Magnesium in PDB 3oyj: Crystal Structure of the Pfv S217Q Mutant Intasome in Complex with Magnesium and the Insti MK2048

The structure of Crystal Structure of the Pfv S217Q Mutant Intasome in Complex with Magnesium and the Insti MK2048, PDB code: 3oyj 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)	38.85 / 2.68
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	160.170, 160.170, 123.700, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 24.1

The structure of Crystal Structure of the Pfv S217Q Mutant Intasome in Complex with Magnesium and the Insti MK2048 also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Zinc	(Zn)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of the Pfv S217Q Mutant Intasome in Complex with Magnesium and the Insti MK2048 (pdb code 3oyj). 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 Pfv S217Q Mutant Intasome in Complex with Magnesium and the Insti MK2048, PDB code: 3oyj:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the Pfv S217Q Mutant Intasome in Complex with Magnesium and the Insti MK2048


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 Pfv S217Q Mutant Intasome in Complex with Magnesium and the Insti MK2048 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg396 b:48.1 occ:1.00 O A:HOH510 2.0 34.6 1.0 OAE A:ZZX398 2.0 44.5 1.0 O A:HOH399 2.0 38.0 1.0 OAG A:ZZX398 2.1 49.5 1.0 OD1 A:ASP185 2.1 45.3 1.0 OD1 A:ASP128 2.2 50.6 1.0 CAS A:ZZX398 2.8 48.9 1.0 CAW A:ZZX398 2.9 48.5 1.0 CAY A:ZZX398 3.1 48.6 1.0 CG A:ASP185 3.1 46.0 1.0 CG A:ASP128 3.3 46.9 1.0 OD2 A:ASP185 3.5 43.9 1.0 N6 D:DA17 3.7 85.1 1.0 MG A:MG397 3.7 32.8 1.0 OD2 A:ASP128 3.7 46.3 1.0 O A:HOH519 4.0 45.7 1.0 NBD A:ZZX398 4.1 49.2 1.0 O A:HOH444 4.2 58.0 1.0 O D:HOH26 4.3 37.3 1.0 CBA A:ZZX398 4.3 48.3 1.0 O A:TYR129 4.3 45.7 1.0 N A:TYR129 4.4 45.8 1.0 N7 D:DA17 4.4 84.8 1.0 O A:HOH508 4.5 51.1 1.0 C6 D:DA17 4.5 85.8 1.0 CB A:ASP185 4.5 46.6 1.0 NBF A:ZZX398 4.5 48.9 1.0 OE2 A:GLU221 4.6 46.5 1.0 CB A:ASP128 4.6 45.9 1.0 CAM A:ZZX398 4.7 48.8 1.0 C5 D:DA17 4.7 85.7 1.0 CA A:ASP128 4.9 45.8 1.0 O D:HOH289 4.9 50.2 1.0 OE1 A:GLN217 5.0 54.4 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the Pfv S217Q Mutant Intasome in Complex with Magnesium and the Insti MK2048


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 Pfv S217Q Mutant Intasome in Complex with Magnesium and the Insti MK2048 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg397 b:32.8 occ:1.00 OE2 A:GLU221 1.9 46.5 1.0 OD2 A:ASP128 2.1 46.3 1.0 O D:HOH26 2.1 37.3 1.0 OAG A:ZZX398 2.1 49.5 1.0 OAF A:ZZX398 2.2 42.3 1.0 OE1 A:GLU221 2.4 48.8 1.0 CD A:GLU221 2.5 46.2 1.0 CAW A:ZZX398 3.0 48.5 1.0 CAZ A:ZZX398 3.1 45.9 1.0 CG A:ASP128 3.1 46.9 1.0 CBA A:ZZX398 3.3 48.3 1.0 OD1 A:ASP128 3.4 50.6 1.0 MG A:MG396 3.7 48.1 1.0 ND2 A:ASN224 3.8 44.6 1.0 O A:HOH510 3.8 34.6 1.0 O A:HOH444 3.9 58.0 1.0 CG A:GLU221 4.0 45.0 1.0 O A:TYR129 4.2 45.7 1.0 N7 D:DA17 4.3 84.8 1.0 OP1 D:DA17 4.3 54.8 1.0 CAY A:ZZX398 4.4 48.6 1.0 CB A:ASP128 4.4 45.9 1.0 NBE A:ZZX398 4.4 45.6 1.0 OD1 A:ASP185 4.5 45.3 1.0 C8 D:DA17 4.6 85.2 1.0 CBB A:ZZX398 4.7 49.9 1.0 O3' D:DC16 4.7 51.1 1.0 OE1 A:GLN217 4.9 54.4 1.0 CB A:GLU221 5.0 44.4 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the Pfv S217Q Mutant Intasome in Complex with Magnesium and the Insti MK2048


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 Pfv S217Q Mutant Intasome in Complex with Magnesium and the Insti MK2048 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg394 b:0.1 occ:1.00 O B:HOH427 1.8 99.0 1.0 O B:HOH395 1.9 72.5 1.0 OD1 B:ASP128 2.2 64.1 1.0 OD1 B:ASP185 2.3 58.3 1.0 CG B:ASP128 3.2 61.5 1.0 CG B:ASP185 3.3 57.3 1.0 OD2 B:ASP185 3.6 58.4 1.0 OD2 B:ASP128 3.6 62.7 1.0 N B:TYR129 4.1 59.5 1.0 CB B:ASP128 4.5 59.9 1.0 O B:HOH426 4.5 61.3 1.0 O B:TYR129 4.5 61.2 1.0 CA B:ASP128 4.6 59.2 1.0 CB B:ASP185 4.6 55.5 1.0 CE2 B:PHE190 4.7 54.1 1.0 C B:ASP128 4.9 59.4 1.0 CA B:TYR129 5.0 59.8 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