Magnesium in PDB 9c29: Hexadecamer of NL4-3 Wt Hiv-1 Intasome

The binding sites of Magnesium atom in the Hexadecamer of NL4-3 Wt Hiv-1 Intasome (pdb code 9c29). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Hexadecamer of NL4-3 Wt Hiv-1 Intasome, PDB code: 9c29:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Hexadecamer of NL4-3 Wt Hiv-1 Intasome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hexadecamer of NL4-3 Wt Hiv-1 Intasome within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg600 b:30.3 occ:1.00 MG A:MG601 3.7 30.6 1.0 O3' R:DA21 3.8 15.0 1.0 CB A:ASP116 4.2 13.6 1.0 CB A:ASP64 4.5 12.3 1.0 O A:CYS65 4.7 22.5 1.0

Magnesium binding site 2 out of 4 in the Hexadecamer of NL4-3 Wt Hiv-1 Intasome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hexadecamer of NL4-3 Wt Hiv-1 Intasome within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:30.6 occ:1.00 O3' R:DA21 2.3 15.0 1.0 O A:CYS65 2.8 22.5 1.0 C3' R:DA21 3.6 7.3 1.0 MG A:MG600 3.7 30.3 1.0 OP1 R:DA21 3.8 7.2 1.0 C4' R:DA21 3.8 9.1 1.0 C A:CYS65 4.0 17.0 1.0 CB A:ASP64 4.3 12.3 1.0 C5' R:DA21 4.4 9.7 1.0 CA A:THR66 4.5 16.0 1.0 C2' R:DA21 4.6 6.2 1.0 CB A:THR66 4.6 17.3 1.0 N A:THR66 4.6 18.2 1.0 N A:CYS65 4.8 14.7 1.0 P R:DA21 4.9 3.4 1.0 O3' R:DC20 5.0 12.7 1.0

Magnesium binding site 3 out of 4 in the Hexadecamer of NL4-3 Wt Hiv-1 Intasome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Hexadecamer of NL4-3 Wt Hiv-1 Intasome within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg600 b:30.3 occ:1.00 MG I:MG601 3.7 30.6 1.0 O3' T:DA21 3.8 15.0 1.0 CB I:ASP116 4.2 13.6 1.0 CB I:ASP64 4.5 12.3 1.0 O I:CYS65 4.7 22.5 1.0

Magnesium binding site 4 out of 4 in the Hexadecamer of NL4-3 Wt Hiv-1 Intasome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Hexadecamer of NL4-3 Wt Hiv-1 Intasome within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg601 b:30.6 occ:1.00 O3' T:DA21 2.3 15.0 1.0 O I:CYS65 2.8 22.5 1.0 C3' T:DA21 3.6 7.3 1.0 MG I:MG600 3.7 30.3 1.0 OP1 T:DA21 3.8 7.2 1.0 C4' T:DA21 3.8 9.1 1.0 C I:CYS65 4.0 17.0 1.0 CB I:ASP64 4.3 12.3 1.0 C5' T:DA21 4.4 9.7 1.0 CA I:THR66 4.5 16.0 1.0 C2' T:DA21 4.6 6.2 1.0 CB I:THR66 4.6 17.3 1.0 N I:THR66 4.6 18.2 1.0 N I:CYS65 4.8 14.7 1.0 P T:DA21 4.9 3.4 1.0 O3' T:DC20 5.0 12.7 1.0

T.Jing, Z.Shan, T.Dinh, A.Biswas, S.Jang, J.Greenwood, M.Li, Z.Zhang, G.Gray, H.J.Shin, B.Zhou, D.Passos, T.S.Strutzenberg, S.Aiyer, L.Andrade, Y.Zhang, Z.Li, R.Craigie, A.N.Engelman, M.Kvaratskhelia, D.Lyumkis. Oligomeric Hiv-1 Integrase Structures Reveal Functional Plasticity For Intasome Assembly and Rna Binding Biorxiv 2025.
ISSN: ISSN 2692-8205
DOI: 10.1101/2024.01.26.577436