Magnesium in PDB 8t8y: Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Adp and 1,4,5-IP3

The structure of Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Adp and 1,4,5-IP3, PDB code: 8t8y 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)	37.80 / 2.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	64.619, 100.61, 105.022, 90, 90, 90
R / Rfree (%)	17.3 / 22.3

The binding sites of Magnesium atom in the Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Adp and 1,4,5-IP3 (pdb code 8t8y). 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 1,4,5-IP3, PDB code: 8t8y:
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 1,4,5-IP3


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 1,4,5-IP3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:17.0 occ:1.00 O A:HOH530 2.0 24.1 1.0 O41 A:I3P404 2.1 29.9 1.0 OD2 A:ASP231 2.1 28.3 1.0 O1A A:ADP401 2.1 27.3 1.0 O A:HOH521 2.2 18.7 1.0 O1B A:ADP401 2.3 31.3 1.0 CG A:ASP231 3.1 31.5 1.0 PA A:ADP401 3.4 29.6 1.0 P4 A:I3P404 3.4 31.1 1.0 CB A:ASP231 3.5 30.9 1.0 PB A:ADP401 3.6 31.9 1.0 O3A A:ADP401 3.7 30.6 1.0 O42 A:I3P404 3.7 30.3 1.0 O A:HOH508 4.2 26.9 1.0 O4 A:I3P404 4.2 30.6 1.0 NZ A:LYS128 4.2 27.2 1.0 OD1 A:ASP231 4.3 31.7 1.0 OG A:SER213 4.3 29.0 1.0 O2A A:ADP401 4.3 30.9 1.0 O A:HOH525 4.4 20.1 1.0 O3B A:ADP401 4.4 30.4 1.0 OD2 A:ASP126 4.5 32.5 1.0 O43 A:I3P404 4.5 28.8 1.0 O A:GLY211 4.5 27.7 1.0 O5' A:ADP401 4.5 27.7 1.0 C5' A:ADP401 4.6 27.7 1.0 O2B A:ADP401 4.6 30.1 1.0 O A:HOH593 4.7 40.9 1.0 CA A:GLY57 4.9 31.8 1.0 CE A:LYS128 4.9 27.8 1.0 CB A:SER213 5.0 28.6 1.0 CA A:ASP231 5.0 30.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Adp and 1,4,5-IP3


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 1,4,5-IP3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:50.6 occ:1.00 O A:HOH517 2.0 30.9 1.0 O A:HOH591 2.1 40.4 1.0 O A:HOH599 2.2 32.0 1.0 O12 A:I3P404 2.2 35.5 1.0 O A:HOH534 2.5 32.1 1.0 P1 A:I3P404 3.6 38.0 1.0 O2 A:I3P404 3.7 35.2 1.0 O13 A:I3P404 3.8 34.5 1.0 O A:HOH510 3.9 32.7 1.0 NZ A:LYS76 4.0 39.2 1.0 O1 A:I3P404 4.2 36.8 1.0 C2 A:I3P404 4.4 34.3 1.0 O A:HOH569 4.4 34.5 1.0 O11 A:I3P404 4.8 34.3 1.0 CE A:LYS76 4.9 39.6 1.0 C1 A:I3P404 4.9 34.1 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