Magnesium in PDB 5uop: Crystal Structure of the Prototype Foamy Virus Intasome with A 2- Pyridinone Aminal Inhibitor (Compound 18)

The structure of Crystal Structure of the Prototype Foamy Virus Intasome with A 2- Pyridinone Aminal Inhibitor (Compound 18), PDB code: 5uop was solved by D.J.Klein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.78 / 2.85
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	158.818, 158.818, 123.797, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 20.3

The structure of Crystal Structure of the Prototype Foamy Virus Intasome with A 2- Pyridinone Aminal Inhibitor (Compound 18) 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 (Compound 18) (pdb code 5uop). 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 (Compound 18), PDB code: 5uop:
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 (Compound 18)


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 (Compound 18) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:50.1 occ:1.00 O1 A:8G4409 1.9 74.4 1.0 O A:HOH501 2.0 94.6 1.0 OD1 A:ASP128 2.1 64.5 1.0 OD2 A:ASP185 2.2 69.5 1.0 O A:HOH513 2.3 64.2 1.0 O A:8G4409 2.3 74.1 1.0 C6 A:8G4409 2.7 73.7 1.0 C7 A:8G4409 3.0 73.1 1.0 CG A:ASP128 3.1 65.0 1.0 CG A:ASP185 3.2 70.2 1.0 OD2 A:ASP128 3.4 65.6 1.0 O2 A:GOL408 3.4 0.3 1.0 OD1 A:ASP185 3.5 68.0 1.0 MG A:MG405 3.7 55.3 1.0 N1 A:8G4409 4.0 74.0 1.0 O A:HOH508 4.1 76.9 1.0 N A:TYR129 4.3 61.5 1.0 O A:TYR129 4.3 62.1 1.0 OE2 A:GLU221 4.4 59.7 1.0 CB A:ASP128 4.4 64.4 1.0 O D:HOH101 4.4 58.6 1.0 C2 A:8G4409 4.4 70.0 1.0 O A:HOH596 4.4 80.5 1.0 CB A:ASP185 4.5 71.0 1.0 C19 A:8G4409 4.6 73.3 1.0 CA A:ASP128 4.7 62.0 1.0 O A:HOH511 4.7 63.0 1.0 C16 A:8G4409 4.7 70.7 1.0 C8 A:8G4409 4.7 73.5 1.0 C18 A:8G4409 4.8 71.9 1.0 C2 A:GOL408 4.8 97.7 1.0 O5 A:8G4409 4.9 65.0 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 (Compound 18)


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 (Compound 18) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:55.3 occ:1.00 O A:8G4409 1.9 74.1 1.0 O5 A:8G4409 2.0 65.0 1.0 OD2 A:ASP128 2.1 65.6 1.0 OE1 A:GLU221 2.1 59.1 1.0 OE2 A:GLU221 2.1 59.7 1.0 O D:HOH101 2.2 58.6 1.0 CD A:GLU221 2.4 58.5 1.0 C1 A:8G4409 3.0 65.3 1.0 C7 A:8G4409 3.0 73.1 1.0 CG A:ASP128 3.1 65.0 1.0 OD1 A:ASP128 3.5 64.5 1.0 C2 A:8G4409 3.5 70.0 1.0 ND2 A:ASN224 3.7 56.3 1.0 MG A:MG404 3.7 50.1 1.0 CG A:GLU221 3.9 56.8 1.0 O A:HOH508 4.1 76.9 1.0 N A:8G4409 4.2 61.5 1.0 C6 A:8G4409 4.2 73.7 1.0 O A:HOH501 4.3 94.6 1.0 O A:TYR129 4.3 62.1 1.0 CB A:ASP128 4.3 64.4 1.0 OP1 D:DA17 4.5 75.6 1.0 O1 A:8G4409 4.5 74.4 1.0 OD2 A:ASP185 4.6 69.5 1.0 C21 A:8G4409 4.7 55.3 1.0 O2 A:GOL408 4.7 0.3 1.0 O3' D:DC16 4.8 70.7 1.0 CB A:GLU221 4.9 58.7 1.0 C3 A:8G4409 4.9 69.9 1.0 O5' D:DA17 4.9 78.3 1.0 CG A:ASN224 5.0 58.4 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 (Compound 18)


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 (Compound 18) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:0.4 occ:1.00 OD2 B:ASP185 2.8 76.4 1.0 OD2 B:ASP128 3.3 82.2 1.0 CG B:ASP185 3.7 75.6 1.0 CB B:ASP185 4.0 72.7 1.0 CG B:ASP128 4.0 79.0 1.0 CB B:PRO214 4.1 0.4 1.0 OD1 B:ASP128 4.1 81.9 1.0 O B:HOH505 4.5 64.4 1.0 CG B:PRO214 4.6 0.6 1.0 OD1 B:ASP185 4.9 77.8 1.0

J.D.Schreier, M.W.Embrey, I.T.Raheem, G.Barbe, L.C.Campeau, D.Dubost, J.Mccabe Dunn, J.Grobler, T.J.Hartingh, D.J.Hazuda, D.Klein, M.D.Miller, K.P.Moore, N.Nguyen, N.Pajkovic, D.A.Powell, V.Rada, J.M.Sanders, J.Sisko, T.G.Steele, J.Wai, A.Walji, M.Xu, P.J.Coleman. Discovery and Optimization of 2-Pyridinone Aminal Integrase Strand Transfer Inhibitors For the Treatment of Hiv. Bioorg. Med. Chem. Lett. V. 27 2038 2017.
ISSN: ESSN 1464-3405
PubMed: 28285916
DOI: 10.1016/J.BMCL.2017.02.039