Magnesium in PDB 3s3m: Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and Dolutegravir (S/GSK1349572)

The structure of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and Dolutegravir (S/GSK1349572), PDB code: 3s3m was solved by S.Hare, P.Cherepanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.15 / 2.49
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	160.140, 160.140, 123.430, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 23.2

The structure of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and Dolutegravir (S/GSK1349572) also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Zinc	(Zn)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and Dolutegravir (S/GSK1349572) (pdb code 3s3m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and Dolutegravir (S/GSK1349572), PDB code: 3s3m:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and Dolutegravir (S/GSK1349572)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and Dolutegravir (S/GSK1349572) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg396 b:43.5 occ:1.00 OD1 A:ASP185 1.9 42.2 1.0 OAE A:DLU398 2.0 41.8 1.0 OAC A:DLU398 2.0 44.1 1.0 OD1 A:ASP128 2.0 37.1 1.0 O A:HOH526 2.0 33.8 1.0 O A:HOH400 2.2 28.1 1.0 CAS A:DLU398 3.0 44.5 1.0 CG A:ASP185 3.0 43.3 1.0 CAW A:DLU398 3.0 42.2 1.0 CG A:ASP128 3.1 39.1 1.0 CAY A:DLU398 3.4 43.0 1.0 OD2 A:ASP185 3.5 44.7 1.0 OD2 A:ASP128 3.6 39.6 1.0 MG A:MG397 3.7 39.6 1.0 O A:HOH452 3.7 44.1 1.0 NBC A:DLU398 4.2 44.2 1.0 OE2 A:GLU221 4.2 40.4 1.0 O A:HOH434 4.3 41.7 1.0 CAZ A:DLU398 4.3 43.0 1.0 CB A:ASP185 4.3 43.7 1.0 O D:HOH18 4.4 37.6 1.0 N A:TYR129 4.4 40.5 1.0 CB A:ASP128 4.4 38.4 1.0 O A:TYR129 4.5 42.5 1.0 O A:HOH524 4.5 37.1 1.0 OAD A:DLU398 4.6 42.0 1.0 CBA A:DLU398 4.7 43.8 1.0 CA A:ASP128 4.7 39.3 1.0 NBD A:DLU398 4.8 43.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and Dolutegravir (S/GSK1349572)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and Dolutegravir (S/GSK1349572) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg397 b:39.6 occ:1.00 OE2 A:GLU221 1.9 40.4 1.0 OE1 A:GLU221 2.0 40.5 1.0 OAD A:DLU398 2.1 42.0 1.0 O D:HOH18 2.1 37.6 1.0 OD2 A:ASP128 2.1 39.6 1.0 CD A:GLU221 2.3 39.7 1.0 OAE A:DLU398 2.3 41.8 1.0 CAZ A:DLU398 2.9 43.0 1.0 CAW A:DLU398 3.0 42.2 1.0 CG A:ASP128 3.1 39.1 1.0 OD1 A:ASP128 3.5 37.1 1.0 ND2 A:ASN224 3.6 40.9 1.0 MG A:MG396 3.7 43.5 1.0 CG A:GLU221 3.8 36.5 1.0 O A:HOH452 3.9 44.1 1.0 O A:HOH526 4.1 33.8 1.0 CAX A:DLU398 4.2 41.1 1.0 O A:TYR129 4.2 42.5 1.0 CAY A:DLU398 4.4 43.0 1.0 OP1 D:DA17 4.4 59.3 1.0 CB A:ASP128 4.4 38.4 1.0 NAP A:DLU398 4.5 37.6 1.0 CB A:GLU221 4.6 37.6 1.0 FAG A:DLU398 4.7 42.8 1.0 OD1 A:ASP185 4.7 42.2 1.0 CA A:GLU221 4.8 37.5 1.0 OAC A:DLU398 4.9 44.1 1.0 CAR A:DLU398 4.9 40.6 1.0 CG A:ASN224 4.9 41.4 1.0 O3' D:DC16 5.0 53.1 1.0

S.Hare, S.J.Smith, M.Metifiot, A.Jaxa-Chamiec, Y.Pommier, S.H.Hughes, P.Cherepanov. Structural and Functional Analyses of the Second-Generation Integrase Strand Transfer Inhibitor Dolutegravir (S/GSK1349572). Mol.Pharmacol. V. 80 565 2011.
ISSN: ISSN 0026-895X
PubMed: 21719464
DOI: 10.1124/MOL.111.073189