Magnesium in PDB 4ikf: Pfv Intasome with Inhibitor Mb-76

The structure of Pfv Intasome with Inhibitor Mb-76, PDB code: 4ikf was solved by O.Taltynov, J.Demeulemeester, B.A.Desimmie, V.Suchaud, M.Billamboz, C.Lion, F.Bailly, Z.Debyser, P.Cotelle, F.Christ, S.V.Strelkov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.85 / 3.40
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	159.070, 159.070, 123.820, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 23

The structure of Pfv Intasome with Inhibitor Mb-76 also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Pfv Intasome with Inhibitor Mb-76 (pdb code 4ikf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Pfv Intasome with Inhibitor Mb-76, PDB code: 4ikf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Pfv Intasome with Inhibitor Mb-76


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pfv Intasome with Inhibitor Mb-76 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:95.5 occ:1.00 O16 D:M76101 1.8 0.2 1.0 OD1 A:ASP128 1.8 0.6 1.0 O18 D:M76101 2.2 79.9 1.0 OD1 A:ASP185 2.4 0.8 1.0 OD2 A:ASP185 2.5 98.2 1.0 CG A:ASP185 2.6 0.9 1.0 N15 D:M76101 2.7 90.5 1.0 C17 D:M76101 2.7 88.1 1.0 CG A:ASP128 2.8 91.2 1.0 OD2 A:ASP128 3.1 89.3 1.0 MG A:MG405 3.8 77.1 1.0 C2 D:DA17 3.9 0.3 1.0 O A:TYR129 3.9 0.3 1.0 N1 D:DA17 3.9 0.5 1.0 N A:TYR129 3.9 87.3 1.0 CB A:ASP185 3.9 0.2 1.0 C13 D:M76101 4.0 87.4 1.0 CB A:ASP128 4.1 82.6 1.0 C19 D:M76101 4.2 87.7 1.0 OE2 A:GLU221 4.4 87.2 1.0 CA A:ASP128 4.4 97.5 1.0 O14 D:M76101 4.4 89.1 1.0 C A:TYR129 4.7 0.3 1.0 C A:ASP128 4.7 96.4 1.0 CA A:TYR129 4.8 86.1 1.0 N3 D:DA17 4.8 0.5 1.0 C20 D:M76101 4.9 86.2 1.0 C6 D:DA17 4.9 0.9 1.0 CB A:TYR129 5.0 91.7 1.0

Magnesium binding site 2 out of 2 in the Pfv Intasome with Inhibitor Mb-76


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pfv Intasome with Inhibitor Mb-76 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:77.1 occ:1.00 O14 D:M76101 1.7 89.1 1.0 OD2 A:ASP128 1.9 89.3 1.0 OE1 A:GLU221 2.0 86.3 1.0 O16 D:M76101 2.2 0.2 1.0 OE2 A:GLU221 2.5 87.2 1.0 C13 D:M76101 2.5 87.4 1.0 CD A:GLU221 2.5 81.0 1.0 N15 D:M76101 2.7 90.5 1.0 CG A:ASP128 2.9 91.2 1.0 ND2 A:ASN224 3.6 83.1 1.0 OD1 A:ASP128 3.6 0.6 1.0 MG A:MG404 3.8 95.5 1.0 C12 D:M76101 3.9 87.3 1.0 OP1 D:DA17 3.9 90.7 1.0 CG A:GLU221 4.0 76.3 1.0 CB A:ASP128 4.0 82.6 1.0 N3 D:M76101 4.1 84.8 1.0 C17 D:M76101 4.1 88.1 1.0 O A:TYR129 4.3 0.3 1.0 O3' D:DC16 4.3 90.3 1.0 N3 D:DA17 4.4 0.5 1.0 C2 D:DA17 4.4 0.3 1.0 C2 D:M76101 4.5 78.2 1.0 CB A:GLU221 4.7 73.0 1.0 P D:DA17 4.8 0.4 1.0 O18 D:M76101 4.8 79.9 1.0 OD1 A:ASP185 4.9 0.8 1.0 CG A:ASN224 4.9 82.2 1.0 CA A:GLU221 4.9 74.9 1.0 C2' D:DC16 5.0 86.6 1.0 C24 D:M76101 5.0 86.6 1.0

B.A.Desimmie, J.Demeulemeester, V.Suchaud, O.Taltynov, M.Billamboz, C.Lion, F.Bailly, S.V.Strelkov, Z.Debyser, P.Cotelle, F.Christ. 2-Hydroxyisoquinoline-1,3(2H,4H)-Diones (Hids), Novel Inhibitors of Hiv Integrase with A High Barrier to Resistance. Acs Chem.Biol. V. 8 1187 2013.
ISSN: ISSN 1554-8929
PubMed: 23517458
DOI: 10.1021/CB4000426