Cadmium in PDB 8t8w: Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Atp

The structure of Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Atp, PDB code: 8t8w 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)	37.17 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	63.084, 104.244, 102.402, 90, 90, 90
R / Rfree (%)	15.9 / 19.5

The binding sites of Cadmium atom in the Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Atp (pdb code 8t8w). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Atp, PDB code: 8t8w:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in the Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Atp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd402 b:26.0 occ:0.60 O2A A:ATP401 2.2 26.3 0.5 O A:HOH565 2.3 21.1 1.0 O2A A:ATP401 2.3 15.1 0.6 OD2 A:ASP231 2.3 20.7 1.0 O A:HOH610 2.3 24.3 1.0 O1B A:ATP401 2.5 13.6 0.6 O3B A:ATP401 2.7 33.1 0.5 O A:HOH503 2.7 48.6 1.0 O A:HOH505 2.9 34.4 1.0 PA A:ATP401 3.3 26.5 0.5 O3A A:ATP401 3.3 30.4 0.5 CG A:ASP231 3.4 18.9 1.0 PB A:ATP401 3.4 30.2 0.5 PA A:ATP401 3.6 18.1 0.6 PB A:ATP401 3.6 18.4 0.6 O2B A:ATP401 3.8 29.4 0.5 CB A:ASP231 3.8 18.6 1.0 O3A A:ATP401 3.8 16.2 0.6 PG A:ATP401 3.9 31.3 0.5 O2G A:ATP401 3.9 34.4 0.5 NZ A:LYS128 4.0 45.1 1.0 O1G A:ATP401 4.1 36.1 0.5 CD A:CD403 4.2 50.5 0.6 O A:HOH666 4.3 49.0 1.0 O3B A:ATP401 4.3 25.0 0.6 O1A A:ATP401 4.3 27.3 0.5 O A:GLY211 4.3 19.1 1.0 O5' A:ATP401 4.4 26.0 0.5 OG A:SER213 4.4 16.9 1.0 O1A A:ATP401 4.5 15.9 0.6 O1G A:ATP401 4.5 25.2 0.6 OD1 A:ASP231 4.5 23.3 1.0 O5' A:ATP401 4.6 18.4 0.6 C5' A:ATP401 4.7 18.6 0.6 C5' A:ATP401 4.7 25.0 0.5 OD2 A:ASP126 4.7 22.3 1.0 O1B A:ATP401 4.8 32.9 0.5 O2B A:ATP401 4.9 17.6 0.6 CE A:LYS128 4.9 41.1 1.0 CB A:SER213 4.9 16.6 1.0 PG A:ATP401 4.9 22.9 0.6 O A:HOH658 5.0 30.9 1.0

Cadmium binding site 2 out of 3 in the Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Atp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd403 b:50.5 occ:0.60 O3G A:ATP401 2.1 22.2 0.6 OD2 A:ASP231 2.5 20.7 1.0 OG A:SER233 2.5 22.1 1.0 O1G A:ATP401 2.5 25.2 0.6 OD1 A:ASP231 2.5 23.3 1.0 O A:HOH658 2.6 30.9 1.0 O2B A:ATP401 2.6 29.4 0.5 PG A:ATP401 2.7 22.9 0.6 CG A:ASP231 2.8 18.9 1.0 O1G A:ATP401 2.9 36.1 0.5 O A:HOH620 3.2 52.0 1.0 O A:HOH503 3.3 48.6 1.0 O3B A:ATP401 3.6 25.0 0.6 CB A:SER233 3.7 21.2 1.0 O3B A:ATP401 3.7 33.1 0.5 PB A:ATP401 3.8 30.2 0.5 PG A:ATP401 4.0 31.3 0.5 O2G A:ATP401 4.0 27.6 0.6 CD A:CD402 4.2 26.0 0.6 CB A:ASP231 4.3 18.6 1.0 O A:HOH575 4.3 16.4 1.0 O1B A:ATP401 4.3 13.6 0.6 O A:HOH549 4.5 51.4 1.0 NZ A:LYS72 4.6 21.1 1.0 PB A:ATP401 4.6 18.4 0.6 N A:SER233 4.6 19.9 1.0 CA A:SER233 4.7 21.5 1.0 O1B A:ATP401 4.8 32.9 0.5 O3A A:ATP401 4.9 30.4 0.5 O3G A:ATP401 4.9 27.3 0.5 CG A:ARG234 5.0 27.7 1.0

Cadmium binding site 3 out of 3 in the Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Atp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd404 b:107.9 occ:1.00 OD2 A:ASP219 2.4 31.3 1.0 OG A:SER223 2.7 34.4 1.0 CG A:ASP219 3.2 27.4 1.0 OD2 A:ASP221 3.4 56.5 1.0 CB A:ASP219 3.7 25.8 1.0 ND2 A:ASN120 3.7 49.1 1.0 OD1 A:ASP221 3.8 44.6 1.0 CG A:ASP221 4.0 49.5 1.0 CB A:SER223 4.1 38.2 1.0 OD1 A:ASP219 4.1 30.8 1.0 CG A:ASN120 4.4 45.7 1.0 CG A:LYS224 4.4 42.5 1.0 N A:ASN120 4.6 31.6 1.0 CB A:ASN120 4.6 39.7 1.0 O A:HOH631 4.8 58.8 1.0 CE A:LYS224 4.9 58.7 1.0 CA A:SER223 5.0 38.9 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