Zinc in PDB 6yes: Crystal Structure of Type I-D Crispr-Cas Nuclease CAS10D

The structure of Crystal Structure of Type I-D Crispr-Cas Nuclease CAS10D, PDB code: 6yes was solved by D.E.Brodersen, L.B.Van, M.C.Manav, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	91.31 / 4.10
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	141.430, 141.430, 223.870, 90.00, 90.00, 90.00
R / Rfree (%)	34.3 / 37

The binding sites of Zinc atom in the Crystal Structure of Type I-D Crispr-Cas Nuclease CAS10D (pdb code 6yes). 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 Type I-D Crispr-Cas Nuclease CAS10D, PDB code: 6yes:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Type I-D Crispr-Cas Nuclease CAS10D


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 Type I-D Crispr-Cas Nuclease CAS10D within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:0.8 occ:1.00 SG A:CYS478 2.0 0.8 1.0 SG A:CYS432 2.4 0.7 1.0 SG A:CYS481 2.4 0.7 1.0 SG A:CYS429 2.6 0.9 1.0 CB A:CYS432 2.9 0.1 1.0 N A:CYS478 3.3 0.2 1.0 CB A:CYS478 3.3 0.7 1.0 CB A:CYS481 3.4 0.5 1.0 N A:CYS432 3.5 0.9 1.0 N A:CYS481 3.5 0.2 1.0 CG1 A:VAL431 3.7 1.0 1.0 CA A:CYS478 3.8 0.3 1.0 CA A:CYS432 3.8 0.2 1.0 CB A:CYS429 3.8 1.0 1.0 O A:CYS478 4.0 0.3 1.0 CA A:CYS481 4.0 0.5 1.0 C A:CYS478 4.2 0.2 1.0 C A:VAL477 4.2 0.6 1.0 CB A:ILE480 4.5 0.4 1.0 CA A:VAL477 4.5 1.0 1.0 C A:ILE480 4.6 0.9 1.0 C A:VAL431 4.7 0.9 1.0 N A:ILE480 4.7 0.6 1.0 C A:CYS432 4.8 0.1 1.0 CB A:VAL477 4.8 0.5 1.0 CA A:ILE480 4.8 0.1 1.0 CB A:VAL431 4.9 0.4 1.0 N A:VAL431 4.9 1.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Type I-D Crispr-Cas Nuclease CAS10D


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 Type I-D Crispr-Cas Nuclease CAS10D within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:0.5 occ:1.00 SG B:CYS478 2.3 0.9 1.0 N B:CYS478 2.9 0.5 1.0 CB B:CYS478 3.3 0.9 1.0 SG B:CYS481 3.5 0.5 1.0 C B:VAL477 3.6 0.7 1.0 CA B:VAL477 3.7 0.4 1.0 CA B:CYS478 3.7 0.1 1.0 N B:VAL477 4.1 0.4 1.0 O B:CYS478 4.4 0.3 1.0 CB B:CYS481 4.5 0.1 1.0 C B:CYS478 4.6 0.3 1.0 O B:VAL477 4.6 0.3 1.0

M.C.Manav, L.B.Van, J.Lin, A.Fuglsang, X.Peng, D.E.Brodersen. Structural Basis For Inhibition of An Archaeal Crispr-Cas Type I-D Large Subunit By An Anti-Crispr Protein. Nat Commun V. 11 5993 2020.
ISSN: ESSN 2041-1723
PubMed: 33239638
DOI: 10.1038/S41467-020-19847-X