Cadmium in PDB 8t8x: Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Amp-Pnp

The structure of Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Amp-Pnp, PDB code: 8t8x 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)	37.27 / 2.59
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	63.489, 103.417, 102.669, 90, 90, 90
R / Rfree (%)	17.8 / 22.9

The binding sites of Cadmium atom in the Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Amp-Pnp (pdb code 8t8x). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Amp-Pnp, PDB code: 8t8x:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Amp-Pnp


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 Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd402 b:59.8 occ:1.00 OD2 A:ASP231 2.3 43.6 1.0 O A:HOH505 2.5 59.5 1.0 O2A A:ANP401 2.7 58.4 1.0 O A:HOH501 2.8 33.2 1.0 N3B A:ANP401 2.9 63.5 1.0 O3A A:ANP401 3.3 52.4 1.0 O1G A:ANP401 3.3 62.8 1.0 CG A:ASP231 3.3 34.1 1.0 O A:HOH566 3.5 42.6 1.0 PA A:ANP401 3.6 51.1 1.0 PB A:ANP401 3.6 49.1 1.0 NZ A:LYS128 3.7 49.0 1.0 PG A:ANP401 3.7 76.3 1.0 CB A:ASP231 3.8 32.1 1.0 CD A:CD403 4.0 55.7 1.0 O A:HOH502 4.1 31.3 1.0 O2 A:PO4407 4.2 89.2 1.0 OG A:SER213 4.2 21.6 1.0 O A:GLY211 4.3 26.1 1.0 O1B A:ANP401 4.4 47.4 1.0 OD1 A:ASP231 4.5 34.8 1.0 OD2 A:ASP126 4.5 29.3 1.0 CE A:LYS128 4.5 46.0 1.0 O1A A:ANP401 4.6 57.2 1.0 O5' A:ANP401 4.7 50.0 1.0 C5' A:ANP401 4.7 48.0 1.0 O2B A:ANP401 4.7 53.6 1.0 O2G A:ANP401 4.8 78.0 1.0 O3G A:ANP401 4.8 69.3 1.0 CB A:SER213 4.9 22.2 1.0 O A:HOH507 4.9 34.0 1.0 CA A:GLY57 4.9 71.3 1.0

Cadmium binding site 2 out of 5 in the Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Amp-Pnp


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 Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd403 b:55.7 occ:1.00 O A:HOH507 2.2 34.0 1.0 OD2 A:ASP231 2.4 43.6 1.0 OD1 A:ASP231 2.6 34.8 1.0 O1B A:ANP401 2.8 47.4 1.0 OG A:SER233 2.8 32.3 1.0 CG A:ASP231 2.8 34.1 1.0 O3G A:ANP401 3.1 69.3 1.0 O A:HOH503 3.2 23.4 1.0 O2 A:PO4407 3.3 89.2 1.0 O4 A:PO4407 3.3 85.1 1.0 PB A:ANP401 3.6 49.1 1.0 PG A:ANP401 3.6 76.3 1.0 N3B A:ANP401 3.6 63.5 1.0 O1G A:ANP401 3.7 62.8 1.0 P A:PO4407 3.8 102.3 1.0 O3A A:ANP401 3.9 52.4 1.0 CB A:SER233 4.0 30.2 1.0 CD A:CD402 4.0 59.8 1.0 O A:HOH504 4.3 26.6 1.0 CB A:ASP231 4.3 32.1 1.0 O1 A:PO4407 4.5 83.4 1.0 NZ A:LYS72 4.5 43.1 1.0 O A:HOH518 4.8 17.3 1.0

Cadmium binding site 3 out of 5 in the Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Amp-Pnp


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 Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd404 b:152.5 occ:1.00 O A:ALA176 2.4 80.5 1.0 C A:ALA176 3.5 72.1 1.0 CA A:ALA176 4.1 70.7 1.0 CB A:ALA176 4.2 73.5 1.0 N A:GLY177 4.7 72.4 1.0

Cadmium binding site 4 out of 5 in the Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd405 b:93.2 occ:1.00 OD2 A:ASP219 2.5 49.3 1.0 OG A:SER223 2.9 52.4 1.0 CG A:ASP219 3.3 41.1 1.0 OD1 A:ASP221 3.5 73.1 1.0 OD1 A:ASN120 3.7 62.4 1.0 CB A:ASP219 3.7 38.3 1.0 OD2 A:ASP221 3.8 72.2 1.0 CG A:ASP221 4.1 80.2 1.0 OD1 A:ASP219 4.2 43.7 1.0 CB A:SER223 4.3 62.5 1.0 NZ A:LYS224 4.4 74.0 1.0 CG A:ASN120 4.5 58.4 1.0 CB A:ASN120 4.7 55.3 1.0 N A:ASN120 4.7 41.4 1.0 O A:ASP221 4.8 71.4 1.0 CG A:LYS224 5.0 55.9 1.0

Cadmium binding site 5 out of 5 in the Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Terrestrivirus Inositol Pyrophosphatase Kinase in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd406 b:173.3 occ:1.00 O4 A:PO4408 2.2 104.0 1.0 O3 A:PO4407 2.5 85.2 1.0 O A:HOH502 2.6 31.3 1.0 O1G A:ANP401 3.3 62.8 1.0 O A:HOH509 3.4 58.7 1.0 O A:HOH565 3.5 41.6 1.0 P A:PO4408 3.5 107.4 1.0 NH1 A:ARG58 3.6 91.9 1.0 O1 A:PO4408 3.7 82.7 1.0 O2G A:ANP401 3.7 78.0 1.0 P A:PO4407 3.7 102.3 1.0 O2 A:PO4407 3.9 89.2 1.0 PG A:ANP401 4.1 76.3 1.0 O A:HOH571 4.2 50.2 1.0 O2 A:PO4408 4.4 93.0 1.0 O A:HOH529 4.4 56.8 1.0 O4 A:PO4407 4.4 85.1 1.0 CZ A:ARG58 4.5 96.5 1.0 O3 A:PO4408 4.6 106.9 1.0 O3G A:ANP401 4.6 69.3 1.0 O A:HOH513 4.8 33.7 1.0 NZ A:LYS128 4.8 49.0 1.0 O1 A:PO4407 4.9 83.4 1.0 CE A:LYS128 4.9 46.0 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