Magnesium in PDB 5frm: Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ384 (Compound 4A)

The structure of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ384 (Compound 4A), PDB code: 5frm was solved by D.P.Maskell, V.E.Pye, P.Cherepanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.90 / 2.58
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	159.737, 159.737, 123.528, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 20.3

The structure of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ384 (Compound 4A) also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
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 XZ384 (Compound 4A) (pdb code 5frm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ384 (Compound 4A), PDB code: 5frm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ384 (Compound 4A)


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 XZ384 (Compound 4A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1377 b:59.1 occ:1.00 NAN D:WA51018 2.0 58.2 1.0 O A:HOH2028 2.1 67.8 1.0 O A:HOH2027 2.1 54.1 1.0 OAD D:WA51018 2.1 58.8 1.0 OD2 A:ASP185 2.2 56.0 1.0 OD1 A:ASP128 2.2 58.3 1.0 CAX D:WA51018 2.8 63.3 1.0 NAY D:WA51018 2.9 70.0 1.0 CAH D:WA51018 3.0 57.9 1.0 CG A:ASP185 3.2 60.5 1.0 CG A:ASP128 3.3 58.9 1.0 OD1 A:ASP185 3.6 65.6 1.0 OD2 A:ASP128 3.7 61.9 1.0 MG A:MG1378 3.9 61.3 1.0 CAW D:WA51018 4.1 63.0 1.0 CAV D:WA51018 4.2 65.6 1.0 N1 D:DA17 4.3 0.2 1.0 CAG D:WA51018 4.3 62.6 1.0 O A:TYR129 4.4 65.6 1.0 N A:TYR129 4.4 55.8 1.0 CB A:ASP185 4.5 53.7 1.0 O A:HOH2029 4.6 54.1 1.0 CB A:ASP128 4.6 59.0 1.0 OE2 A:GLU221 4.6 58.7 1.0 O A:HOH2026 4.6 68.5 1.0 C2 D:DA17 4.7 97.0 1.0 OAC D:WA51018 4.7 62.2 1.0 CAK D:WA51018 4.8 54.1 1.0 CA A:ASP128 4.9 54.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ384 (Compound 4A)


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 XZ384 (Compound 4A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1378 b:61.3 occ:1.00 OAD D:WA51018 2.0 58.8 1.0 O A:HOH2029 2.1 54.1 1.0 OE2 A:GLU221 2.1 58.7 1.0 OE1 A:GLU221 2.1 56.7 1.0 OAC D:WA51018 2.1 62.2 1.0 OD2 A:ASP128 2.1 61.9 1.0 CD A:GLU221 2.4 50.8 1.0 NAY D:WA51018 2.8 70.0 1.0 CAV D:WA51018 2.8 65.6 1.0 CG A:ASP128 3.1 58.9 1.0 OD1 A:ASP128 3.5 58.3 1.0 ND2 A:ASN224 3.9 55.4 1.0 MG A:MG1377 3.9 59.1 1.0 CG A:GLU221 3.9 53.9 1.0 CAX D:WA51018 4.1 63.3 1.0 CAU D:WA51018 4.2 69.9 1.0 O A:TYR129 4.3 65.6 1.0 O A:HOH2028 4.4 67.8 1.0 CB A:ASP128 4.4 59.0 1.0 OP1 D:DA17 4.5 75.7 1.0 NAO D:WA51018 4.5 66.4 1.0 FAF D:WA51018 4.5 59.9 1.0 NAN D:WA51018 4.6 58.2 1.0 CB A:GLU221 4.7 50.1 1.0 OD2 A:ASP185 4.8 56.0 1.0 O3' D:DC16 4.8 73.0 1.0 C2 D:DA17 4.9 97.0 1.0 CAP D:WA51018 4.9 62.5 1.0 CA A:GLU221 4.9 57.0 1.0

X.Z.Zhao, S.J.Smith, D.P.Maskell, M.Metifiot, V.E.Pye, K.Fesen, C.Marchand, Y.Pommier, P.Cherepanov, S.H.Hughes, T.R.J.Burke. Hiv-1 Integrase Strand Transfer Inhibitors with Reduced Susceptibility to Drug Resistant Mutant Integrases. Acs Chem.Biol. V. 11 1074 2016.
ISSN: ISSN 1554-8929
PubMed: 26808478
DOI: 10.1021/ACSCHEMBIO.5B00948