Magnesium in PDB 8vbe: 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 8vbe). 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: 8vbe:
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:41.1 occ:1.00 O A:VAL111 2.1 72.3 1.0 O1A A:DTP601 2.1 81.7 1.0 OD2 A:ASP185 2.3 71.7 1.0 OD1 A:ASP110 2.3 75.8 1.0 O1G A:DTP601 2.4 76.7 1.0 O2B A:DTP601 2.5 68.8 1.0 C A:VAL111 3.2 68.0 1.0 PA A:DTP601 3.5 84.1 1.0 CG A:ASP110 3.5 77.2 1.0 CG A:ASP185 3.5 71.6 1.0 PB A:DTP601 3.6 77.9 1.0 PG A:DTP601 3.7 85.3 1.0 O3A A:DTP601 3.8 65.2 1.0 O3B A:DTP601 3.9 75.8 1.0 OD2 A:ASP110 4.0 73.9 1.0 N A:VAL111 4.0 62.7 1.0 OD1 A:ASP185 4.1 72.3 1.0 N A:GLY112 4.1 69.0 1.0 CA A:GLY112 4.2 69.9 1.0 CA A:VAL111 4.2 61.0 1.0 C5' A:DTP601 4.2 64.7 1.0 O5' A:DTP601 4.4 71.8 1.0 O2A A:DTP601 4.5 74.9 1.0 O3G A:DTP601 4.6 73.8 1.0 N A:ASP113 4.6 72.7 1.0 CB A:ASP185 4.6 65.1 1.0 MG A:MG603 4.6 77.4 1.0 NZ A:LYS220 4.7 76.8 1.0 CB A:ASP110 4.7 70.5 1.0 C A:ASP110 4.7 70.2 1.0 CB A:ALA114 4.7 59.2 1.0 O2G A:DTP601 4.7 73.3 1.0 C A:GLY112 4.7 72.9 1.0 CB A:VAL111 4.8 64.6 1.0 N A:ALA114 4.8 60.1 1.0 O1B A:DTP601 5.0 81.0 1.0 O3' F:DA34 5.0 75.9 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:77.4 occ:1.00 OD2 A:ASP110 2.4 73.9 1.0 O3' F:DA34 2.7 75.9 1.0 CG A:ASP110 3.4 77.2 1.0 O1A A:DTP601 3.7 81.7 1.0 OD1 A:ASP110 3.8 75.8 1.0 C3' F:DA34 3.8 60.7 1.0 O2A A:DTP601 4.1 74.9 1.0 OD2 A:ASP186 4.2 84.1 1.0 O5' F:DA34 4.2 63.5 1.0 NZ A:LYS220 4.4 76.8 1.0 PA A:DTP601 4.4 84.1 1.0 C5' F:DA34 4.6 58.7 1.0 MG A:MG602 4.6 41.1 1.0 CB A:ASP110 4.6 70.5 1.0 C4' F:DA34 4.7 59.8 1.0 OP1 F:DA34 4.7 69.8 1.0 OD1 A:ASP185 4.7 72.3 1.0 OD2 A:ASP185 4.9 71.7 1.0 CG A:ASP186 5.0 78.9 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