Magnesium in PDB 8t8v: Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Adp

The structure of Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Adp, PDB code: 8t8v 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)	36.92 / 1.96
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	61.706, 104.656, 102.502, 90, 90, 90
R / Rfree (%)	19.9 / 23.2

The binding sites of Magnesium atom in the Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Adp (pdb code 8t8v). 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, PDB code: 8t8v:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:12.8 occ:1.00 O1A A:ADP401 1.9 14.8 1.0 O A:HOH530 2.1 11.8 1.0 O A:HOH533 2.1 11.5 1.0 O1B A:ADP401 2.2 17.7 1.0 OD2 A:ASP231 2.2 12.9 1.0 O1 A:PO4404 2.2 23.9 1.0 CG A:ASP231 3.2 13.1 1.0 PA A:ADP401 3.2 15.0 1.0 PB A:ADP401 3.3 17.7 1.0 P A:PO4404 3.4 28.0 1.0 O3A A:ADP401 3.6 15.9 1.0 CB A:ASP231 3.6 12.9 1.0 O4 A:PO4404 3.7 27.6 1.0 O3 A:PO4404 3.8 26.2 1.0 O3B A:ADP401 3.9 19.0 1.0 OG A:SER213 4.1 11.2 1.0 O2A A:ADP401 4.2 15.3 1.0 NZ A:LYS128 4.3 20.7 1.0 O5' A:ADP401 4.3 14.9 1.0 OD1 A:ASP231 4.4 13.7 1.0 O A:GLY211 4.4 14.7 1.0 OD2 A:ASP126 4.5 13.2 1.0 C5' A:ADP401 4.5 14.5 1.0 O2B A:ADP401 4.6 18.1 1.0 O2 A:PO4404 4.7 27.2 1.0 O A:HOH501 4.8 53.6 1.0 CB A:SER213 4.8 11.1 1.0 CA A:GLY57 4.8 25.4 1.0 O A:HOH642 4.8 29.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Terrestrivirus 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 Inositol Pyrophosphatase Kinase in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:38.2 occ:1.00 O A:HOH520 2.1 19.1 1.0 O A:HOH584 2.2 33.3 1.0 O A:HOH602 2.3 28.5 1.0 O A:HOH657 2.3 36.5 1.0 O A:HOH539 2.3 23.8 1.0 O A:HOH521 2.5 36.5 1.0 OD1 A:ASN228 3.9 12.4 1.0 OD2 A:ASP226 4.1 13.1 1.0 O A:HOH572 4.2 39.7 1.0 OE2 A:GLU113 4.2 16.0 1.0 O A:HOH605 4.2 37.5 1.0 OE1 A:GLU113 4.4 14.5 1.0 O A:HOH522 4.4 18.8 1.0 CG A:ASN228 4.5 11.9 1.0 ND2 A:ASN228 4.5 11.6 1.0 O A:LYS96 4.6 19.0 1.0 O A:LYS97 4.6 13.9 1.0 NZ A:LYS194 4.6 12.5 1.0 O A:VAL99 4.7 13.3 1.0 CD A:GLU113 4.7 15.1 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