Magnesium in PDB 1biu: Hiv-1 Integrase Core Domain Complexed with Mg++

The structure of Hiv-1 Integrase Core Domain Complexed with Mg++, PDB code: 1biu was solved by Y.Goldgur, F.Dyda, A.B.Hickman, T.M.Jenkins, R.Craigie, D.R.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	76.220, 46.910, 140.270, 90.00, 105.13, 90.00
R / Rfree (%)	19.8 / 26.5

The binding sites of Magnesium atom in the Hiv-1 Integrase Core Domain Complexed with Mg++ (pdb code 1biu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Hiv-1 Integrase Core Domain Complexed with Mg++, PDB code: 1biu:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Hiv-1 Integrase Core Domain Complexed with Mg++


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hiv-1 Integrase Core Domain Complexed with Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1244 b:1.0 occ:1.00 O A:HOH1279 1.6 45.0 1.0 O A:HOH1283 1.6 59.4 1.0 H2 A:HOH1279 2.2 0.0 1.0 H1 A:HOH1283 2.4 0.0 1.0 H1 A:HOH1279 2.5 0.0 1.0 H2 A:HOH1283 2.6 0.0 1.0 O A:CYS65 2.8 33.6 1.0 OD1 A:ASP64 3.6 30.3 1.0 OD2 A:ASP64 3.9 34.0 1.0 O A:HOH1330 3.9 39.3 1.0 C A:CYS65 4.0 29.4 1.0 H A:CYS65 4.0 0.0 1.0 CG A:ASP64 4.1 32.8 1.0 HE2 A:HIS67 4.1 0.0 1.0 H1 A:HOH1330 4.4 0.0 1.0 OD2 A:ASP116 4.5 40.0 1.0 N A:CYS65 4.6 22.3 1.0 H2 A:HOH1330 4.7 0.0 1.0 CA A:CYS65 4.7 25.0 1.0 NE2 A:HIS67 4.8 31.0 1.0 CB A:CYS65 4.9 16.3 1.0 N A:THR66 5.0 29.3 1.0

Magnesium binding site 2 out of 3 in the Hiv-1 Integrase Core Domain Complexed with Mg++


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hiv-1 Integrase Core Domain Complexed with Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1399 b:39.6 occ:1.00 OD2 B:ASP116 2.1 26.8 1.0 OD1 B:ASP64 2.3 28.3 1.0 CG B:ASP116 3.2 26.4 1.0 CG B:ASP64 3.3 24.9 1.0 H B:CYS65 3.6 0.0 1.0 OD1 B:ASP116 3.6 29.9 1.0 OD2 B:ASP64 3.7 30.8 1.0 H2 B:HOH1439 4.0 0.0 1.0 O B:HOH1444 4.2 30.1 1.0 O B:HOH1409 4.2 26.6 1.0 O B:CYS65 4.2 34.3 1.0 O B:HOH1439 4.3 21.1 1.0 CB B:ASP116 4.5 25.1 1.0 N B:CYS65 4.5 30.0 1.0 CB B:ASP64 4.7 28.1 1.0 H2 B:HOH1409 4.8 0.0 1.0 H1 B:HOH1444 4.8 0.0 1.0 H2 B:HOH1444 4.8 0.0 1.0 H1 B:HOH1409 4.9 0.0 1.0

Magnesium binding site 3 out of 3 in the Hiv-1 Integrase Core Domain Complexed with Mg++


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Hiv-1 Integrase Core Domain Complexed with Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1437 b:46.5 occ:1.00 O C:HOH1484 1.5 50.1 1.0 OD2 C:ASP116 2.3 37.0 1.0 H1 C:HOH1484 2.3 0.0 1.0 OD1 C:ASP64 2.3 33.0 1.0 H2 C:HOH1484 2.4 0.0 1.0 CG C:ASP64 3.3 32.2 1.0 CG C:ASP116 3.4 28.1 1.0 OD2 C:ASP64 3.5 32.1 1.0 H C:CYS65 3.6 0.0 1.0 OD1 C:ASP116 3.9 30.9 1.0 O C:HOH1457 4.0 25.6 1.0 O C:CYS65 4.1 30.6 1.0 N C:CYS65 4.5 21.6 1.0 O C:HOH1458 4.5 19.3 1.0 H1 C:HOH1457 4.6 0.0 1.0 CB C:ASP116 4.7 25.8 1.0 CB C:ASP64 4.7 26.5 1.0 H2 C:HOH1457 4.8 0.0 1.0 H1 C:HOH1458 4.8 0.0 1.0

Y.Goldgur, F.Dyda, A.B.Hickman, T.M.Jenkins, R.Craigie, D.R.Davies. Three New Structures of the Core Domain of Hiv-1 Integrase: An Active Site That Binds Magnesium. Proc.Natl.Acad.Sci.Usa V. 95 9150 1998.
ISSN: ISSN 0027-8424
PubMed: 9689049
DOI: 10.1073/PNAS.95.16.9150