Magnesium in PDB 8t92: Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Adp and Scyllo-D-(1,2,3,4)-IP4

The structure of Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Adp and Scyllo-D-(1,2,3,4)-IP4, PDB code: 8t92 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)	37.33 / 2.30
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	62.532, 104.128, 103.862, 90, 90, 90
R / Rfree (%)	16.8 / 22.8

The binding sites of Magnesium atom in the Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Adp and Scyllo-D-(1,2,3,4)-IP4 (pdb code 8t92). 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-D-(1,2,3,4)-IP4, PDB code: 8t92:
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-D-(1,2,3,4)-IP4


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-D-(1,2,3,4)-IP4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:21.3 occ:1.00 OD2 A:ASP231 1.9 22.7 1.0 O A:HOH534 2.0 21.4 1.0 O1B A:ADP401 2.0 23.9 1.0 O1A A:ADP401 2.1 21.2 1.0 O A:HOH507 2.1 29.0 1.0 O A:HOH502 2.3 21.6 1.0 CG A:ASP231 3.0 20.7 1.0 PB A:ADP401 3.1 27.6 1.0 PA A:ADP401 3.3 22.4 1.0 O1 A:PO4405 3.3 77.6 1.0 CB A:ASP231 3.5 20.1 1.0 O3A A:ADP401 3.5 22.9 1.0 O3B A:ADP401 3.5 23.5 1.0 O A:HOH506 3.7 26.2 1.0 OD1 A:ASP231 4.0 21.4 1.0 MG A:MG403 4.1 27.6 1.0 O A:GLY211 4.2 23.9 1.0 O2A A:ADP401 4.2 26.3 1.0 O24 A:XID404 4.3 37.4 1.0 OG A:SER213 4.3 21.9 1.0 O5' A:ADP401 4.4 24.2 1.0 O2B A:ADP401 4.5 24.7 1.0 OD2 A:ASP126 4.5 21.8 1.0 C5' A:ADP401 4.6 21.8 1.0 O A:HOH575 4.6 40.2 1.0 P A:PO4405 4.6 116.8 1.0 O3 A:PO4405 4.8 111.3 1.0 CB A:SER213 4.8 21.1 1.0 CA A:GLY57 5.0 43.0 1.0 CA A:ASP231 5.0 19.9 1.0 O A:HOH535 5.0 25.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Adp and Scyllo-D-(1,2,3,4)-IP4


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-D-(1,2,3,4)-IP4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:27.6 occ:1.00 O A:HOH512 1.8 32.0 1.0 O A:HOH535 2.1 25.1 1.0 O A:HOH506 2.1 26.2 1.0 OD1 A:ASP231 2.2 21.4 1.0 O3B A:ADP401 2.3 23.5 1.0 OD2 A:ASP231 2.5 22.7 1.0 CG A:ASP231 2.7 20.7 1.0 OG A:SER233 2.9 35.4 1.0 PB A:ADP401 3.5 27.6 1.0 O1B A:ADP401 3.8 23.9 1.0 O24 A:XID404 4.0 37.4 1.0 MG A:MG402 4.1 21.3 1.0 O23 A:XID404 4.2 51.3 1.0 O34 A:XID404 4.2 38.4 1.0 CB A:ASP231 4.2 20.1 1.0 NZ A:LYS72 4.2 24.2 1.0 CB A:SER233 4.2 27.0 1.0 O A:HOH507 4.4 29.0 1.0 O A:HOH518 4.5 16.5 1.0 O2B A:ADP401 4.5 24.7 1.0 O A:HOH575 4.5 40.2 1.0 P4 A:XID404 4.7 37.2 1.0 O33 A:XID404 4.7 51.6 1.0 O3A A:ADP401 4.7 22.9 1.0 CA A:ASP231 4.8 19.9 1.0 P3 A:XID404 4.8 68.3 1.0 N A:SER233 4.9 25.6 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