Magnesium in PDB 4ztf: Crystal Structure of the Prototype Foamy Virus Intasome with A 2- Pyridinone Aminal Inhibitor

The structure of Crystal Structure of the Prototype Foamy Virus Intasome with A 2- Pyridinone Aminal Inhibitor, PDB code: 4ztf was solved by D.J.Klein, S.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.86 / 2.70
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	159.450, 159.450, 124.090, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 21.5

The structure of Crystal Structure of the Prototype Foamy Virus Intasome with A 2- Pyridinone Aminal Inhibitor 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 Prototype Foamy Virus Intasome with A 2- Pyridinone Aminal Inhibitor (pdb code 4ztf). 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 Intasome with A 2- Pyridinone Aminal Inhibitor, PDB code: 4ztf:
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 Intasome with A 2- Pyridinone Aminal Inhibitor


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 Intasome with A 2- Pyridinone Aminal Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:54.2 occ:1.00 O1 A:X2P404 1.9 66.5 1.0 OD1 A:ASP128 2.1 55.5 1.0 OD2 A:ASP185 2.1 61.6 1.0 O A:HOH521 2.1 53.2 1.0 O A:HOH549 2.2 72.6 1.0 O A:X2P404 2.3 67.2 1.0 C6 A:X2P404 2.8 67.0 1.0 C7 A:X2P404 3.0 66.9 1.0 CG A:ASP185 3.1 62.2 1.0 CG A:ASP128 3.1 56.0 1.0 OD1 A:ASP185 3.4 60.0 1.0 OD2 A:ASP128 3.5 56.7 1.0 MG A:MG406 3.8 52.0 1.0 N1 A:X2P404 4.1 67.5 1.0 O A:HOH522 4.2 66.2 1.0 N A:TYR129 4.3 54.4 1.0 O A:TYR129 4.3 55.0 1.0 O D:HOH101 4.4 46.4 1.0 O A:HOH593 4.4 60.4 1.0 C2 A:X2P404 4.4 65.5 1.0 CB A:ASP128 4.5 55.5 1.0 CB A:ASP185 4.5 63.1 1.0 OE2 A:GLU221 4.5 57.6 1.0 C15 A:X2P404 4.6 58.8 1.0 C14 A:X2P404 4.6 59.1 1.0 O A:HOH587 4.7 70.6 1.0 CA A:ASP128 4.8 53.6 1.0 O A:HOH504 4.8 62.6 1.0 C16 A:X2P404 4.8 60.6 1.0 C8 A:X2P404 4.9 64.8 1.0 O A:HOH589 4.9 73.1 1.0 O4 A:X2P404 4.9 65.2 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the Prototype Foamy Virus Intasome with A 2- Pyridinone Aminal Inhibitor


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 Intasome with A 2- Pyridinone Aminal Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:52.0 occ:1.00 O4 A:X2P404 2.0 65.2 1.0 OE2 A:GLU221 2.0 57.6 1.0 OE1 A:GLU221 2.1 57.1 1.0 OD2 A:ASP128 2.1 56.7 1.0 O A:X2P404 2.1 67.2 1.0 O D:HOH101 2.2 46.4 1.0 CD A:GLU221 2.3 56.4 1.0 C1 A:X2P404 3.0 63.7 1.0 CG A:ASP128 3.2 56.0 1.0 C7 A:X2P404 3.2 66.9 1.0 C2 A:X2P404 3.5 65.5 1.0 OD1 A:ASP128 3.6 55.5 1.0 ND2 A:ASN224 3.7 52.5 1.0 CG A:GLU221 3.8 54.8 1.0 MG A:MG405 3.8 54.2 1.0 O A:HOH522 4.1 66.2 1.0 N A:X2P404 4.2 57.7 1.0 O A:TYR129 4.4 55.0 1.0 C6 A:X2P404 4.4 67.0 1.0 CB A:ASP128 4.5 55.5 1.0 OP1 D:DA17 4.5 68.2 1.0 O A:HOH549 4.5 72.6 1.0 OD2 A:ASP185 4.6 61.6 1.0 C18 A:X2P404 4.6 49.0 1.0 O1 A:X2P404 4.7 66.5 1.0 CB A:GLU221 4.8 56.6 1.0 O3' D:DC16 4.8 63.9 1.0 CB A:PRO214 4.9 56.4 1.0 CA A:GLU221 4.9 54.9 1.0 C2' D:DC16 4.9 57.7 1.0 C24 A:X2P404 5.0 45.0 1.0 C3 A:X2P404 5.0 64.7 1.0 O5' D:DA17 5.0 72.1 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the Prototype Foamy Virus Intasome with A 2- Pyridinone Aminal Inhibitor


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 Intasome with A 2- Pyridinone Aminal Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:0.5 occ:1.00 OD2 B:ASP185 2.8 69.7 1.0 OD2 B:ASP128 3.2 75.9 1.0 OD1 B:ASP128 3.4 75.6 1.0 CG B:ASP128 3.6 72.7 1.0 CG B:ASP185 4.0 68.8 1.0 O B:HOH505 4.3 64.2 1.0 CB B:ASP185 4.7 66.0 1.0 O B:HOH506 4.8 62.2 1.0 OD1 B:ASP185 4.9 71.0 1.0

I.T.Raheem, A.M.Walji, D.Klein, J.M.Sanders, D.A.Powell, P.Abeywickrema, G.Barbe, A.Bennet, S.D.Clas, D.Dubost, M.Embrey, J.Grobler, M.J.Hafey, T.J.Hartingh, D.J.Hazuda, M.D.Miller, K.P.Moore, N.Pajkovic, S.Patel, V.Rada, P.Rearden, J.D.Schreier, J.Sisko, T.G.Steele, J.F.Truchon, J.Wai, M.Xu, P.J.Coleman. Discovery of 2-Pyridinone Aminals: A Prodrug Strategy to Advance A Second Generation of Hiv-1 Integrase Strand Transfer Inhibitors. J.Med.Chem. V. 58 8154 2015.
ISSN: ISSN 0022-2623
PubMed: 26397965
DOI: 10.1021/ACS.JMEDCHEM.5B01037