Magnesium in PDB 8w34: Hiv-1 Intasome Core Assembled with Wild-Type Integrase, 1F

The structure of Hiv-1 Intasome Core Assembled with Wild-Type Integrase, 1F also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Hiv-1 Intasome Core Assembled with Wild-Type Integrase, 1F (pdb code 8w34). 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 Intasome Core Assembled with Wild-Type Integrase, 1F, PDB code: 8w34:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Hiv-1 Intasome Core Assembled with Wild-Type Integrase, 1F


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hiv-1 Intasome Core Assembled with Wild-Type Integrase, 1F within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:35.1 occ:1.00 OD2 A:ASP116 2.0 36.1 1.0 OAC A:DLU302 2.0 42.3 1.0 OD1 A:ASP64 2.0 38.0 1.0 OAE A:DLU302 2.2 44.0 1.0 CG A:ASP64 3.0 37.0 1.0 CAS A:DLU302 3.1 39.9 1.0 CG A:ASP116 3.2 37.0 1.0 CAW A:DLU302 3.3 38.7 1.0 OD2 A:ASP64 3.4 39.9 1.0 MG A:MG304 3.5 40.7 1.0 CAY A:DLU302 3.6 37.9 1.0 OD1 A:ASP116 3.9 42.2 1.0 O A:CYS65 4.0 44.5 1.0 N A:CYS65 4.1 35.4 1.0 N1 F:DA21 4.1 40.4 0.5 NBC A:DLU302 4.2 33.4 1.0 CB A:ASP116 4.3 30.3 1.0 CB A:ASP64 4.4 32.1 1.0 C2 F:DA21 4.5 40.0 0.5 OE2 A:GLU152 4.5 36.9 1.0 CBA A:DLU302 4.5 33.5 1.0 CAZ A:DLU302 4.5 39.5 1.0 CA A:ASP64 4.7 29.9 1.0 OAD A:DLU302 4.7 42.3 1.0 C A:CYS65 4.8 35.2 1.0 CA A:CYS65 4.9 31.5 1.0 C A:ASP64 5.0 33.3 1.0 NBD A:DLU302 5.0 36.4 1.0 C6 F:DA21 5.0 39.4 0.5

Magnesium binding site 2 out of 4 in the Hiv-1 Intasome Core Assembled with Wild-Type Integrase, 1F


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hiv-1 Intasome Core Assembled with Wild-Type Integrase, 1F within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:40.7 occ:1.00 OD2 A:ASP64 2.0 39.9 1.0 OAE A:DLU302 2.1 44.0 1.0 OAD A:DLU302 2.2 42.3 1.0 OE2 A:GLU152 2.4 36.9 1.0 OE1 A:GLU152 2.4 37.3 1.0 CD A:GLU152 2.7 36.6 1.0 CAZ A:DLU302 2.9 39.5 1.0 CAW A:DLU302 2.9 38.7 1.0 CG A:ASP64 3.1 37.0 1.0 OD1 A:ASP64 3.5 38.0 1.0 MG A:MG303 3.5 35.1 1.0 ND2 A:ASN155 3.7 32.8 1.0 OP1 F:DA21 4.0 39.0 0.5 C5' F:DA21 4.0 41.1 0.5 OP1 F:DA21 4.1 39.0 0.5 C2 F:DA21 4.2 40.0 0.5 CAY A:DLU302 4.2 37.9 1.0 CAX A:DLU302 4.2 36.8 1.0 CG A:GLU152 4.3 34.8 1.0 CB A:ASP64 4.4 32.1 1.0 OAC A:DLU302 4.4 42.3 1.0 O A:CYS65 4.5 44.5 1.0 O3' F:DC20 4.5 41.1 1.0 N3 F:DA21 4.6 39.8 0.5 FAG A:DLU302 4.7 46.1 1.0 NAP A:DLU302 4.7 37.4 1.0 P F:DA21 4.8 41.1 0.5 CAS A:DLU302 4.9 39.9 1.0 N1 F:DA21 4.9 40.4 0.5 O5' F:DA21 4.9 42.0 0.5 P F:DA21 4.9 40.5 0.5 OD2 A:ASP116 4.9 36.1 1.0 CG A:ASN155 5.0 34.5 1.0 CAR A:DLU302 5.0 38.4 1.0 C2' F:DC20 5.0 36.3 1.0

Magnesium binding site 3 out of 4 in the Hiv-1 Intasome Core Assembled with Wild-Type Integrase, 1F


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Hiv-1 Intasome Core Assembled with Wild-Type Integrase, 1F within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg303 b:36.3 occ:1.00 OD2 I:ASP116 2.0 36.4 1.0 OAC I:DLU302 2.0 42.1 1.0 OD1 I:ASP64 2.0 39.6 1.0 OAE I:DLU302 2.2 43.5 1.0 CG I:ASP64 3.0 37.6 1.0 CAS I:DLU302 3.1 40.5 1.0 CG I:ASP116 3.3 38.8 1.0 CAW I:DLU302 3.3 39.2 1.0 OD2 I:ASP64 3.3 40.5 1.0 MG I:MG304 3.5 40.8 1.0 CAY I:DLU302 3.6 38.5 1.0 O I:CYS65 4.0 45.4 1.0 OD1 I:ASP116 4.0 44.9 1.0 N1 O:DA21 4.1 40.5 0.5 N I:CYS65 4.2 36.1 1.0 NBC I:DLU302 4.2 34.5 1.0 CB I:ASP116 4.3 32.5 1.0 CB I:ASP64 4.4 33.3 1.0 OE2 I:GLU152 4.4 36.7 1.0 C2 O:DA21 4.4 40.1 0.5 CAZ I:DLU302 4.5 39.5 1.0 CBA I:DLU302 4.5 35.4 1.0 CA I:ASP64 4.7 31.4 1.0 OAD I:DLU302 4.7 42.7 1.0 C I:CYS65 4.8 35.1 1.0 C6 O:DA21 4.9 39.7 0.5 CA I:CYS65 5.0 31.2 1.0 NBD I:DLU302 5.0 36.6 1.0 C I:ASP64 5.0 34.4 1.0

Magnesium binding site 4 out of 4 in the Hiv-1 Intasome Core Assembled with Wild-Type Integrase, 1F


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Hiv-1 Intasome Core Assembled with Wild-Type Integrase, 1F within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg304 b:40.8 occ:1.00 OD2 I:ASP64 2.0 40.5 1.0 OAE I:DLU302 2.1 43.5 1.0 OAD I:DLU302 2.2 42.7 1.0 OE2 I:GLU152 2.2 36.7 1.0 OE1 I:GLU152 2.4 37.9 1.0 CD I:GLU152 2.6 36.6 1.0 CAW I:DLU302 2.9 39.2 1.0 CAZ I:DLU302 2.9 39.5 1.0 CG I:ASP64 3.1 37.6 1.0 OD1 I:ASP64 3.5 39.6 1.0 MG I:MG303 3.5 36.3 1.0 ND2 I:ASN155 3.6 33.2 1.0 OP1 O:DA21 4.1 38.3 0.5 C5' O:DA21 4.1 41.1 0.5 C2 O:DA21 4.1 40.1 0.5 CG I:GLU152 4.1 34.6 1.0 CAY I:DLU302 4.2 38.5 1.0 OP1 O:DA21 4.2 38.2 0.5 CAX I:DLU302 4.2 37.1 1.0 CB I:ASP64 4.4 33.3 1.0 OAC I:DLU302 4.4 42.1 1.0 O I:CYS65 4.5 45.4 1.0 O3' O:DC20 4.5 40.4 1.0 N3 O:DA21 4.6 39.9 0.5 FAG I:DLU302 4.7 45.1 1.0 NAP I:DLU302 4.7 37.3 1.0 CAS I:DLU302 4.8 40.5 1.0 N1 O:DA21 4.9 40.5 0.5 P O:DA21 4.9 41.4 0.5 CG I:ASN155 5.0 34.4 1.0 CB I:GLU152 5.0 31.5 1.0 P O:DA21 5.0 41.2 0.5 CAR I:DLU302 5.0 38.3 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