Zinc in PDB 8wai: Structure of RVY_06210 at 1.45 Angstrom Resolution

The structure of Structure of RVY_06210 at 1.45 Angstrom Resolution, PDB code: 8wai 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)	40.58 / 1.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.96, 82.161, 145.065, 90, 90, 90
R / Rfree (%)	16.8 / 19.2

The binding sites of Zinc atom in the Structure of RVY_06210 at 1.45 Angstrom Resolution (pdb code 8wai). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of RVY_06210 at 1.45 Angstrom Resolution, PDB code: 8wai:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of RVY_06210 at 1.45 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of RVY_06210 at 1.45 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:16.6 occ:1.00 OE1 A:GLU70 2.0 16.7 1.0 OE2 A:GLU31 2.0 16.8 1.0 ND1 A:HIS73 2.1 16.7 1.0 OD2 A:ASP142 2.2 24.2 1.0 OD1 A:ASP142 2.4 23.5 1.0 CG A:ASP142 2.6 18.2 1.0 CD A:GLU31 2.9 20.8 1.0 CD A:GLU70 3.0 18.7 1.0 CE1 A:HIS73 3.0 16.4 1.0 OE1 A:GLU31 3.1 23.6 1.0 CG A:HIS73 3.2 13.6 1.0 O A:HOH404 3.2 22.8 0.6 OE2 A:GLU70 3.3 22.4 1.0 ZN A:ZN302 3.4 19.2 0.5 O A:HOH467 3.5 21.5 0.6 CB A:HIS73 3.5 15.3 1.0 OH A:TYR119 3.9 18.1 1.0 CB A:ASP142 4.1 13.1 1.0 NE2 A:HIS73 4.2 15.2 1.0 CD2 A:HIS73 4.3 15.2 1.0 CG A:GLU31 4.3 18.2 1.0 CG A:GLU70 4.3 15.5 1.0 CE1 A:TYR119 4.3 17.8 1.0 OD2 A:ASP115 4.4 15.0 0.3 CZ A:TYR119 4.5 17.9 1.0 CA A:GLU70 4.6 14.7 1.0 CB A:GLU70 4.8 15.9 1.0 ND1 A:HIS145 5.0 17.4 1.0 CA A:ASP142 5.0 14.8 1.0 CE1 A:HIS145 5.0 15.1 1.0

Zinc binding site 2 out of 4 in the Structure of RVY_06210 at 1.45 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of RVY_06210 at 1.45 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:19.2 occ:0.53 OE2 A:GLU70 1.7 22.4 1.0 O A:HOH404 2.0 22.8 0.6 OE1 A:GLU112 2.0 21.6 1.0 O A:HOH467 2.1 21.5 0.6 OD2 A:ASP115 2.1 15.0 0.3 OE2 A:GLU112 2.4 25.7 1.0 CD A:GLU112 2.5 19.8 1.0 OD1 A:ASP142 2.7 23.5 1.0 CD A:GLU70 2.8 18.7 1.0 CG A:ASP142 3.1 18.2 1.0 OE1 A:GLU70 3.2 16.7 1.0 CG A:ASP115 3.4 23.5 0.3 ZN A:ZN301 3.4 16.6 1.0 OD2 A:ASP142 3.6 24.2 1.0 OD2 A:ASP115 3.7 30.8 0.7 ND1 A:HIS145 3.8 17.4 1.0 CB A:ASP142 3.8 13.1 1.0 CG A:GLU112 4.0 15.3 1.0 CG A:GLU70 4.1 15.5 1.0 OD1 A:ASP115 4.2 28.5 0.3 CB A:ASP115 4.2 27.7 0.3 OE1 A:GLU31 4.3 23.6 1.0 CB A:ASP115 4.3 27.8 0.7 CA A:GLU112 4.5 18.2 1.0 CA A:ASP142 4.5 14.8 1.0 CG A:ASP115 4.5 31.4 0.7 CB A:GLU112 4.6 16.5 1.0 CB A:ALA34 4.7 17.8 1.0 CE1 A:HIS145 4.7 15.1 1.0 OE2 A:GLU31 4.7 16.8 1.0 CG A:HIS145 4.8 14.0 1.0 CE2 A:TYR38 4.9 15.5 1.0 CB A:HIS145 4.9 13.9 1.0

Zinc binding site 3 out of 4 in the Structure of RVY_06210 at 1.45 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of RVY_06210 at 1.45 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:17.9 occ:0.54 OE2 B:GLU70 1.8 25.9 1.0 OD2 B:ASP115 1.9 31.4 1.0 OE1 B:GLU112 2.0 19.7 1.0 O B:HOH404 2.0 24.7 1.0 OE2 B:GLU112 2.4 26.1 1.0 CD B:GLU112 2.5 18.8 1.0 OD1 B:ASP142 2.5 26.5 1.0 CD B:GLU70 2.8 19.7 1.0 CG B:ASP115 3.0 32.1 1.0 CG B:ASP142 3.1 21.5 1.0 OE1 B:GLU70 3.3 20.4 1.0 ZN B:ZN302 3.4 17.1 1.0 OD1 B:ASP115 3.5 34.3 1.0 OD2 B:ASP142 3.7 24.8 1.0 CB B:ASP142 3.8 15.0 1.0 ND1 B:HIS145 3.8 16.5 1.0 CG B:GLU112 4.0 16.8 1.0 CG B:GLU70 4.1 17.0 1.0 CB B:ASP115 4.2 24.0 1.0 O B:HOH512 4.2 18.5 0.4 OE1 B:GLU31 4.3 24.6 1.0 CA B:GLU112 4.4 17.1 1.0 CA B:ASP142 4.4 14.7 1.0 CB B:GLU112 4.5 16.9 1.0 CE1 B:HIS145 4.6 15.9 1.0 CB B:ALA34 4.7 18.0 1.0 OE2 B:GLU31 4.7 18.3 1.0 CG B:HIS145 4.8 14.3 1.0 CB B:HIS145 4.9 14.9 1.0 CE2 B:TYR38 4.9 15.0 1.0 N B:GLU112 5.0 14.5 1.0

Zinc binding site 4 out of 4 in the Structure of RVY_06210 at 1.45 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of RVY_06210 at 1.45 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:17.1 occ:1.00 OE1 B:GLU70 2.0 20.4 1.0 OE2 B:GLU31 2.0 18.3 1.0 ND1 B:HIS73 2.1 16.9 1.0 OD2 B:ASP142 2.3 24.8 1.0 OD1 B:ASP142 2.3 26.5 1.0 CG B:ASP142 2.6 21.5 1.0 CD B:GLU31 2.9 23.8 1.0 CD B:GLU70 3.0 19.7 1.0 CE1 B:HIS73 3.0 17.3 1.0 OE1 B:GLU31 3.1 24.6 1.0 CG B:HIS73 3.2 15.4 1.0 O B:HOH404 3.3 24.7 1.0 OE2 B:GLU70 3.3 25.9 1.0 ZN B:ZN301 3.4 17.9 0.5 CB B:HIS73 3.6 15.8 1.0 OH B:TYR119 4.0 17.0 1.0 CB B:ASP142 4.1 15.0 1.0 NE2 B:HIS73 4.2 16.9 1.0 CD2 B:HIS73 4.3 16.9 1.0 CG B:GLU31 4.3 18.1 1.0 OD2 B:ASP115 4.3 31.4 1.0 CG B:GLU70 4.3 17.0 1.0 CE1 B:TYR119 4.4 17.2 1.0 OD1 B:ASP115 4.5 34.3 1.0 CZ B:TYR119 4.6 16.0 1.0 CA B:GLU70 4.6 16.6 1.0 CG B:ASP115 4.7 32.1 1.0 CB B:GLU70 4.8 16.1 1.0 CA B:ASP142 4.9 14.7 1.0 ND1 B:HIS145 4.9 16.5 1.0 CE1 B:HIS145 5.0 15.9 1.0

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