Magnesium in PDB 8w09: Hiv-1 Wild-Type Intasome Core

The structure of Hiv-1 Wild-Type Intasome Core also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Fluorine	(F)	4 atoms

The binding sites of Magnesium atom in the Hiv-1 Wild-Type Intasome Core (pdb code 8w09). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Hiv-1 Wild-Type Intasome Core, PDB code: 8w09:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Hiv-1 Wild-Type Intasome Core


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hiv-1 Wild-Type Intasome Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:9.5 occ:1.00 OD2 A:ASP116 2.0 35.0 1.0 OD1 A:ASP64 2.1 38.4 1.0 OAC A:DLU304 2.1 39.8 1.0 OAE A:DLU304 2.2 39.9 1.0 CG A:ASP64 3.1 37.0 1.0 CG A:ASP116 3.2 34.9 1.0 CAS A:DLU304 3.2 32.1 1.0 CAW A:DLU304 3.3 37.6 1.0 OD2 A:ASP64 3.5 41.1 1.0 MG A:MG302 3.5 41.6 1.0 CAY A:DLU304 3.7 29.9 1.0 OD1 A:ASP116 3.7 41.7 1.0 O A:CYS65 3.9 39.0 1.0 N A:CYS65 4.2 29.4 1.0 NBC A:DLU304 4.3 23.9 1.0 CB A:ASP116 4.4 30.3 1.0 CB A:ASP64 4.4 29.6 1.0 CAZ A:DLU304 4.5 34.0 1.0 CBA A:DLU304 4.6 28.8 1.0 OAD A:DLU304 4.7 38.7 1.0 OE2 A:GLU152 4.7 23.6 1.0 CA A:ASP64 4.8 27.4 1.0 C A:CYS65 4.8 28.5 1.0 CA A:CYS65 4.9 27.1 1.0 N7 F:DA21 5.0 28.8 0.7 C A:ASP64 5.0 30.7 1.0 CE2 A:PHE121 5.0 33.9 1.0

Magnesium binding site 2 out of 4 in the Hiv-1 Wild-Type Intasome Core


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hiv-1 Wild-Type Intasome Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:41.6 occ:1.00 OD2 A:ASP64 2.0 41.1 1.0 OAE A:DLU304 2.1 39.9 1.0 OAD A:DLU304 2.1 38.7 1.0 OE2 A:GLU152 2.4 23.6 1.0 OE1 A:GLU152 2.5 39.0 1.0 CD A:GLU152 2.8 30.9 1.0 CAZ A:DLU304 2.9 34.0 1.0 CAW A:DLU304 2.9 37.6 1.0 CG A:ASP64 3.0 37.0 1.0 OD1 A:ASP64 3.4 38.4 1.0 OP1 F:DA21 3.5 32.3 0.7 MG A:MG301 3.5 9.5 1.0 C5' F:DA21 3.6 33.8 0.3 ND2 A:ASN155 4.1 25.7 1.0 C4' F:DA21 4.1 32.5 0.3 CAX A:DLU304 4.2 26.4 1.0 CAY A:DLU304 4.3 29.9 1.0 CG A:GLU152 4.3 30.1 1.0 O A:CYS65 4.3 39.0 1.0 CB A:ASP64 4.3 29.6 1.0 FAG A:DLU304 4.4 38.5 1.0 OAC A:DLU304 4.6 39.8 1.0 NAP A:DLU304 4.6 28.2 1.0 OD2 A:ASP116 4.6 35.0 1.0 O5' F:DA21 4.7 36.2 0.3 C8 F:DA21 4.7 30.2 0.7 O4' F:DA21 4.8 34.4 0.3 N7 F:DA21 4.8 28.8 0.7 P F:DA21 4.8 33.7 0.7 CAR A:DLU304 4.9 28.2 1.0 CAS A:DLU304 4.9 32.1 1.0 OP1 F:DA21 4.9 31.9 0.3 O3' F:DC20 5.0 32.7 1.0

Magnesium binding site 3 out of 4 in the Hiv-1 Wild-Type Intasome Core


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Hiv-1 Wild-Type Intasome Core within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg301 b:11.6 occ:1.00 OD2 I:ASP116 2.0 33.6 1.0 OD1 I:ASP64 2.1 31.9 1.0 OAC I:DLU304 2.1 34.7 1.0 OAE I:DLU304 2.2 37.1 1.0 CAS I:DLU304 3.1 30.0 1.0 CG I:ASP64 3.1 31.7 1.0 CG I:ASP116 3.2 30.7 1.0 CAW I:DLU304 3.3 35.2 1.0 MG I:MG302 3.5 39.5 1.0 OD2 I:ASP64 3.6 37.4 1.0 CAY I:DLU304 3.6 26.6 1.0 OD1 I:ASP116 3.7 37.5 1.0 O I:CYS65 4.0 39.2 1.0 N I:CYS65 4.1 26.9 1.0 NBC I:DLU304 4.2 22.5 1.0 CB I:ASP116 4.4 25.2 1.0 CB I:ASP64 4.4 24.5 1.0 CAZ I:DLU304 4.4 31.8 1.0 OE2 I:GLU152 4.5 21.1 1.0 CBA I:DLU304 4.6 28.3 1.0 OAD I:DLU304 4.7 35.3 1.0 CA I:ASP64 4.7 23.9 1.0 C I:CYS65 4.8 25.8 1.0 CA I:CYS65 4.9 21.3 1.0 CE2 I:PHE121 4.9 28.9 1.0 C I:ASP64 4.9 30.3 1.0 NBD I:DLU304 5.0 14.8 1.0

Magnesium binding site 4 out of 4 in the Hiv-1 Wild-Type Intasome Core


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Hiv-1 Wild-Type Intasome Core within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg302 b:39.5 occ:1.00 OD2 I:ASP64 2.0 37.4 1.0 OAE I:DLU304 2.1 37.1 1.0 OAD I:DLU304 2.1 35.3 1.0 OE2 I:GLU152 2.3 21.1 1.0 OE1 I:GLU152 2.4 37.3 1.0 CD I:GLU152 2.7 27.6 1.0 CAZ I:DLU304 2.8 31.8 1.0 CAW I:DLU304 2.9 35.2 1.0 CG I:ASP64 3.0 31.7 1.0 OD1 I:ASP64 3.3 31.9 1.0 OP1 O:DA21 3.4 29.0 0.7 C5' O:DA21 3.5 31.4 0.3 MG I:MG301 3.5 11.6 1.0 ND2 I:ASN155 3.9 25.3 1.0 C4' O:DA21 4.1 30.9 0.3 CAX I:DLU304 4.2 24.0 1.0 CG I:GLU152 4.2 22.5 1.0 CAY I:DLU304 4.2 26.6 1.0 O I:CYS65 4.3 39.2 1.0 CB I:ASP64 4.3 24.5 1.0 FAG I:DLU304 4.4 38.0 1.0 OAC I:DLU304 4.5 34.7 1.0 NAP I:DLU304 4.6 25.8 1.0 C8 O:DA21 4.6 29.7 0.7 N7 O:DA21 4.6 28.1 0.7 O5' O:DA21 4.6 33.9 0.3 OD2 I:ASP116 4.7 33.6 1.0 P O:DA21 4.8 35.6 0.7 OP1 O:DA21 4.8 32.7 0.3 O4' O:DA21 4.9 31.5 0.3 CAS I:DLU304 4.9 30.0 1.0 CAR I:DLU304 4.9 26.1 1.0

M.Li, R.Yang, X.Chen, H.Wang, R.Ghirlando, E.K.Dimitriadis, R.Craigie. Hiv-1 Integrase Assembles Multiple Species of Stable Synaptic Complex Intasomes That Are Active For Concerted Dna Integration in Vitro. J.Mol.Biol. 68557 2024.
ISSN: ESSN 1089-8638
PubMed: 38582148
DOI: 10.1016/J.JMB.2024.168557