Magnesium in PDB 3f9k: Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd

The structure of Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd, PDB code: 3f9k was solved by S.Hare, P.Cherepanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.99 / 3.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	201.360, 202.500, 280.480, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 23.4

The structure of Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd also contains other interesting chemical elements:

Zinc

(Zn)

24 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Magnesium atom in the Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd (pdb code 3f9k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 24 binding sites of Magnesium where determined in the Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd, PDB code: 3f9k:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 24 in the Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg211 b:19.5 occ:1.00 OD2 A:ASP116 2.2 47.6 1.0 OD1 A:ASP64 2.4 46.1 1.0 CG A:ASP64 3.2 42.9 1.0 OD2 A:ASP64 3.2 44.4 1.0 CG A:ASP116 3.3 47.7 1.0 OD1 A:ASP116 3.8 47.8 1.0 O A:CYS65 3.9 42.8 1.0 N A:CYS65 4.3 42.1 1.0 CB A:ASP116 4.6 47.9 1.0 CB A:ASP64 4.6 41.0 1.0 C A:CYS65 4.8 42.5 1.0 CA A:CYS65 4.9 42.8 1.0

Magnesium binding site 2 out of 24 in the Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg211 b:39.6 occ:1.00 OD2 B:ASP116 2.1 42.0 1.0 OD1 B:ASP64 2.1 48.4 1.0 CG B:ASP64 3.1 44.9 1.0 CG B:ASP116 3.2 41.1 1.0 OD2 B:ASP64 3.3 46.9 1.0 OD1 B:ASP116 3.7 41.9 1.0 O B:CYS65 4.0 45.9 1.0 N B:CYS65 4.2 44.4 1.0 CB B:ASP116 4.4 40.2 1.0 CB B:ASP64 4.5 42.5 1.0 C B:CYS65 4.8 45.5 1.0 CA B:ASP64 4.9 41.9 1.0 CA B:CYS65 4.9 45.5 1.0 CE2 B:PHE121 4.9 34.8 1.0

Magnesium binding site 3 out of 24 in the Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg211 b:14.9 occ:1.00 OD2 E:ASP116 2.2 47.5 1.0 OD1 E:ASP64 2.2 46.1 1.0 CG E:ASP64 3.1 42.9 1.0 CG E:ASP116 3.2 47.7 1.0 OD2 E:ASP64 3.3 44.4 1.0 OD1 E:ASP116 3.6 47.7 1.0 O E:CYS65 3.9 42.9 1.0 N E:CYS65 4.2 42.1 1.0 CB E:ASP116 4.5 47.9 1.0 CB E:ASP64 4.5 41.0 1.0 CE2 E:PHE121 4.8 53.2 1.0 C E:CYS65 4.8 42.5 1.0 CA E:CYS65 4.8 42.8 1.0 CB E:CYS65 4.9 43.2 1.0 CA E:ASP64 4.9 40.8 1.0

Magnesium binding site 4 out of 24 in the Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg211 b:29.9 occ:1.00 OD2 F:ASP116 2.2 42.0 1.0 OD1 F:ASP64 2.4 48.4 1.0 CG F:ASP64 3.3 44.9 1.0 CG F:ASP116 3.3 41.0 1.0 OD2 F:ASP64 3.4 46.8 1.0 OD1 F:ASP116 3.9 41.8 1.0 O F:CYS65 4.0 45.9 1.0 N F:CYS65 4.3 44.4 1.0 CB F:ASP116 4.5 40.3 1.0 CB F:ASP64 4.7 42.5 1.0 C F:CYS65 4.9 45.5 1.0

Magnesium binding site 5 out of 24 in the Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg211 b:20.6 occ:1.00 OD2 I:ASP116 2.1 47.6 1.0 OD1 I:ASP64 2.4 46.1 1.0 CG I:ASP116 3.1 47.7 1.0 CG I:ASP64 3.2 43.0 1.0 OD2 I:ASP64 3.4 44.4 1.0 OD1 I:ASP116 3.5 47.7 1.0 O I:CYS65 4.1 42.9 1.0 N I:CYS65 4.3 42.0 1.0 CB I:ASP116 4.4 47.9 1.0 CB I:ASP64 4.6 41.0 1.0 CE2 I:PHE121 4.8 53.2 1.0 C I:CYS65 5.0 42.5 1.0

Magnesium binding site 6 out of 24 in the Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg211 b:52.8 occ:1.00 OD1 J:ASP64 2.1 48.4 1.0 OD2 J:ASP116 2.2 42.0 1.0 CG J:ASP64 2.8 44.9 1.0 OD2 J:ASP64 2.9 46.9 1.0 CG J:ASP116 3.4 41.1 1.0 O J:CYS65 3.8 45.9 1.0 OD1 J:ASP116 4.1 41.9 1.0 N J:CYS65 4.2 44.4 1.0 CB J:ASP64 4.3 42.5 1.0 CB J:ASP116 4.6 40.3 1.0 C J:CYS65 4.7 45.5 1.0 CA J:ASP64 4.8 41.9 1.0 CA J:CYS65 4.9 45.5 1.0

Magnesium binding site 7 out of 24 in the Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg211 b:24.6 occ:1.00 OD2 M:ASP116 2.1 47.6 1.0 OD1 M:ASP64 2.3 46.1 1.0 CG M:ASP64 3.1 42.9 1.0 OD2 M:ASP64 3.2 44.3 1.0 CG M:ASP116 3.2 47.7 1.0 OD1 M:ASP116 3.7 47.8 1.0 O M:CYS65 3.9 42.9 1.0 N M:CYS65 4.3 42.1 1.0 CB M:ASP116 4.5 47.9 1.0 CB M:ASP64 4.5 41.0 1.0 C M:CYS65 4.9 42.5 1.0 CE2 M:PHE121 4.9 53.2 1.0 CA M:CYS65 5.0 42.8 1.0

Magnesium binding site 8 out of 24 in the Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg211 b:33.4 occ:1.00 OD1 N:ASP64 1.9 48.4 1.0 OD2 N:ASP116 2.4 42.0 1.0 CG N:ASP64 2.9 44.9 1.0 OD2 N:ASP64 3.2 46.9 1.0 CG N:ASP116 3.5 41.0 1.0 O N:CYS65 3.6 45.9 1.0 N N:CYS65 3.7 44.4 1.0 OD1 N:ASP116 3.9 41.8 1.0 CB N:ASP64 4.2 42.4 1.0 C N:CYS65 4.4 45.5 1.0 CA N:CYS65 4.4 45.5 1.0 CA N:ASP64 4.5 41.9 1.0 CB N:CYS65 4.6 45.9 1.0 C N:ASP64 4.6 43.1 1.0 CE2 N:PHE121 4.7 34.8 1.0 CB N:ASP116 4.7 40.2 1.0

Magnesium binding site 9 out of 24 in the Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd within 5.0Å range: probe atom residue distance (Å) B Occ Q:Mg211 b:20.8 occ:1.00 OD2 Q:ASP116 2.1 47.6 1.0 OD1 Q:ASP64 2.5 46.1 1.0 CG Q:ASP116 3.2 47.7 1.0 CG Q:ASP64 3.4 42.9 1.0 OD2 Q:ASP64 3.5 44.4 1.0 OD1 Q:ASP116 3.6 47.7 1.0 O Q:CYS65 4.1 42.9 1.0 CB Q:ASP116 4.4 47.9 1.0 N Q:CYS65 4.5 42.1 1.0 CB Q:ASP64 4.8 41.0 1.0

Magnesium binding site 10 out of 24 in the Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg211 b:14.5 occ:1.00 OD2 R:ASP116 2.3 42.0 1.0 OD1 R:ASP64 2.3 48.4 1.0 CG R:ASP64 3.2 44.9 1.0 OD2 R:ASP64 3.3 46.8 1.0 CG R:ASP116 3.4 41.0 1.0 O R:CYS65 3.8 46.0 1.0 OD1 R:ASP116 3.9 41.9 1.0 N R:CYS65 4.2 44.4 1.0 CB R:ASP64 4.6 42.5 1.0 CB R:ASP116 4.6 40.2 1.0 C R:CYS65 4.7 45.5 1.0 CA R:CYS65 4.9 45.5 1.0 CA R:ASP64 5.0 41.9 1.0 CB R:CYS65 5.0 45.9 1.0

S.Hare, M.C.Shun, S.S.Gupta, E.Valkov, A.Engelman, P.Cherepanov. A Novel Co-Crystal Structure Affords the Design of Gain-of-Function Lentiviral Integrase Mutants in the Presence of Modified PSIP1/Ledgf/P75 Plos Pathog. V. 5 E1000 2009.
ISSN: ISSN 1553-7366
PubMed: 19132083
DOI: 10.1371/JOURNAL.PPAT.1000259