Magnesium in PDB 3oyd: Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti GS9160

The structure of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti GS9160, PDB code: 3oyd 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)	39.88 / 2.54
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	159.530, 159.530, 123.580, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 23.4

The structure of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti GS9160 also contains other interesting chemical elements:

Fluorine	(F)	1 atom
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 the Insti GS9160 (pdb code 3oyd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti GS9160, PDB code: 3oyd:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti GS9160


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 the Insti GS9160 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg396 b:43.3 occ:1.00 O A:HOH400 2.0 43.6 1.0 OD1 A:ASP185 2.1 45.2 1.0 NAQ A:ZZV398 2.1 44.2 1.0 OAF A:ZZV398 2.1 47.3 1.0 OD1 A:ASP128 2.1 45.2 1.0 O A:HOH525 2.2 39.6 1.0 CAU A:ZZV398 2.8 46.0 1.0 CAZ A:ZZV398 2.9 46.0 1.0 CG A:ASP185 3.1 47.6 1.0 CAI A:ZZV398 3.1 46.2 1.0 CG A:ASP128 3.2 45.6 1.0 OD2 A:ASP185 3.4 48.5 1.0 OD2 A:ASP128 3.6 47.4 1.0 MG A:MG397 3.9 48.7 1.0 O A:HOH453 3.9 50.1 1.0 N6 D:DA17 4.2 71.5 1.0 CAW A:ZZV398 4.2 45.9 1.0 N A:TYR129 4.2 45.7 1.0 CAY A:ZZV398 4.3 45.8 1.0 O A:TYR129 4.3 46.6 1.0 CAH A:ZZV398 4.4 44.6 1.0 CB A:ASP185 4.4 48.6 1.0 CB A:ASP128 4.4 45.7 1.0 O A:HOH399 4.5 36.9 1.0 OE2 A:GLU221 4.6 42.5 1.0 CA A:ASP128 4.7 45.6 1.0 N7 D:DA17 4.7 71.5 1.0 CAN A:ZZV398 4.9 45.8 1.0 CE2 A:PHE190 4.9 55.1 1.0 OAC A:ZZV398 4.9 44.7 1.0 C6 D:DA17 5.0 72.3 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti GS9160


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 the Insti GS9160 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg397 b:48.7 occ:1.00 OAC A:ZZV398 1.9 44.7 1.0 OD2 A:ASP128 1.9 47.4 1.0 O A:HOH399 1.9 36.9 1.0 OE2 A:GLU221 2.0 42.5 1.0 OE1 A:GLU221 2.2 41.9 1.0 OAF A:ZZV398 2.2 47.3 1.0 CD A:GLU221 2.4 43.4 1.0 CAR A:ZZV398 2.9 46.6 1.0 CG A:ASP128 3.0 45.6 1.0 CAU A:ZZV398 3.2 46.0 1.0 CAW A:ZZV398 3.3 45.9 1.0 OD1 A:ASP128 3.4 45.2 1.0 ND2 A:ASN224 3.7 44.8 1.0 MG A:MG396 3.9 43.3 1.0 CG A:GLU221 3.9 41.8 1.0 O A:HOH453 4.1 50.1 1.0 O A:TYR129 4.1 46.6 1.0 NBB A:ZZV398 4.1 45.9 1.0 O A:HOH525 4.1 39.6 1.0 CB A:ASP128 4.2 45.7 1.0 OP1 D:DA17 4.4 54.1 1.0 CAZ A:ZZV398 4.5 46.0 1.0 O3' D:DC16 4.6 48.9 1.0 OD1 A:ASP185 4.6 45.2 1.0 CAO A:ZZV398 4.7 43.6 1.0 CAV A:ZZV398 4.7 44.9 1.0 N7 D:DA17 4.8 71.5 1.0 CB A:GLU221 4.8 43.1 1.0 CA A:GLU221 4.9 42.9 1.0 C2' D:DC16 4.9 43.1 1.0 C8 D:DA17 4.9 72.4 1.0 NAQ A:ZZV398 4.9 44.2 1.0 CG A:ASN224 5.0 43.1 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti GS9160


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti GS9160 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg394 b:96.0 occ:1.00 OD1 B:ASP128 2.3 65.0 1.0 OD1 B:ASP185 2.4 54.4 1.0 CG B:ASP185 3.1 53.7 1.0 OD2 B:ASP185 3.2 55.6 1.0 CG B:ASP128 3.4 62.5 1.0 O B:HOH407 3.8 47.4 1.0 OD2 B:ASP128 3.9 65.7 1.0 N B:TYR129 4.2 58.9 1.0 CE2 B:PHE190 4.3 58.5 1.0 CB B:ASP185 4.6 52.4 1.0 CB B:ASP128 4.6 59.1 1.0 O B:TYR129 4.7 61.4 1.0 CA B:ASP128 4.7 58.1 1.0 CA B:GLY187 4.9 58.1 1.0 C B:ASP128 5.0 58.4 1.0

S.Hare, A.M.Vos, R.F.Clayton, J.W.Thuring, M.D.Cummings, P.Cherepanov. Molecular Mechanisms of Retroviral Integrase Inhibition and the Evolution of Viral Resistance. Proc.Natl.Acad.Sci.Usa V. 107 20057 2010.
ISSN: ISSN 0027-8424
PubMed: 21030679
DOI: 10.1073/PNAS.1010246107