Magnesium in PDB 8t96: Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Adp and Scyllo-IP5

The structure of Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Adp and Scyllo-IP5, PDB code: 8t96 was solved by G.Zong, H.Wang, S.B.Shears, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.57 / 2.36
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	63.562, 103.358, 104.193, 90, 90, 90
R / Rfree (%)	16.8 / 22.6

The binding sites of Magnesium atom in the Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Adp and Scyllo-IP5 (pdb code 8t96). 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 Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Adp and Scyllo-IP5, PDB code: 8t96:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Adp and Scyllo-IP5


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 Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Adp and Scyllo-IP5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:63.2 occ:1.00 O A:HOH512 2.2 49.6 1.0 O1B A:ADP401 2.2 68.1 1.0 OD2 A:ASP231 2.3 45.0 1.0 O A:HOH511 2.3 45.2 1.0 O1A A:ADP401 2.3 53.9 1.0 O1 A:PO4405 2.6 112.8 1.0 O A:HOH507 3.0 76.2 1.0 CG A:ASP231 3.4 42.9 1.0 PB A:ADP401 3.5 68.4 1.0 PA A:ADP401 3.6 49.6 1.0 O3A A:ADP401 3.9 53.2 1.0 CB A:ASP231 3.9 40.4 1.0 O3B A:ADP401 3.9 59.7 1.0 P A:PO4405 4.0 119.0 1.0 O35 A:K7V404 4.0 77.4 1.0 MG A:MG403 4.1 65.1 1.0 OG A:SER213 4.2 36.2 1.0 O A:GLY211 4.2 48.4 1.0 O4 A:PO4405 4.3 98.4 1.0 OD2 A:ASP126 4.4 39.1 1.0 OD1 A:ASP231 4.5 41.1 1.0 O3 A:PO4405 4.5 104.8 1.0 O5' A:ADP401 4.6 47.8 1.0 O A:HOH505 4.6 68.6 1.0 O2A A:ADP401 4.6 54.6 1.0 O2B A:ADP401 4.7 63.8 1.0 C5' A:ADP401 4.7 44.2 1.0 CB A:SER213 4.8 34.0 1.0 O A:HOH530 4.9 65.5 1.0 CA A:GLY57 4.9 66.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Adp and Scyllo-IP5


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 Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Adp and Scyllo-IP5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:65.1 occ:1.00 O A:HOH507 2.2 76.2 1.0 O3B A:ADP401 2.2 59.7 1.0 O A:HOH530 2.5 65.5 1.0 O46 A:K7V404 2.6 105.1 1.0 OD2 A:ASP231 2.6 45.0 1.0 OD1 A:ASP231 2.6 41.1 1.0 CG A:ASP231 3.0 42.9 1.0 OG A:SER233 3.0 56.1 1.0 PB A:ADP401 3.3 68.4 1.0 O1B A:ADP401 3.5 68.1 1.0 P6 A:K7V404 3.9 91.8 1.0 O16 A:K7V404 4.0 99.4 1.0 O25 A:K7V404 4.1 83.9 1.0 O2B A:ADP401 4.1 63.8 1.0 MG A:MG402 4.1 63.2 1.0 O35 A:K7V404 4.1 77.4 1.0 CB A:SER233 4.2 45.5 1.0 O A:HOH505 4.2 68.6 1.0 NZ A:LYS72 4.4 43.0 1.0 O36 A:K7V404 4.4 103.8 1.0 CB A:ASP231 4.5 40.4 1.0 O3A A:ADP401 4.6 53.2 1.0 P5 A:K7V404 4.7 75.3 1.0 O1A A:ADP401 4.9 53.9 1.0 O A:HOH586 4.9 51.5 1.0 O A:HOH535 5.0 36.3 1.0

G.Zong, H.Wang, S.B.Shears. Biochemical and Structural Characterization of A Giant Virus Inositol Pyrophosphate Kinase Embo J. 2023.
ISSN: ESSN 1460-2075