Magnesium in PDB 8w2r: Hiv-1 P5-in Intasome Core

The structure of Hiv-1 P5-in Intasome Core also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Hiv-1 P5-in Intasome Core (pdb code 8w2r). 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 P5-in Intasome Core, PDB code: 8w2r:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Hiv-1 P5-in 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 P5-in Intasome Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:29.9 occ:1.00 OD2 A:ASP116 2.0 52.8 1.0 OD1 A:ASP64 2.1 56.2 1.0 OAC A:DLU304 2.1 57.6 1.0 OAE A:DLU304 2.1 53.1 1.0 CG A:ASP64 2.9 51.0 1.0 CG A:ASP116 3.1 51.9 1.0 CAS A:DLU304 3.1 57.4 1.0 OD2 A:ASP64 3.2 55.3 1.0 CAW A:DLU304 3.2 56.7 1.0 MG A:MG302 3.4 33.8 1.0 CAY A:DLU304 3.6 54.2 1.0 OD1 A:ASP116 3.7 54.8 1.0 O A:CYS65 4.0 62.7 1.0 CB A:ASP116 4.1 42.7 1.0 NBC A:DLU304 4.1 51.5 1.0 N A:CYS65 4.3 37.9 1.0 CB A:ASP64 4.3 37.1 1.0 CAZ A:DLU304 4.4 49.4 1.0 OE2 A:GLU152 4.4 36.8 1.0 CBA A:DLU304 4.5 50.5 1.0 OAD A:DLU304 4.6 47.4 1.0 CA A:ASP64 4.7 43.5 1.0 N6 F:DA21 4.8 65.6 1.0 NBD A:DLU304 4.9 42.8 1.0 CE2 A:PHE121 4.9 45.8 1.0 C A:CYS65 4.9 52.2 1.0 C A:ASP64 5.0 41.0 1.0

Magnesium binding site 2 out of 4 in the Hiv-1 P5-in 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 P5-in Intasome Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:33.8 occ:1.00 OD2 A:ASP64 2.0 55.3 1.0 OAE A:DLU304 2.1 53.1 1.0 OAD A:DLU304 2.1 47.4 1.0 OE2 A:GLU152 2.4 36.8 1.0 OE1 A:GLU152 2.5 36.3 1.0 CD A:GLU152 2.8 39.7 1.0 CAZ A:DLU304 2.9 49.4 1.0 CAW A:DLU304 2.9 56.7 1.0 CG A:ASP64 3.0 51.0 1.0 MG A:MG301 3.4 29.9 1.0 OD1 A:ASP64 3.4 56.2 1.0 O A:CYS65 4.0 62.7 1.0 ND2 A:ASN155 4.0 40.0 1.0 OP1 F:DA21 4.1 61.5 1.0 CAX A:DLU304 4.2 44.0 1.0 CAY A:DLU304 4.2 54.2 1.0 CG A:GLU152 4.3 32.4 1.0 CB A:ASP64 4.3 37.1 1.0 OAC A:DLU304 4.5 57.6 1.0 NAP A:DLU304 4.7 47.2 1.0 O3' F:DC20 4.7 60.5 1.0 OD2 A:ASP116 4.8 52.8 1.0 CAS A:DLU304 4.9 57.4 1.0 FAG A:DLU304 4.9 56.5 1.0 CAR A:DLU304 5.0 47.1 1.0 P F:DA21 5.0 66.2 1.0

Magnesium binding site 3 out of 4 in the Hiv-1 P5-in 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 P5-in Intasome Core within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg301 b:26.2 occ:1.00 OD2 I:ASP116 2.0 54.2 1.0 OD1 I:ASP64 2.1 56.2 1.0 OAC I:DLU304 2.1 55.3 1.0 OAE I:DLU304 2.1 52.6 1.0 CG I:ASP64 3.0 50.9 1.0 CG I:ASP116 3.1 54.0 1.0 CAS I:DLU304 3.1 56.8 1.0 CAW I:DLU304 3.2 56.6 1.0 OD2 I:ASP64 3.3 55.0 1.0 MG I:MG302 3.4 32.3 1.0 CAY I:DLU304 3.6 53.8 1.0 OD1 I:ASP116 3.8 55.2 1.0 O I:CYS65 4.0 63.3 1.0 CB I:ASP116 4.1 46.5 1.0 NBC I:DLU304 4.1 50.7 1.0 OE2 I:GLU152 4.2 35.8 1.0 N I:CYS65 4.3 41.0 1.0 CAZ I:DLU304 4.4 47.0 1.0 CB I:ASP64 4.4 36.0 1.0 CBA I:DLU304 4.5 50.1 1.0 OAD I:DLU304 4.6 45.0 1.0 CA I:ASP64 4.7 43.9 1.0 N6 O:DA21 4.7 64.4 1.0 NBD I:DLU304 4.9 41.8 1.0 CE2 I:PHE121 4.9 45.6 1.0 C I:CYS65 4.9 51.8 1.0 C6 O:DA21 5.0 65.0 1.0

Magnesium binding site 4 out of 4 in the Hiv-1 P5-in 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 P5-in Intasome Core within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg302 b:32.3 occ:1.00 OD2 I:ASP64 2.0 55.0 1.0 OAE I:DLU304 2.0 52.6 1.0 OAD I:DLU304 2.1 45.0 1.0 OE2 I:GLU152 2.3 35.8 1.0 OE1 I:GLU152 2.4 36.3 1.0 CD I:GLU152 2.7 37.4 1.0 CAZ I:DLU304 2.9 47.0 1.0 CAW I:DLU304 2.9 56.6 1.0 CG I:ASP64 3.0 50.9 1.0 MG I:MG301 3.4 26.2 1.0 OD1 I:ASP64 3.5 56.2 1.0 ND2 I:ASN155 3.9 40.5 1.0 O I:CYS65 4.0 63.3 1.0 OP1 O:DA21 4.1 61.1 1.0 CG I:GLU152 4.2 30.9 1.0 CAX I:DLU304 4.2 42.8 1.0 CAY I:DLU304 4.2 53.8 1.0 CB I:ASP64 4.3 36.0 1.0 OAC I:DLU304 4.5 55.3 1.0 O3' O:DC20 4.7 60.8 1.0 NAP I:DLU304 4.7 47.1 1.0 OD2 I:ASP116 4.8 54.2 1.0 CAS I:DLU304 4.8 56.8 1.0 P O:DA21 4.9 69.3 1.0 FAG I:DLU304 4.9 55.6 1.0 CAR I:DLU304 4.9 46.9 1.0 CG I:ASN155 5.0 44.2 1.0 CB I:GLU152 5.0 26.9 1.0 C8 O:DA21 5.0 61.4 1.0 N7 O:DA21 5.0 59.0 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