Zinc in PDB 8d1v: Cryo-Em Structure of Guide Rna and Target Rna Bound CAS7-11

The binding sites of Zinc atom in the Cryo-Em Structure of Guide Rna and Target Rna Bound CAS7-11 (pdb code 8d1v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Cryo-Em Structure of Guide Rna and Target Rna Bound CAS7-11, PDB code: 8d1v:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Cryo-Em Structure of Guide Rna and Target Rna Bound CAS7-11


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 Guide Rna and Target Rna Bound CAS7-11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1701 b:69.8 occ:1.00 SG A:CYS1312 2.3 42.3 1.0 SG A:CYS1345 2.3 42.8 1.0 SG A:CYS965 2.3 16.2 1.0 SG A:CYS1342 2.3 16.5 1.0 CB A:CYS1342 3.2 24.2 1.0 CB A:CYS1345 3.3 13.5 1.0 CB A:CYS1312 3.3 39.3 1.0 CB A:CYS965 3.5 17.0 1.0 N A:CYS1312 3.8 41.8 1.0 N A:CYS1342 3.8 26.0 1.0 CA A:CYS1342 4.1 20.9 1.0 N A:CYS965 4.1 14.6 1.0 CA A:CYS1312 4.2 39.7 1.0 N A:CYS1345 4.2 12.8 1.0 CA A:CYS1345 4.3 10.7 1.0 CA A:CYS965 4.3 17.4 1.0 CG A:ARG967 4.5 10.2 1.0 NH2 A:ARG876 4.6 37.1 1.0 C A:CYS1342 4.8 22.6 1.0 NE A:ARG876 4.8 37.8 1.0 C A:PRO1311 4.8 37.5 1.0 O A:CYS1342 4.9 24.7 1.0 O A:CYS965 4.9 21.4 1.0 C A:CYS965 4.9 21.2 1.0 CZ A:ARG876 4.9 38.7 1.0 CA A:PRO1311 5.0 35.7 1.0 C A:LEU1341 5.0 32.7 1.0

Zinc binding site 2 out of 4 in the Cryo-Em Structure of Guide Rna and Target Rna Bound CAS7-11


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 Guide Rna and Target Rna Bound CAS7-11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1702 b:78.0 occ:1.00 CB A:CYS708 1.8 42.8 1.0 ND1 A:HIS703 2.1 48.7 1.0 SG A:CYS706 2.3 64.5 1.0 SG A:CYS711 2.3 40.1 1.0 SG A:CYS708 2.3 47.8 1.0 CE1 A:HIS703 2.4 49.8 1.0 CA A:CYS708 3.2 42.0 1.0 CG A:HIS703 3.4 48.0 1.0 CB A:CYS706 3.5 58.0 1.0 CB A:CYS711 3.7 31.4 1.0 NE2 A:HIS703 3.7 49.0 1.0 N A:CYS708 3.8 47.1 1.0 CB A:HIS703 4.2 48.6 1.0 CD2 A:HIS703 4.2 47.3 1.0 N A:CYS711 4.2 33.9 1.0 C A:CYS708 4.3 39.6 1.0 CA A:HIS703 4.6 52.4 1.0 CA A:CYS711 4.6 28.8 1.0 OE1 A:GLU693 4.6 59.9 1.0 C A:GLU707 4.7 56.1 1.0 CA A:CYS706 4.8 58.8 1.0 C A:CYS706 4.8 57.1 1.0 O A:CYS708 4.8 42.0 1.0 N A:LEU709 5.0 34.2 1.0

Zinc binding site 3 out of 4 in the Cryo-Em Structure of Guide Rna and Target Rna Bound CAS7-11


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 Guide Rna and Target Rna Bound CAS7-11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1703 b:80.5 occ:1.00 SG A:CYS477 2.3 37.7 1.0 SG A:CYS463 2.3 49.2 1.0 SG A:CYS474 2.3 31.9 1.0 SG A:CYS472 2.3 43.9 1.0 CB A:CYS472 3.1 34.8 1.0 CB A:CYS477 3.3 25.6 1.0 CB A:CYS474 3.4 29.4 1.0 CB A:CYS463 3.5 36.3 1.0 N A:CYS477 4.1 22.1 1.0 N A:CYS474 4.2 30.9 1.0 CA A:CYS477 4.3 19.3 1.0 CB A:ALA465 4.3 44.9 1.0 CA A:CYS474 4.3 29.7 1.0 CA A:CYS472 4.4 37.5 1.0 CA A:CYS463 4.5 37.3 1.0 C A:CYS472 4.5 35.0 1.0 O A:CYS472 4.7 38.9 1.0 C A:CYS474 4.9 29.8 1.0 N A:MET473 4.9 33.2 1.0 O A:CYS474 5.0 33.3 1.0

Zinc binding site 4 out of 4 in the Cryo-Em Structure of Guide Rna and Target Rna Bound CAS7-11


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of Guide Rna and Target Rna Bound CAS7-11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1704 b:93.5 occ:1.00 SG A:CYS86 2.3 54.1 1.0 SG A:CYS126 2.3 54.3 1.0 SG A:CYS123 2.3 59.6 1.0 SG A:CYS115 2.3 59.0 1.0 CB A:CYS115 3.3 54.8 1.0 CB A:CYS123 3.4 52.9 1.0 CB A:CYS126 3.5 48.3 1.0 CB A:CYS86 3.6 51.3 1.0 N A:CYS115 3.8 54.9 1.0 N A:CYS123 3.9 56.0 1.0 N A:CYS86 4.1 51.7 1.0 CA A:CYS115 4.2 54.6 1.0 CA A:CYS123 4.2 55.1 1.0 N A:CYS126 4.2 48.0 1.0 CA A:CYS86 4.4 51.0 1.0 NH1 A:ARG131 4.4 53.6 1.0 CA A:CYS126 4.5 49.0 1.0 O A:CYS123 4.7 55.6 1.0 C A:CYS123 4.7 55.9 1.0 O A:CYS86 4.8 53.6 1.0 C A:CYS86 4.8 51.1 1.0 C A:PRO114 4.9 52.5 1.0

H.N.Goswami, J.Rai, A.Das, H.Li. Molecular Mechanism of Active CAS7-11 in Processing Crispr Rna and Interfering Target Rna. Elife V. 11 2022.
ISSN: ESSN 2050-084X
PubMed: 36190192
DOI: 10.7554/ELIFE.81678