Magnesium in PDB 6rwn: Sivrcm Intasome in Complex with Dolutegravir

The structure of Sivrcm Intasome in Complex with Dolutegravir also contains other interesting chemical elements:

Fluorine	(F)	4 atoms
Zinc	(Zn)	8 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Magnesium atom in the Sivrcm Intasome in Complex with Dolutegravir (pdb code 6rwn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Sivrcm Intasome in Complex with Dolutegravir, PDB code: 6rwn:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Sivrcm Intasome in Complex with Dolutegravir


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Sivrcm Intasome in Complex with Dolutegravir within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:9.6 occ:1.00 O A:HOH402 2.0 11.4 1.0 OAC A:DLU303 2.0 9.6 1.0 O A:HOH401 2.0 13.7 1.0 OAE A:DLU303 2.1 9.6 1.0 OD2 A:ASP116 2.1 7.8 1.0 OD1 A:ASP64 2.1 6.4 1.0 CG A:ASP64 3.1 6.4 1.0 CAS A:DLU303 3.1 9.6 1.0 CAW A:DLU303 3.2 9.6 1.0 CG A:ASP116 3.2 7.8 1.0 OD2 A:ASP64 3.4 6.4 1.0 MG A:MG305 3.5 4.9 1.0 CAY A:DLU303 3.6 9.6 1.0 OD1 A:ASP116 3.7 7.8 1.0 NBC A:DLU303 4.2 9.6 1.0 O A:HOH403 4.2 7.8 1.0 O A:CYS65 4.4 12.1 1.0 CAZ A:DLU303 4.4 9.6 1.0 CB A:ASP116 4.5 7.8 1.0 CB A:ASP64 4.5 6.4 1.0 N A:CYS65 4.5 12.1 1.0 CBA A:DLU303 4.5 9.6 1.0 OE2 A:GLU152 4.6 9.6 1.0 OAD A:DLU303 4.7 9.6 1.0 CA A:ASP64 4.8 6.4 1.0 N7 T:DA21 4.9 20.5 1.0 NBD A:DLU303 5.0 9.6 1.0 O A:HOH404 5.0 16.0 1.0

Magnesium binding site 2 out of 4 in the Sivrcm Intasome in Complex with Dolutegravir


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Sivrcm Intasome in Complex with Dolutegravir within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg305 b:4.9 occ:1.00 OAD A:DLU303 2.0 9.6 1.0 O A:HOH403 2.0 7.8 1.0 OE1 A:GLU152 2.0 9.6 1.0 OE2 A:GLU152 2.0 9.6 1.0 OD2 A:ASP64 2.1 6.4 1.0 OAE A:DLU303 2.1 9.6 1.0 CD A:GLU152 2.3 9.6 1.0 CAZ A:DLU303 2.7 9.6 1.0 CAW A:DLU303 2.8 9.6 1.0 CG A:ASP64 3.1 6.4 1.0 OD1 A:ASP64 3.5 6.4 1.0 MG A:MG304 3.5 9.6 1.0 CG A:GLU152 3.8 9.6 1.0 O A:HOH402 4.1 11.4 1.0 CAX A:DLU303 4.1 9.6 1.0 CAY A:DLU303 4.2 9.6 1.0 CB A:ASP64 4.4 6.4 1.0 NAP A:DLU303 4.4 9.6 1.0 OAC A:DLU303 4.5 9.6 1.0 FAG A:DLU303 4.6 9.6 1.0 O A:CYS65 4.6 12.1 1.0 CB A:GLU152 4.7 9.6 1.0 OD2 A:ASP116 4.7 7.8 1.0 ND2 A:ASN155 4.7 5.5 1.0 CAR A:DLU303 4.8 9.6 1.0 OP1 T:DA21 4.9 20.5 1.0 CAS A:DLU303 4.9 9.6 1.0

Magnesium binding site 3 out of 4 in the Sivrcm Intasome in Complex with Dolutegravir


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Sivrcm Intasome in Complex with Dolutegravir within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg304 b:9.1 occ:1.00 O I:HOH403 2.0 10.8 1.0 O I:HOH401 2.0 14.0 1.0 OAC I:DLU303 2.0 11.0 1.0 OAE I:DLU303 2.1 11.0 1.0 OD2 I:ASP116 2.1 8.0 1.0 OD1 I:ASP64 2.1 6.5 1.0 CG I:ASP64 3.1 6.5 1.0 CAS I:DLU303 3.1 11.0 1.0 CAW I:DLU303 3.2 11.0 1.0 CG I:ASP116 3.2 8.0 1.0 OD2 I:ASP64 3.4 6.5 1.0 MG I:MG305 3.5 4.9 1.0 CAY I:DLU303 3.6 11.0 1.0 OD1 I:ASP116 3.7 8.0 1.0 O I:HOH402 4.1 6.4 1.0 NBC I:DLU303 4.2 11.0 1.0 O I:CYS65 4.4 12.3 1.0 CAZ I:DLU303 4.4 11.0 1.0 CB I:ASP116 4.5 8.0 1.0 CB I:ASP64 4.5 6.5 1.0 N I:CYS65 4.5 12.3 1.0 CBA I:DLU303 4.5 11.0 1.0 OE2 I:GLU152 4.6 10.2 1.0 OAD I:DLU303 4.7 11.0 1.0 CA I:ASP64 4.8 6.5 1.0 N7 W:DA21 4.9 20.4 1.0 NBD I:DLU303 5.0 11.0 1.0

Magnesium binding site 4 out of 4 in the Sivrcm Intasome in Complex with Dolutegravir


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Sivrcm Intasome in Complex with Dolutegravir within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg305 b:4.9 occ:1.00 OE2 I:GLU152 2.0 10.2 1.0 O I:HOH402 2.0 6.4 1.0 OAD I:DLU303 2.0 11.0 1.0 OD2 I:ASP64 2.1 6.5 1.0 OE1 I:GLU152 2.1 10.2 1.0 OAE I:DLU303 2.1 11.0 1.0 CD I:GLU152 2.3 10.2 1.0 CAZ I:DLU303 2.8 11.0 1.0 CAW I:DLU303 2.8 11.0 1.0 CG I:ASP64 3.1 6.5 1.0 OD1 I:ASP64 3.5 6.5 1.0 MG I:MG304 3.5 9.1 1.0 CG I:GLU152 3.9 10.2 1.0 O I:HOH403 4.1 10.8 1.0 CAX I:DLU303 4.1 11.0 1.0 CAY I:DLU303 4.2 11.0 1.0 CB I:ASP64 4.4 6.5 1.0 NAP I:DLU303 4.4 11.0 1.0 OAC I:DLU303 4.5 11.0 1.0 FAG I:DLU303 4.6 11.0 1.0 O I:CYS65 4.6 12.3 1.0 OD2 I:ASP116 4.7 8.0 1.0 CB I:GLU152 4.7 10.2 1.0 ND2 I:ASN155 4.8 8.6 1.0 CAR I:DLU303 4.8 11.0 1.0 CAS I:DLU303 4.8 11.0 1.0 OP1 W:DA21 4.9 20.4 1.0

P.Cherepanov, N.Nans, N.J.Cook. Structural Basis of Second-Generation Hiv Integrase Inhibitor Action and Viral Resistance Science 2020.
ISSN: ESSN 1095-9203
DOI: 10.1126/SCIENCE.AAY4919