Magnesium in PDB 8t8u: Crystal Structure of Terrestrivirus Full-Length Inositol Pyrophosphatase Kinase in Complex with Adp

The structure of Crystal Structure of Terrestrivirus Full-Length Inositol Pyrophosphatase Kinase in Complex with Adp, PDB code: 8t8u 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)	36.96 / 2.01
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	61.929, 104.902, 102.395, 90, 90, 90
R / Rfree (%)	17.4 / 20.4

The binding sites of Magnesium atom in the Crystal Structure of Terrestrivirus Full-Length Inositol Pyrophosphatase Kinase in Complex with Adp (pdb code 8t8u). 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 Full-Length Inositol Pyrophosphatase Kinase in Complex with Adp, PDB code: 8t8u:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Terrestrivirus Full-Length Inositol Pyrophosphatase Kinase in Complex with Adp


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 Full-Length Inositol Pyrophosphatase Kinase in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:22.2 occ:1.00 O1A A:ADP401 2.0 23.7 1.0 O A:HOH533 2.1 18.4 1.0 O1B A:ADP401 2.1 26.9 1.0 O1 A:PO4404 2.2 34.5 1.0 OD2 A:ASP231 2.2 21.3 1.0 O A:HOH536 2.2 20.9 1.0 CG A:ASP231 3.2 21.4 1.0 PA A:ADP401 3.3 24.3 1.0 P A:PO4404 3.3 41.3 1.0 PB A:ADP401 3.3 27.2 1.0 O3A A:ADP401 3.5 25.5 1.0 CB A:ASP231 3.6 20.5 1.0 O2 A:PO4404 3.7 40.8 1.0 O4 A:PO4404 3.7 36.8 1.0 O A:HOH544 4.0 51.0 1.0 O3B A:ADP401 4.1 28.1 1.0 NZ A:LYS128 4.1 27.7 1.0 OG A:SER213 4.2 16.8 1.0 O2A A:ADP401 4.3 25.3 1.0 O5' A:ADP401 4.3 24.8 1.0 OD1 A:ASP231 4.3 22.5 1.0 O A:HOH522 4.4 58.0 1.0 O A:GLY211 4.4 20.9 1.0 C5' A:ADP401 4.5 24.4 1.0 OD2 A:ASP126 4.5 20.0 1.0 O2B A:ADP401 4.5 26.4 1.0 O3 A:PO4404 4.6 40.9 1.0 CA A:GLY57 4.8 34.1 1.0 CB A:SER213 4.9 16.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Terrestrivirus Full-Length Inositol Pyrophosphatase Kinase in Complex with Adp


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 Full-Length Inositol Pyrophosphatase Kinase in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:38.1 occ:1.00 O A:HOH575 2.0 35.6 1.0 O A:HOH552 2.0 27.6 1.0 O A:HOH578 2.1 32.1 1.0 O A:HOH532 2.2 30.9 1.0 O A:HOH595 2.2 31.6 1.0 O A:HOH667 2.4 41.0 1.0 O A:HOH617 4.1 40.0 1.0 OE2 A:GLU113 4.1 23.4 1.0 OD1 A:ASN228 4.1 18.3 1.0 OE1 A:GLU113 4.2 20.2 1.0 OD2 A:ASP226 4.2 19.3 1.0 O A:HOH524 4.3 26.3 1.0 O A:HOH599 4.4 35.9 1.0 CD A:GLU113 4.5 21.4 1.0 O A:LYS96 4.6 25.1 1.0 O A:VAL99 4.7 18.8 1.0 CG A:ASN228 4.7 17.7 1.0 ND2 A:ASN228 4.7 17.6 1.0 O A:LYS97 4.9 19.2 1.0 NZ A:LYS194 4.9 17.3 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