Magnesium in PDB 6vdk: Cryoem Structure of Hiv-1 Conserved Intasome Core

The structure of Cryoem Structure of Hiv-1 Conserved Intasome Core also contains other interesting chemical elements:

Fluorine

(F)

4 atoms

The binding sites of Magnesium atom in the Cryoem Structure of Hiv-1 Conserved Intasome Core (pdb code 6vdk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Cryoem Structure of Hiv-1 Conserved Intasome Core, PDB code: 6vdk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Cryoem Structure of Hiv-1 Conserved Intasome Core


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryoem Structure of Hiv-1 Conserved Intasome Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:0.4 occ:1.00 OD2 A:ASP64 2.1 0.1 1.0 OAE A:DLU303 2.1 0.7 1.0 OAC A:DLU303 2.3 0.7 1.0 OD1 A:ASP64 2.3 0.1 1.0 OD2 A:ASP116 2.5 0.6 1.0 CG A:ASP64 2.5 0.1 1.0 CAS A:DLU303 3.3 0.7 1.0 CAW A:DLU303 3.4 0.7 1.0 CG A:ASP116 3.5 0.6 1.0 O A:CYS65 3.6 0.8 1.0 MG A:MG302 3.8 0.9 1.0 OD1 A:ASP116 3.8 0.6 1.0 CAY A:DLU303 3.9 0.7 1.0 CB A:ASP64 4.0 0.1 1.0 OE2 A:GLU152 4.3 0.5 1.0 NBC A:DLU303 4.4 0.7 1.0 SG A:CYS65 4.5 0.8 1.0 CAZ A:DLU303 4.6 0.7 1.0 N A:CYS65 4.7 0.8 1.0 C A:CYS65 4.7 0.8 1.0 CBA A:DLU303 4.8 0.7 1.0 CB A:ASP116 4.8 0.6 1.0 OAD A:DLU303 4.8 0.7 1.0 CA A:ASP64 4.9 0.1 1.0

Magnesium binding site 2 out of 4 in the Cryoem Structure of Hiv-1 Conserved Intasome Core


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryoem Structure of Hiv-1 Conserved Intasome Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:0.9 occ:1.00 OE1 A:GLU152 2.0 0.5 1.0 OAD A:DLU303 2.2 0.7 1.0 OAE A:DLU303 2.4 0.7 1.0 CD A:GLU152 2.6 0.5 1.0 OE2 A:GLU152 2.7 0.5 1.0 CAZ A:DLU303 2.9 0.7 1.0 CAW A:DLU303 3.0 0.7 1.0 OD2 A:ASP64 3.1 0.1 1.0 MG A:MG301 3.8 0.4 1.0 C2 H:DA21 4.0 0.5 1.0 CG A:GLU152 4.0 0.5 1.0 CG A:ASP64 4.2 0.1 1.0 CAX A:DLU303 4.3 0.7 1.0 O A:CYS65 4.4 0.8 1.0 OP1 H:DA21 4.4 0.5 1.0 N1 H:DA21 4.4 0.5 1.0 N3 H:DA21 4.5 0.5 1.0 CAY A:DLU303 4.5 0.7 1.0 NAP A:DLU303 4.6 0.7 1.0 CB A:GLU152 4.6 0.5 1.0 ND2 A:ASN155 4.7 0.8 1.0 OAC A:DLU303 4.9 0.7 1.0 O3' H:DC20 4.9 0.8 1.0 CAR A:DLU303 5.0 0.7 1.0

Magnesium binding site 3 out of 4 in the Cryoem Structure of Hiv-1 Conserved Intasome Core


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryoem Structure of Hiv-1 Conserved Intasome Core within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:0.9 occ:1.00 OAE C:DLU303 1.9 0.8 1.0 OD2 C:ASP116 2.2 0.0 1.0 OAC C:DLU303 2.6 0.8 1.0 OD1 C:ASP64 2.7 0.7 1.0 CAW C:DLU303 2.9 0.8 1.0 OD2 C:ASP64 3.0 0.7 1.0 MG C:MG302 3.1 0.9 1.0 CG C:ASP64 3.2 0.7 1.0 CG C:ASP116 3.2 0.0 1.0 CAS C:DLU303 3.3 0.8 1.0 OE2 C:GLU152 3.4 0.1 1.0 CAY C:DLU303 3.6 0.8 1.0 OD1 C:ASP116 3.8 0.0 1.0 CAZ C:DLU303 4.1 0.8 1.0 CB C:ASP116 4.3 0.0 1.0 OAD C:DLU303 4.3 0.8 1.0 O C:CYS65 4.4 0.9 1.0 NBC C:DLU303 4.5 0.8 1.0 CD C:GLU152 4.5 0.1 1.0 CB C:ASP64 4.6 0.7 1.0 NBD C:DLU303 4.9 0.8 1.0 OE1 C:GLU152 4.9 0.1 1.0

Magnesium binding site 4 out of 4 in the Cryoem Structure of Hiv-1 Conserved Intasome Core


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryoem Structure of Hiv-1 Conserved Intasome Core within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg302 b:0.9 occ:1.00 OAE C:DLU303 2.1 0.8 1.0 OD2 C:ASP64 2.2 0.7 1.0 OE1 C:GLU152 2.4 0.1 1.0 OAD C:DLU303 2.6 0.8 1.0 OE2 C:GLU152 2.6 0.1 1.0 CD C:GLU152 2.9 0.1 1.0 CAW C:DLU303 3.0 0.8 1.0 CAZ C:DLU303 3.1 0.8 1.0 MG C:MG301 3.1 0.9 1.0 CG C:ASP64 3.4 0.7 1.0 OP1 F:DA21 3.8 0.0 1.0 OD1 C:ASP64 3.8 0.7 1.0 O C:CYS65 3.9 0.9 1.0 ND2 C:ASN155 4.3 0.5 1.0 CG C:GLU152 4.4 0.1 1.0 CAY C:DLU303 4.5 0.8 1.0 OAC C:DLU303 4.6 0.8 1.0 CAX C:DLU303 4.6 0.8 1.0 CB C:ASP64 4.6 0.7 1.0 C2 F:DA21 4.8 0.0 1.0 NAP C:DLU303 5.0 0.8 1.0

M.Li, X.Chen, H.Wang, K.Jurado, A.Engelman, R.Craigie. A Peptide Derived From Ledgf Stimulates Hiv-1 Dna Integration and Facilitates Intasome Structural Studies J.Mol.Biol. 2020.
ISSN: ESSN 1089-8638