Cadmium in PDB 8x1k: Structure of RVY_06210 at 2.55 Angstrom Resolution

The structure of Structure of RVY_06210 at 2.55 Angstrom Resolution, PDB code: 8x1k was solved by S.Kato, Y.Fukuda, T.Inoue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.53 / 2.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.152, 80.372, 105.025, 90, 90, 90
R / Rfree (%)	21.8 / 27

The binding sites of Cadmium atom in the Structure of RVY_06210 at 2.55 Angstrom Resolution (pdb code 8x1k). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Structure of RVY_06210 at 2.55 Angstrom Resolution, PDB code: 8x1k:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Structure of RVY_06210 at 2.55 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of RVY_06210 at 2.55 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd501 b:105.7 occ:1.00 OE2 A:GLU51 2.6 81.7 1.0 OE1 A:GLU90 2.6 83.1 1.0 OD2 A:ASP162 2.7 87.1 1.0 OE1 A:GLU51 2.8 78.1 1.0 ND1 A:HIS93 2.8 86.9 1.0 OD1 A:ASP162 3.0 82.7 1.0 CD A:GLU51 3.0 83.8 1.0 CD A:CD502 3.1 99.1 0.8 CG A:ASP162 3.2 86.4 1.0 CD A:GLU90 3.6 83.8 1.0 CG A:HIS93 3.7 85.8 1.0 OH A:TYR139 3.7 76.9 1.0 CB A:HIS93 3.7 81.8 1.0 CE1 A:HIS93 3.8 90.9 1.0 OE2 A:GLU90 3.9 91.0 1.0 CE2 A:TYR139 4.3 77.3 1.0 OD1 A:ASP135 4.3 78.4 1.0 CZ A:TYR139 4.5 83.3 1.0 CG A:GLU51 4.5 81.0 1.0 CB A:ASP162 4.6 82.4 1.0 CG A:ASP135 4.7 83.1 1.0 OD2 A:ASP135 4.8 89.0 1.0 CA A:GLU90 4.9 80.7 1.0 CD2 A:HIS93 4.9 93.3 1.0 NE2 A:HIS93 4.9 93.7 1.0 CG A:GLU90 4.9 85.8 1.0

Cadmium binding site 2 out of 5 in the Structure of RVY_06210 at 2.55 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of RVY_06210 at 2.55 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd502 b:99.1 occ:0.77 OD1 A:ASP135 2.5 78.4 1.0 OE1 A:GLU132 2.6 79.3 1.0 OD1 A:ASP162 2.6 82.7 1.0 OE2 A:GLU90 2.9 91.0 1.0 OE1 A:GLU90 3.0 83.1 1.0 CD A:CD501 3.1 105.7 1.0 CD A:GLU90 3.2 83.8 1.0 CD A:GLU132 3.3 81.5 1.0 CG A:ASP135 3.3 83.1 1.0 OE2 A:GLU132 3.3 77.2 1.0 CG A:ASP162 3.5 86.4 1.0 OD2 A:ASP135 3.6 89.0 1.0 OD2 A:ASP162 3.9 87.1 1.0 OE1 A:GLU51 4.3 78.1 1.0 CB A:ALA54 4.4 87.6 1.0 CG A:GLU90 4.4 85.8 1.0 CD2 A:HIS165 4.5 86.1 1.0 CB A:ASP135 4.6 80.5 1.0 CB A:ASP162 4.6 82.4 1.0 CA A:GLU132 4.7 83.5 1.0 CG A:GLU132 4.7 75.3 1.0 O A:LEU131 4.8 79.2 1.0 CG A:HIS165 4.9 85.4 1.0

Cadmium binding site 3 out of 5 in the Structure of RVY_06210 at 2.55 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of RVY_06210 at 2.55 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd501 b:101.3 occ:0.82 OE1 B:GLU90 2.5 94.6 1.0 OD1 B:ASP162 2.6 84.3 1.0 OD2 B:ASP162 2.6 79.7 1.0 ND1 B:HIS93 2.6 95.3 1.0 OE1 B:GLU51 2.7 97.3 1.0 CG B:ASP162 2.9 84.4 1.0 CD B:CD502 2.9 106.9 0.8 OE2 B:GLU51 3.0 89.7 1.0 CD B:GLU51 3.2 94.4 1.0 CD B:GLU90 3.4 91.1 1.0 OE2 B:GLU90 3.5 89.6 1.0 CG B:HIS93 3.5 95.5 1.0 CE1 B:HIS93 3.6 87.4 1.0 CB B:HIS93 3.7 92.2 1.0 OD1 B:ASP135 4.1 98.7 1.0 OH B:TYR139 4.2 89.6 1.0 CB B:ASP162 4.3 88.2 1.0 NE2 B:HIS93 4.6 92.7 1.0 CD2 B:HIS93 4.6 97.0 1.0 CG B:GLU51 4.7 90.4 1.0 CE1 B:TYR139 4.7 86.3 1.0 CG B:GLU90 4.8 94.7 1.0 CA B:GLU90 4.8 93.8 1.0 ND1 B:HIS165 4.8 81.6 1.0 CG B:ASP135 4.9 94.4 1.0 CE1 B:HIS165 4.9 85.3 1.0 CZ B:TYR139 4.9 87.8 1.0

Cadmium binding site 4 out of 5 in the Structure of RVY_06210 at 2.55 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of RVY_06210 at 2.55 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd502 b:106.9 occ:0.82 OE1 B:GLU132 2.5 83.5 1.0 OD1 B:ASP135 2.7 98.7 1.0 OE2 B:GLU90 2.8 89.6 1.0 CD B:CD501 2.9 101.3 0.8 OD1 B:ASP162 3.0 84.3 1.0 CG B:ASP135 3.2 94.4 1.0 CD B:GLU132 3.2 84.5 1.0 OE2 B:GLU132 3.3 88.7 1.0 CG B:ASP162 3.3 84.4 1.0 OD2 B:ASP135 3.3 99.0 1.0 CD B:GLU90 3.5 91.1 1.0 OE1 B:GLU90 3.5 94.6 1.0 OD2 B:ASP162 3.7 79.7 1.0 CB B:ASP162 4.0 88.2 1.0 ND1 B:HIS165 4.2 81.6 1.0 CB B:ASP135 4.3 83.6 1.0 OE2 B:GLU51 4.3 89.7 1.0 CB B:ALA54 4.4 94.6 1.0 CG B:GLU132 4.7 80.1 1.0 CA B:GLU132 4.8 85.1 1.0 CA B:ASP162 4.8 79.0 1.0 CG B:GLU90 4.9 94.7 1.0 CE1 B:HIS165 5.0 85.3 1.0 O B:LEU131 5.0 85.9 1.0

Cadmium binding site 5 out of 5 in the Structure of RVY_06210 at 2.55 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of RVY_06210 at 2.55 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd503 b:118.4 occ:0.63 OD2 B:ASP233 2.9 129.4 1.0 OD1 B:ASP233 3.0 128.3 1.0 CG B:ASP233 3.2 129.6 1.0 O B:VAL234 4.4 128.7 1.0 CB B:ASP233 4.6 122.6 1.0 OG1 B:THR236 4.8 116.8 1.0 CA B:ASP233 4.8 120.2 1.0

S.Kato, Y.Fukuda, T.Inoue. Metabolite Phosphatase From Anhydrobiotic Tardigrades To Be Published.