Magnesium in PDB 1bl3: Catalytic Domain of Hiv-1 Integrase

The structure of Catalytic Domain of Hiv-1 Integrase, PDB code: 1bl3 was solved by S.Maignan, J.P.Guilloteau, Q.Zhou-Liu, C.Clement-Mella, V.Mikol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	99.100, 72.500, 79.400, 90.00, 108.00, 90.00
R / Rfree (%)	21.6 / 27.9

The binding sites of Magnesium atom in the Catalytic Domain of Hiv-1 Integrase (pdb code 1bl3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Catalytic Domain of Hiv-1 Integrase, PDB code: 1bl3:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Catalytic Domain of Hiv-1 Integrase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Catalytic Domain of Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:45.7 occ:1.00 O A:HOH552 2.2 40.7 1.0 OD2 A:ASP116 2.4 52.5 1.0 O A:HOH550 2.4 32.3 1.0 OD1 A:ASP64 2.4 30.3 1.0 O A:HOH557 2.4 53.8 1.0 O A:HOH555 2.5 58.3 1.0 CG A:ASP64 3.5 47.0 1.0 CG A:ASP116 3.5 37.4 1.0 O A:CYS65 3.7 31.1 1.0 OD2 A:ASP64 3.8 44.9 1.0 O A:HOH506 3.9 37.2 1.0 N A:CYS65 4.0 27.4 1.0 OD1 A:ASP116 4.0 34.0 1.0 O A:HOH536 4.4 32.2 1.0 C A:CYS65 4.5 24.8 1.0 CB A:CYS65 4.5 29.5 1.0 CA A:CYS65 4.6 25.6 1.0 CE2 A:PHE121 4.7 34.4 1.0 CB A:ASP116 4.8 31.7 1.0 CB A:ASP64 4.8 37.2 1.0 OE2 A:GLU92 5.0 38.6 1.0 C A:ASP64 5.0 31.7 1.0 CA A:ASP64 5.0 29.3 1.0

Magnesium binding site 2 out of 3 in the Catalytic Domain of Hiv-1 Integrase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Catalytic Domain of Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:52.4 occ:1.00 OD1 B:ASP64 2.3 60.1 1.0 O B:HOH538 2.4 65.8 1.0 O B:HOH536 2.8 47.9 1.0 OD2 B:ASP116 2.9 48.8 1.0 CG B:ASP64 3.1 62.8 1.0 OD2 B:ASP64 3.3 50.0 1.0 O B:CYS65 3.5 37.1 1.0 N B:CYS65 3.7 38.8 1.0 CG B:ASP116 4.0 45.3 1.0 C B:CYS65 4.3 38.1 1.0 CA B:CYS65 4.3 39.6 1.0 OD1 B:ASP116 4.3 53.0 1.0 CB B:CYS65 4.3 34.8 1.0 CB B:ASP64 4.4 47.0 1.0 O B:HOH506 4.7 36.1 1.0 CA B:ASP64 4.7 40.6 1.0 C B:ASP64 4.7 42.8 1.0 CE2 B:PHE121 4.7 40.9 1.0 OE2 B:GLU92 5.0 59.5 1.0

Magnesium binding site 3 out of 3 in the Catalytic Domain of Hiv-1 Integrase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Catalytic Domain of Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:35.7 occ:1.00 O C:HOH540 2.2 38.5 1.0 OD1 C:ASP64 2.2 27.5 1.0 O C:HOH532 2.3 45.7 1.0 O C:HOH555 2.3 49.3 1.0 OD2 C:ASP116 2.3 41.9 1.0 O C:HOH508 2.5 50.9 1.0 CG C:ASP64 3.2 23.5 1.0 CG C:ASP116 3.5 45.3 1.0 OD2 C:ASP64 3.5 28.4 1.0 O C:HOH558 3.9 59.6 1.0 OD1 C:ASP116 3.9 44.2 1.0 O C:CYS65 4.0 39.0 1.0 O C:HOH545 4.1 34.3 1.0 N C:CYS65 4.1 23.2 1.0 O C:HOH526 4.4 31.2 1.0 CB C:ASP64 4.6 25.6 1.0 CB C:ASP116 4.7 35.9 1.0 CE2 C:PHE121 4.8 31.6 1.0 CA C:ASP64 4.8 19.9 1.0 C C:CYS65 4.9 25.2 1.0 CA C:CYS65 4.9 21.4 1.0 OE2 C:GLU92 4.9 31.1 1.0 CB C:CYS65 4.9 17.3 1.0

S.Maignan, J.P.Guilloteau, Q.Zhou-Liu, C.Clement-Mella, V.Mikol. Crystal Structures of the Catalytic Domain of Hiv-1 Integrase Free and Complexed with Its Metal Cofactor: High Level of Similarity of the Active Site with Other Viral Integrases. J.Mol.Biol. V. 282 359 1998.
ISSN: ISSN 0022-2836
PubMed: 9735293
DOI: 10.1006/JMBI.1998.2002