Zinc in PDB 7c7l: Cryo-Em Structure of the CAS12F1-Sgrna-Target Dna Complex

The binding sites of Zinc atom in the Cryo-Em Structure of the CAS12F1-Sgrna-Target Dna Complex (pdb code 7c7l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Cryo-Em Structure of the CAS12F1-Sgrna-Target Dna Complex, PDB code: 7c7l:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Cryo-Em Structure of the CAS12F1-Sgrna-Target Dna Complex


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 the CAS12F1-Sgrna-Target Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:81.5 occ:1.00 ND1 A:HIS53 2.0 97.2 1.0 SG A:CYS69 2.3 80.5 1.0 SG A:CYS50 2.4 94.4 1.0 SG A:CYS72 2.4 79.1 1.0 CE1 A:HIS53 2.9 0.6 1.0 CG A:HIS53 3.1 0.1 1.0 CB A:CYS69 3.3 77.0 1.0 N A:CYS72 3.4 78.1 1.0 CB A:CYS72 3.5 76.6 1.0 CB A:CYS50 3.5 98.2 1.0 CB A:HIS53 3.6 97.3 1.0 C A:PHE71 3.9 77.5 1.0 CA A:CYS72 3.9 80.0 1.0 NE2 A:HIS53 4.1 0.4 1.0 N A:CYS50 4.1 91.9 1.0 CD2 A:HIS53 4.2 0.2 1.0 CB A:PHE71 4.3 99.7 1.0 CA A:CYS50 4.3 97.1 1.0 O A:PHE71 4.4 79.0 1.0 CA A:PHE71 4.5 92.8 1.0 N A:PHE71 4.6 95.4 1.0 CA A:CYS69 4.7 77.0 1.0 N A:HIS53 4.7 89.5 1.0 CA A:HIS53 4.8 90.3 1.0 O A:CYS50 4.9 95.0 1.0 C A:CYS50 4.9 95.5 1.0

Zinc binding site 2 out of 3 in the Cryo-Em Structure of the CAS12F1-Sgrna-Target Dna Complex


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 the CAS12F1-Sgrna-Target Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:0.9 occ:1.00 SG A:CYS478 2.3 1.0 1.0 SG A:CYS475 2.3 1.0 1.0 SG A:CYS503 2.3 0.5 1.0 SG A:CYS500 2.3 0.1 1.0 CB A:CYS500 3.1 0.3 1.0 CB A:CYS475 3.2 0.2 1.0 CB A:CYS478 3.2 0.4 1.0 CB A:CYS503 3.3 0.7 1.0 N A:CYS503 3.8 0.3 1.0 N A:CYS478 3.9 0.9 1.0 CA A:CYS503 4.0 0.1 1.0 CA A:CYS478 4.0 0.2 1.0 C A:LYS502 4.2 0.9 1.0 N A:GLY479 4.4 0.9 1.0 CA A:CYS500 4.6 0.5 1.0 C A:CYS478 4.6 0.2 1.0 CB A:LYS502 4.6 1.0 1.0 CA A:CYS475 4.6 1.0 1.0 CB A:HIS480 4.6 0.8 1.0 C A:CYS503 4.6 0.0 1.0 N A:LYS502 4.7 0.6 1.0 N A:HIS480 4.7 1.0 1.0 O A:LYS502 4.7 0.8 1.0 CA A:LYS502 4.7 0.1 1.0 C A:CYS500 5.0 0.2 1.0

Zinc binding site 3 out of 3 in the Cryo-Em Structure of the CAS12F1-Sgrna-Target Dna Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of the CAS12F1-Sgrna-Target Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:0.0 occ:1.00 SG B:CYS503 2.3 0.3 1.0 SG B:CYS500 2.3 1.0 1.0 SG B:CYS478 2.3 1.0 1.0 SG B:CYS475 2.3 0.6 1.0 CB B:CYS500 3.1 0.7 1.0 CB B:CYS475 3.1 0.7 1.0 CB B:CYS478 3.2 0.5 1.0 CB B:CYS503 3.2 1.0 1.0 N B:CYS478 3.8 0.9 1.0 N B:CYS503 3.9 0.8 1.0 CA B:CYS478 4.0 0.2 1.0 N B:GLY479 4.1 1.0 1.0 CA B:CYS503 4.1 0.4 1.0 C B:CYS478 4.5 0.2 1.0 CA B:CYS500 4.6 0.1 1.0 N B:HIS480 4.6 0.3 1.0 CA B:CYS475 4.6 0.0 1.0 C B:LYS477 4.7 0.6 1.0 C B:CYS503 4.8 0.7 1.0 CB B:LYS477 4.9 0.9 1.0 N B:ASN504 5.0 0.8 1.0

S.N.Takeda, R.Nakagawa, S.Okazaki, H.Hirano, K.Kobayashi, T.Kusakizako, T.Nishizawa, K.Yamashita, H.Nishimasu, O.Nureki. Structure of the Miniature Type V-F Crispr-Cas Effector Enzyme Mol.Cell V. 81 2020.
ISSN: ISSN 1097-2765
DOI: 10.1016/J.MOLCEL.2020.11.035