Magnesium in PDB 3oyf: Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti L-870,810

The structure of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti L-870,810, PDB code: 3oyf 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)	38.65 / 2.51
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	159.340, 159.340, 123.260, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 23.2

The structure of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti L-870,810 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 L-870,810 (pdb code 3oyf). 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 L-870,810, PDB code: 3oyf:
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 L-870,810


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 L-870,810 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg396 b:37.2 occ:1.00 NAR A:ZYP398 2.0 40.2 1.0 OD1 A:ASP185 2.0 38.1 1.0 O A:HOH545 2.1 29.9 1.0 OD1 A:ASP128 2.1 37.0 1.0 O A:HOH401 2.2 29.4 1.0 OAD A:ZYP398 2.3 39.6 1.0 CBB A:ZYP398 2.8 41.3 1.0 CAG A:ZYP398 2.9 40.9 1.0 CAX A:ZYP398 3.0 42.0 1.0 CG A:ASP128 3.1 36.8 1.0 CG A:ASP185 3.1 38.1 1.0 OD2 A:ASP128 3.5 38.2 1.0 OD2 A:ASP185 3.5 40.3 1.0 O A:HOH462 3.7 43.9 1.0 MG A:MG397 3.7 38.6 1.0 CBA A:ZYP398 4.2 41.5 1.0 O A:TYR129 4.3 37.8 1.0 CAF A:ZYP398 4.3 39.9 1.0 N6 D:DA17 4.3 48.2 1.0 O A:HOH400 4.3 33.8 1.0 N A:TYR129 4.3 36.2 1.0 OE2 A:GLU221 4.3 32.8 1.0 CAY A:ZYP398 4.4 42.8 1.0 N7 D:DA17 4.4 46.5 1.0 CB A:ASP128 4.4 36.2 1.0 O A:HOH440 4.4 45.3 1.0 CB A:ASP185 4.4 38.5 1.0 O A:HOH543 4.4 39.9 1.0 OAA A:ZYP398 4.5 46.8 1.0 CAL A:ZYP398 4.7 41.7 1.0 CA A:ASP128 4.8 36.5 1.0 C5 D:DA17 4.9 47.6 1.0 C6 D:DA17 4.9 48.2 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 L-870,810


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 L-870,810 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg397 b:38.6 occ:1.00 OAA A:ZYP398 1.6 46.8 1.0 OAD A:ZYP398 2.0 39.6 1.0 OE2 A:GLU221 2.0 32.8 1.0 OD2 A:ASP128 2.0 38.2 1.0 OE1 A:GLU221 2.1 35.4 1.0 O A:HOH400 2.1 33.8 1.0 CD A:GLU221 2.3 33.8 1.0 CAU A:ZYP398 2.7 44.3 1.0 CAX A:ZYP398 3.0 42.0 1.0 CG A:ASP128 3.1 36.8 1.0 CAY A:ZYP398 3.4 42.8 1.0 ND2 A:ASN224 3.6 33.7 1.0 OD1 A:ASP128 3.6 37.0 1.0 MG A:MG396 3.7 37.2 1.0 NAT A:ZYP398 3.7 42.5 1.0 CG A:GLU221 3.8 33.8 1.0 O A:HOH462 3.9 43.9 1.0 O A:HOH545 4.1 29.9 1.0 O A:TYR129 4.2 37.8 1.0 CBB A:ZYP398 4.3 41.3 1.0 CB A:ASP128 4.4 36.2 1.0 OP1 D:DA17 4.4 40.1 1.0 O3' D:DC16 4.6 37.1 1.0 NAR A:ZYP398 4.6 40.2 1.0 N7 D:DA17 4.7 46.5 1.0 CB A:GLU221 4.7 34.1 1.0 OD1 A:ASP185 4.7 38.1 1.0 C8 D:DA17 4.7 46.7 1.0 NAS A:ZYP398 4.7 42.5 1.0 CAJ A:ZYP398 4.8 39.0 1.0 C2' D:DC16 4.8 32.2 1.0 CA A:GLU221 4.8 34.0 1.0 CG A:ASN224 4.9 34.6 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 L-870,810


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 L-870,810 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg394 b:80.3 occ:1.00 O B:HOH432 2.1 70.7 1.0 OD1 B:ASP185 2.3 44.5 1.0 OD1 B:ASP128 2.3 53.2 1.0 O B:HOH395 2.4 64.1 1.0 CG B:ASP185 3.1 44.7 1.0 OD2 B:ASP185 3.3 46.8 1.0 CG B:ASP128 3.4 51.2 1.0 O B:HOH407 3.7 40.5 1.0 OD2 B:ASP128 3.8 52.6 1.0 O B:HOH431 4.2 77.4 1.0 N B:TYR129 4.4 49.2 1.0 CB B:ASP185 4.5 44.0 1.0 CE2 B:PHE190 4.6 49.1 1.0 CB B:ASP128 4.7 48.8 1.0 O B:TYR129 4.7 51.4 1.0 CA B:ASP128 4.8 48.0 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