Zinc in PDB 9i8y: SPCAS12CAS12F1 in Complex with Sgrna and Cognate Dna

The binding sites of Zinc atom in the SPCAS12CAS12F1 in Complex with Sgrna and Cognate Dna (pdb code 9i8y). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the SPCAS12CAS12F1 in Complex with Sgrna and Cognate Dna, PDB code: 9i8y:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the SPCAS12CAS12F1 in Complex with Sgrna and Cognate Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of SPCAS12CAS12F1 in Complex with Sgrna and Cognate Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:170.3 occ:1.00 SG A:CYS398 2.3 149.1 1.0 SG A:CYS395 2.3 150.5 1.0 SG A:CYS376 2.3 138.3 1.0 SG A:CYS379 2.3 140.1 1.0 CB A:CYS376 2.8 129.7 1.0 CB A:CYS395 3.0 139.9 1.0 CB A:CYS398 3.5 145.0 1.0 CB A:CYS379 3.5 135.4 1.0 N A:CYS379 4.0 134.9 1.0 N A:CYS398 4.2 145.9 1.0 CA A:CYS379 4.3 135.1 1.0 CA A:CYS376 4.3 123.7 1.0 CA A:CYS398 4.4 147.8 1.0 CA A:CYS395 4.5 139.5 1.0 CB A:TYR400 4.8 136.7 1.0 N A:GLY380 4.9 131.6 1.0 N A:GLY399 5.0 143.9 1.0 C A:CYS379 5.0 136.7 1.0 CB A:MET378 5.0 127.1 1.0

Zinc binding site 2 out of 3 in the SPCAS12CAS12F1 in Complex with Sgrna and Cognate Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of SPCAS12CAS12F1 in Complex with Sgrna and Cognate Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:119.6 occ:1.00 SG B:CYS376 2.3 92.8 1.0 SG B:CYS398 2.3 121.2 1.0 SG B:CYS379 2.3 96.6 1.0 SG B:CYS395 2.3 98.0 1.0 CB B:CYS376 3.1 88.8 1.0 CB B:CYS398 3.6 107.4 1.0 CB B:CYS395 3.7 95.7 1.0 CB B:CYS379 3.8 99.1 1.0 N B:CYS398 3.9 101.6 1.0 N B:CYS379 4.2 99.0 1.0 CA B:CYS398 4.2 104.1 1.0 OE1 B:GLN397 4.3 103.5 1.0 CB B:TYR400 4.5 99.3 1.0 CB B:GLN397 4.5 103.8 1.0 CA B:CYS379 4.5 99.0 1.0 CA B:CYS376 4.5 85.9 1.0 CB B:TYR381 4.7 95.5 1.0 C B:GLN397 4.8 102.9 1.0 C B:CYS398 4.8 104.9 1.0 CA B:CYS395 4.8 96.8 1.0 CB B:MET378 4.9 100.7 1.0 N B:TYR400 4.9 104.1 1.0 O B:CYS395 4.9 104.6 1.0 N B:GLY399 4.9 103.6 1.0

Zinc binding site 3 out of 3 in the SPCAS12CAS12F1 in Complex with Sgrna and Cognate Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of SPCAS12CAS12F1 in Complex with Sgrna and Cognate Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:135.1 occ:1.00 SG B:CYS409 2.3 114.1 1.0 SG B:CYS419 2.3 123.3 1.0 SG B:CYS422 2.3 112.5 1.0 SG B:CYS406 2.3 111.7 1.0 CB B:CYS406 2.8 107.7 1.0 CB B:CYS409 3.0 107.9 1.0 CB B:CYS419 3.2 114.7 1.0 CB B:CYS422 3.3 112.1 1.0 N B:CYS409 3.7 100.5 1.0 N B:CYS422 3.8 115.4 1.0 CA B:CYS409 3.9 103.7 1.0 CA B:CYS422 4.2 112.3 1.0 CA B:CYS406 4.3 105.2 1.0 CB B:GLU421 4.5 118.7 1.0 CA B:CYS419 4.7 113.7 1.0 C B:ASN408 4.7 99.3 1.0 CB B:ASN408 4.7 94.9 1.0 C B:GLU421 4.7 116.0 1.0 C B:CYS406 4.8 100.5 1.0 C B:CYS409 4.8 104.4 1.0 N B:GLU421 4.9 116.1 1.0 N B:ASN408 4.9 94.4 1.0 CA B:GLU421 5.0 116.4 1.0 N B:ARG410 5.0 102.7 1.0

J.Madariaga-Marcos, M.Baltramonaitis, S.Henkel-Heinecke, D.J.Kauert, P.Irmisch, G.Bigelyte-Stankeviciene, A.Silanskas, T.Karvelis, V.Siksnys, G.Sasnauskas, R.Seidel. Structural and Mechanistic Insights Into the Sequential Dsdna Cleavage By SPCAS12F1. Nucleic Acids Res. V. 53 2025.
ISSN: ESSN 1362-4962
PubMed: 40650969
DOI: 10.1093/NAR/GKAF588