Magnesium in PDB 8vbf: 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 8vbf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Kinetic Intermediate States of Hiv-1 Rt Dna Synthesis Captured By Cryo-Em, PDB code: 8vbf:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 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:Mg603 b:99.3 occ:1.00 O6 A:POP602 2.1 102.9 0.5 OD2 A:ASP110 2.2 105.5 1.0 O A:VAL111 2.3 100.6 1.0 O3G A:DTP601 2.3 100.0 0.3 OD2 A:ASP185 2.4 100.8 1.0 O1A A:DTP601 2.5 100.6 0.3 O1B A:DTP601 2.5 102.8 0.3 OP1 F:DA35 3.0 102.5 0.7 CG A:ASP110 3.2 104.8 1.0 P2 A:POP602 3.3 103.5 0.5 C A:VAL111 3.4 93.5 1.0 NZ A:LYS220 3.4 102.4 0.5 CG A:ASP185 3.5 98.8 1.0 MG A:MG604 3.5 97.7 0.4 PB A:DTP601 3.5 104.5 0.3 O3A A:DTP601 3.5 102.1 0.3 PA A:DTP601 3.6 109.3 0.3 PG A:DTP601 3.6 105.7 0.3 OD1 A:ASP110 3.7 102.0 1.0 NZ A:LYS220 3.8 102.9 0.5 O A:POP602 3.8 104.7 0.5 O3B A:DTP601 3.8 101.5 0.3 O2 A:POP602 3.8 103.8 0.5 OD1 A:ASP185 3.8 100.3 1.0 O3 A:POP602 3.9 104.7 0.5 O5 A:POP602 3.9 102.5 0.5 P1 A:POP602 4.0 108.7 0.5 N A:VAL111 4.1 91.0 1.0 P F:DA35 4.3 118.3 0.7 CE A:LYS220 4.3 103.2 0.5 N A:GLY112 4.3 100.6 1.0 CB A:ASP110 4.3 98.8 1.0 C5' F:DA35 4.3 100.8 0.7 O4 A:POP602 4.3 103.1 0.5 CA A:VAL111 4.3 93.7 1.0 CA A:GLY112 4.3 102.0 1.0 O2A A:DTP601 4.4 107.2 0.3 O5' F:DA35 4.4 106.9 0.7 O1G A:DTP601 4.4 103.7 0.3 C A:ASP110 4.4 90.7 1.0 N A:ASP113 4.5 108.4 1.0 O2G A:DTP601 4.6 104.8 0.3 CE A:LYS220 4.6 102.7 0.5 CD A:LYS220 4.6 103.8 0.5 CD A:LYS220 4.7 103.5 0.5 CB A:ASP185 4.7 94.0 1.0 O5' A:DTP601 4.8 104.3 0.3 C5' A:DTP601 4.8 100.2 0.3 CA A:ASP110 4.8 87.9 1.0 C A:GLY112 4.8 109.1 1.0 O2B A:DTP601 4.8 102.4 0.3 O3' F:DA34 4.9 99.0 1.0 N A:ALA114 4.9 82.0 1.0 CB A:ALA114 4.9 87.4 1.0 O A:ASP110 4.9 97.3 1.0 CB A:VAL111 5.0 92.0 1.0

Magnesium binding site 2 out of 3 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:Mg604 b:97.7 occ:0.39 OD1 A:ASP185 2.0 100.3 1.0 OD1 A:ASP110 2.2 102.0 1.0 O1A A:DTP601 2.5 100.6 0.3 O3' F:DA34 2.7 99.0 1.0 OP1 F:DA35 2.8 102.5 0.7 CG A:ASP185 2.9 98.8 1.0 CG A:ASP110 3.0 104.8 1.0 OD2 A:ASP110 3.1 105.5 1.0 OD2 A:ASP185 3.2 100.8 1.0 P F:DA35 3.4 118.3 0.7 PA A:DTP601 3.5 109.3 0.3 MG A:MG603 3.5 99.3 1.0 O2A A:DTP601 3.5 107.2 0.3 MG F:MG101 3.6 100.9 1.0 C3' F:DA34 3.8 93.8 1.0 C4' F:DA34 3.9 87.8 1.0 C5' F:DA34 4.1 92.5 1.0 C5' F:DA35 4.1 100.8 0.7 N A:ASP186 4.1 100.5 1.0 O5' F:DA35 4.2 106.9 0.7 C A:ASP185 4.3 94.0 1.0 O5' A:DTP601 4.3 104.3 0.3 CB A:ASP185 4.3 94.0 1.0 CB A:ASP186 4.3 96.2 1.0 CB A:ASP110 4.4 98.8 1.0 C5' A:DTP601 4.4 100.2 0.3 CA A:ASP186 4.5 98.9 1.0 OP2 F:DA35 4.6 107.4 0.7 CG A:ASP186 4.6 101.3 1.0 O A:ASP185 4.6 97.5 1.0 NZ A:LYS220 4.7 102.4 0.5 CA A:ASP185 4.7 91.6 1.0 N A:ASP185 4.7 94.0 1.0 O6 A:POP602 4.7 102.9 0.5 O3A A:DTP601 4.8 102.1 0.3 C2' F:DA34 4.8 97.6 1.0 OD1 A:ASP186 4.8 104.2 1.0 CA A:ASP110 4.9 87.9 1.0

Magnesium binding site 3 out of 3 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 3 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 F:Mg101 b:100.9 occ:1.00 C5' F:DA34 3.3 92.5 1.0 O2A A:DTP601 3.5 107.2 0.3 MG A:MG604 3.6 97.7 0.4 OP1 F:DA35 3.6 102.5 0.7 OD1 A:ASP110 3.8 102.0 1.0 NZ A:LYS220 3.9 102.4 0.5 OP1 F:DA34 4.0 94.7 1.0 O3' F:DA34 4.1 99.0 1.0 O5' F:DA34 4.1 95.7 1.0 P F:DA35 4.1 118.3 0.7 OP2 F:DA35 4.2 107.4 0.7 CG A:ASP110 4.2 104.8 1.0 OD2 A:ASP110 4.2 105.5 1.0 C4' F:DA34 4.4 87.8 1.0 P F:DA34 4.4 101.3 1.0 C3' F:DA34 4.6 93.8 1.0 PA A:DTP601 4.7 109.3 0.3 OP2 F:DA34 4.7 94.7 1.0 O1A A:DTP601 4.7 100.6 0.3 CE A:LYS220 4.8 102.7 0.5

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