Zinc in PDB 5isy: Crystal Structure of Nudix Family Protein with Nad

All present enzymatic activity of Crystal Structure of Nudix Family Protein with Nad:
3.6.1.22;

The structure of Crystal Structure of Nudix Family Protein with Nad, PDB code: 5isy was solved by D.Zhang, Z.Guan, T.Zou, P.Yin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.00 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.411, 98.702, 113.739, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 24.4

The binding sites of Zinc atom in the Crystal Structure of Nudix Family Protein with Nad (pdb code 5isy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Nudix Family Protein with Nad, PDB code: 5isy:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Nudix Family Protein with Nad


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Nudix Family Protein with Nad within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:34.0 occ:1.00 SG A:CYS98 2.3 22.3 1.0 CB A:CYS101 2.4 44.3 1.0 CB A:CYS119 2.4 23.2 1.0 SG A:CYS101 2.5 38.2 1.0 CB A:CYS116 3.0 29.0 1.0 CB A:CYS98 3.1 21.1 1.0 N A:CYS119 3.3 28.2 1.0 CA A:CYS119 3.4 32.5 1.0 CA A:CYS101 3.8 35.1 1.0 N A:CYS101 4.1 30.9 1.0 C A:CYS119 4.4 34.1 1.0 CA A:CYS116 4.5 28.2 1.0 C A:HIS118 4.6 37.1 1.0 CA A:CYS98 4.6 25.0 1.0 CB A:TYR100 4.6 20.9 1.0 O A:CYS119 4.8 35.0 1.0 CB A:HIS118 4.8 40.9 1.0 C A:CYS101 4.8 31.6 1.0 C A:TYR100 4.9 30.6 1.0 N A:HIS118 4.9 37.5 1.0 CB A:HIS103 5.0 27.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Nudix Family Protein with Nad


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Nudix Family Protein with Nad within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:28.6 occ:1.00 SG C:CYS119 2.2 28.1 1.0 SG C:CYS116 2.3 24.2 1.0 SG C:CYS101 2.3 21.4 1.0 SG C:CYS98 2.4 19.7 1.0 CB C:CYS98 3.1 19.8 1.0 CB C:CYS116 3.2 19.9 1.0 CB C:CYS119 3.3 27.3 1.0 CB C:CYS101 3.3 21.6 1.0 N C:CYS119 3.8 32.4 1.0 N C:CYS101 3.8 23.2 1.0 CA C:CYS119 4.1 31.9 1.0 CA C:CYS101 4.1 24.6 1.0 CB C:TYR100 4.5 20.5 1.0 CA C:CYS98 4.6 23.0 1.0 CA C:CYS116 4.6 38.8 1.0 C C:CYS119 4.7 40.6 1.0 N C:GLY102 4.7 26.0 1.0 C C:CYS101 4.7 21.8 1.0 N C:ARG120 4.9 45.6 1.0 C C:HIS118 4.9 35.7 1.0 C C:TYR100 4.9 23.2 1.0 CB C:HIS118 4.9 31.9 1.0

D.Zhang, Y.Liu, Q.Wang, Z.Guan, J.Wang, J.Liu, T.Zou, P.Yin. Structural Basis of Prokaryotic Nad-Rna Decapping By Nudc Cell Res. V. 26 1062 2016.
ISSN: ISSN 1001-0602
PubMed: 27561816
DOI: 10.1038/CR.2016.98