Magnesium in PDB 8vbc: 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 8vbc). 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: 8vbc:
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:97.7 occ:1.00 O A:VAL111 2.0 95.4 1.0 OD2 A:ASP110 2.3 125.0 1.0 OD2 A:ASP185 2.4 115.7 1.0 O2B A:DTP603 2.4 109.2 0.7 O1A A:DTP603 2.5 112.9 0.7 O3G A:DTP603 2.5 117.2 0.3 O1G A:DTP603 2.6 116.9 0.7 C A:VAL111 3.2 92.5 1.0 CG A:ASP110 3.2 123.8 1.0 CG A:ASP185 3.6 116.6 1.0 PB A:DTP603 3.7 109.8 0.7 O5' A:DTP603 3.8 115.9 0.3 PA A:DTP603 3.8 117.2 0.7 PG A:DTP603 3.9 116.5 0.3 OD1 A:ASP110 3.9 118.0 1.0 CA A:GLY112 3.9 105.1 1.0 N A:GLY112 3.9 102.1 1.0 PG A:DTP603 4.0 116.1 0.7 O3A A:DTP603 4.1 110.7 0.7 N A:VAL111 4.1 101.2 1.0 O1G A:DTP603 4.2 114.5 0.3 CA A:VAL111 4.2 97.2 1.0 CB A:ALA114 4.2 97.7 1.0 O3B A:DTP603 4.2 114.7 0.7 CB A:ASP110 4.2 117.2 1.0 C A:ASP110 4.3 116.4 1.0 OD1 A:ASP185 4.4 115.5 1.0 NZ A:LYS220 4.4 118.7 1.0 CB A:ASP185 4.5 107.0 1.0 C4' A:DTP603 4.5 114.6 0.3 C A:GLY112 4.5 113.9 1.0 O A:ASP110 4.5 118.1 1.0 C5' A:DTP603 4.6 114.1 0.7 O2A A:DTP603 4.6 115.5 0.3 N A:ASP113 4.6 116.2 1.0 C5' A:DTP603 4.6 113.4 0.3 N A:ALA114 4.7 98.3 1.0 PA A:DTP603 4.7 121.3 0.3 O3B A:DTP603 4.8 116.3 0.3 O2A A:DTP603 4.8 116.0 0.7 O3A A:DTP603 4.8 115.7 0.3 O5' A:DTP603 4.8 116.1 0.7 CB A:VAL111 4.8 91.1 1.0 CA A:ASP110 4.8 112.2 1.0 O3G A:DTP603 4.9 109.3 0.7 O2G A:DTP603 4.9 109.5 0.3 CE A:LYS220 5.0 121.4 1.0 O1B A:DTP603 5.0 111.5 0.7 O2G A:DTP603 5.0 116.5 0.7 CA A:ALA114 5.0 102.4 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:132.0 occ:1.00 O3' F:DG33 2.2 116.8 1.0 O2A A:DTP603 2.6 115.5 0.3 OD1 A:ASP110 3.4 118.0 1.0 C3' F:DG33 3.5 110.6 1.0 O5' F:DG33 3.6 105.1 1.0 OD2 A:ASP110 3.8 125.0 1.0 CG A:ASP110 3.8 123.8 1.0 PA A:DTP603 3.9 121.3 0.3 NZ A:LYS220 4.1 118.7 1.0 O2A A:DTP603 4.2 116.0 0.7 O1A A:DTP603 4.4 112.9 0.7 C4' F:DG33 4.4 107.9 1.0 O5' A:DTP603 4.4 115.9 0.3 O2B A:DTP603 4.5 112.0 0.3 C5' F:DG33 4.6 102.8 1.0 OP1 F:DG33 4.6 108.3 1.0 P F:DG33 4.6 101.4 1.0 O1A A:DTP603 4.7 116.0 0.3 C2' F:DG33 4.7 104.8 1.0 PA A:DTP603 4.8 117.2 0.7 OD2 A:ASP186 4.9 121.9 1.0 CB A:ASP110 4.9 117.2 1.0 CG A:ASP186 5.0 122.1 1.0 OP2 F:DG33 5.0 110.2 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