Zinc in PDB 9lgi: Cryo-Em Structure of A Type II-D Crispr-CAS9 in Complex with Single- Guided Rna and Double-Stranded Dna

The binding sites of Zinc atom in the Cryo-Em Structure of A Type II-D Crispr-CAS9 in Complex with Single- Guided Rna and Double-Stranded Dna (pdb code 9lgi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryo-Em Structure of A Type II-D Crispr-CAS9 in Complex with Single- Guided Rna and Double-Stranded Dna, PDB code: 9lgi:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of A Type II-D Crispr-CAS9 in Complex with Single- Guided Rna and Double-Stranded Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of A Type II-D Crispr-CAS9 in Complex with Single- Guided Rna and Double-Stranded Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:137.4 occ:1.00 SG A:CYS371 2.3 32.8 1.0 SG A:CYS406 2.3 89.5 1.0 SG A:CYS374 2.3 86.6 1.0 SG A:CYS409 2.3 61.4 1.0 CB A:CYS371 3.2 64.3 1.0 CB A:CYS374 3.6 76.2 1.0 CB A:CYS406 3.8 77.6 1.0 N A:CYS406 3.9 73.2 1.0 CB A:CYS409 3.9 64.4 1.0 N A:CYS374 4.0 75.3 1.0 CG A:LYS376 4.3 81.0 1.0 CA A:CYS374 4.4 72.2 1.0 CA A:CYS406 4.5 76.6 1.0 CB A:TYR373 4.7 73.3 1.0 CA A:CYS371 4.7 62.1 1.0 N A:CYS409 4.8 78.0 1.0 C A:CYS405 4.9 77.3 1.0 CA A:CYS405 4.9 76.5 1.0 N A:SER407 5.0 85.5 1.0 C A:TYR373 5.0 73.5 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of A Type II-D Crispr-CAS9 in Complex with Single- Guided Rna and Double-Stranded Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of A Type II-D Crispr-CAS9 in Complex with Single- Guided Rna and Double-Stranded Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:126.6 occ:1.00 ND1 A:HIS279 2.1 100.4 1.0 CE1 A:HIS279 2.2 99.0 1.0 SG A:CYS192 2.3 98.8 1.0 SG A:CYS189 2.3 101.7 1.0 SG A:CYS276 2.4 112.4 1.0 CG A:HIS279 3.3 98.8 1.0 CB A:CYS189 3.4 90.2 1.0 NE2 A:HIS279 3.4 95.7 1.0 CB A:CYS276 3.7 98.2 1.0 N A:CYS192 3.7 94.5 1.0 CB A:CYS192 3.9 94.1 1.0 CD2 A:HIS279 3.9 98.9 1.0 N A:CYS276 4.1 101.3 1.0 CB A:VAL191 4.1 93.7 1.0 CB A:HIS279 4.3 97.6 1.0 CA A:CYS192 4.3 91.7 1.0 CG2 A:VAL191 4.5 89.6 1.0 CA A:CYS276 4.5 97.3 1.0 N A:VAL191 4.5 92.5 1.0 CA A:VAL191 4.7 92.2 1.0 C A:VAL191 4.7 93.5 1.0 CA A:CYS189 4.8 87.1 1.0 CD1 A:PHE275 4.8 82.9 1.0 O A:CYS192 4.9 92.6 1.0 C A:CYS192 4.9 91.9 1.0

K.Wang, J.Wang, X.Yang, W.Sun, G.Sheng, Y.Wang. Structural Insights Into Type II-D CAS9 and Its Robust Cleavage Activity. Nat Commun V. 16 7396 2025.
ISSN: ESSN 2041-1723
PubMed: 40790018
DOI: 10.1038/S41467-025-62128-8