.4 110.4 0.2 C5' A:DTP603 4.4 110.2 0.2 C5' A:DTP603 4.4 112.2 0.8 PB A:DTP603 4.5 108.9 0.2 O5' A:DTP603 4.5 113.7 0.8 O2G A:DTP603 4.5 103.8 0.8 O1A A:DTP603 4.5 108.3 0.2 O3B A:DTP603 4.5 109.7 0.2 O1G A:DTP603 4.6 111.9 0.8 O2A A:DTP603 4.6 110.4 0.8 N A:ASP113 4.6 96.5 1.0 CB A:ALA114 4.6 93.0 1.0 CE A:LYS220 4.7 114.3 1.0 CA A:ASP110 4.7 98.1 1.0 C A:GLY112 4.7 103.9 1.0 O A:ASP110 4.8 111.6 1.0 N A:ALA114 4.9 92.7 1.0 MG A:MG602 4.9 123.5 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:Mg602 b:123.5 occ:1.00 O3' F:DG33 2.5 115.2 1.0 OD1 A:ASP110 2.5 103.3 1.0 O2B A:DTP603 2.6 109.4 0.2 O1A A:DTP603 3.2 108.3 0.2 CG A:ASP110 3.6 110.5 1.0 PB A:DTP603 3.8 108.9 0.2 O1A A:DTP603 3.9 113.3 0.8 C3' F:DG33 3.9 106.8 1.0 OD2 A:ASP110 4.0 112.3 1.0 O3A A:DTP603 4.1 109.3 0.2 O2A A:DTP603 4.1 110.4 0.8 O5' F:DG33 4.2 99.6 1.0 PA A:DTP603 4.3 110.4 0.2 O1B A:DTP603 4.4 109.3 0.2 PA A:DTP603 4.5 111.9 0.8 NZ A:LYS220 4.6 111.8 1.0 OD1 A:ASP186 4.7 114.8 1.0 C4' F:DG33 4.8 104.5 1.0 CB A:ASP110 4.9 106.7 1.0 MG A:MG601 4.9 94.1 1.0 C5' F:DG33 4.9 99.1 1.0 C2' F:DG33 5.0 99.9 1.0 OP1 F:DG33 5.0 105.6 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