Zinc in PDB 8wm4: Cryo-Em Structure of DICAS7-11 in Complex with Crrna

The binding sites of Zinc atom in the Cryo-Em Structure of DICAS7-11 in Complex with Crrna (pdb code 8wm4). 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 DICAS7-11 in Complex with Crrna, PDB code: 8wm4:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Cryo-Em Structure of DICAS7-11 in Complex with Crrna


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 DICAS7-11 in Complex with Crrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1701 b:203.6 occ:1.00 SG A:CYS126 2.3 162.0 1.0 SG A:CYS115 2.3 166.9 1.0 SG A:CYS86 2.3 164.0 1.0 SG A:CYS123 2.3 160.8 1.0 CB A:CYS86 3.1 162.2 1.0 CB A:CYS126 3.3 159.5 1.0 CB A:CYS123 3.6 157.5 1.0 N A:CYS126 3.7 158.7 1.0 CA A:CYS126 3.9 159.2 1.0 N A:CYS86 4.1 162.8 1.0 CB A:CYS115 4.1 164.1 1.0 NH1 A:ARG131 4.2 160.4 1.0 CA A:CYS86 4.2 162.3 1.0 N A:CYS123 4.6 158.7 1.0 CA A:CYS123 4.6 158.2 1.0 O A:CYS115 4.6 164.9 1.0 C A:PHE125 4.7 148.9 1.0 CZ A:ARG131 4.7 160.2 1.0 C A:CYS85 4.7 158.6 1.0 CB A:PHE125 4.8 148.6 1.0 N A:CYS115 4.9 164.5 1.0 CA A:CYS115 5.0 164.1 1.0

Zinc binding site 2 out of 4 in the Cryo-Em Structure of DICAS7-11 in Complex with Crrna


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 DICAS7-11 in Complex with Crrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1702 b:153.4 occ:1.00 SG A:CYS477 2.3 100.8 1.0 SG A:CYS463 2.3 141.7 1.0 CB A:CYS463 2.6 139.9 1.0 NH1 A:ARG452 3.7 59.1 1.0 CB A:CYS474 3.8 111.2 1.0 CB A:CYS477 4.0 94.2 1.0 CA A:CYS463 4.1 139.8 1.0 SG A:CYS472 4.1 121.7 1.0 SG A:CYS474 4.2 115.5 1.0 N A:CYS477 4.2 96.8 1.0 NE2 A:GLN456 4.3 76.6 1.0 CB A:ALA465 4.5 142.8 1.0 CB A:THR476 4.5 91.1 1.0 CA A:CYS477 4.6 94.1 1.0 C A:CYS463 4.8 140.0 1.0 CB A:CYS472 4.8 124.3 1.0 N A:CYS463 4.9 138.4 1.0 C A:THR476 5.0 90.8 1.0 CZ A:ARG452 5.0 61.2 1.0

Zinc binding site 3 out of 4 in the Cryo-Em Structure of DICAS7-11 in Complex with Crrna


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 DICAS7-11 in Complex with Crrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1703 b:205.4 occ:1.00 ND1 A:HIS703 2.1 156.9 1.0 SG A:CYS711 2.3 109.5 1.0 SG A:CYS708 2.3 124.8 1.0 SG A:CYS706 2.3 153.3 1.0 CE1 A:HIS703 3.0 154.7 1.0 CB A:CYS711 3.1 107.0 1.0 CG A:HIS703 3.1 155.4 1.0 CA A:HIS703 3.4 156.7 1.0 CB A:HIS703 3.5 156.7 1.0 CB A:CYS708 3.5 130.1 1.0 N A:CYS711 3.9 108.4 1.0 CA A:CYS711 4.1 104.1 1.0 CB A:CYS706 4.1 152.8 1.0 C A:HIS703 4.1 155.8 1.0 NE2 A:HIS703 4.2 153.4 1.0 CD2 A:HIS703 4.2 153.1 1.0 N A:CYS708 4.2 134.0 1.0 O A:HIS703 4.4 154.9 1.0 O A:CYS706 4.4 153.8 1.0 CA A:CYS708 4.4 134.4 1.0 N A:HIS703 4.5 156.5 1.0 C A:CYS706 4.7 153.3 1.0 CA A:CYS706 4.9 153.7 1.0 C A:CYS708 4.9 132.9 1.0 N A:SER704 5.0 164.7 1.0

Zinc binding site 4 out of 4 in the Cryo-Em Structure of DICAS7-11 in Complex with Crrna


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 DICAS7-11 in Complex with Crrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1704 b:130.6 occ:1.00 SG A:CYS1342 2.3 60.9 1.0 SG A:CYS1345 2.3 93.7 1.0 SG A:CYS965 2.3 57.2 1.0 SG A:CYS1312 2.3 112.5 1.0 CB A:CYS1345 3.2 65.8 1.0 CB A:CYS1312 3.3 99.6 1.0 CB A:CYS1342 3.4 68.2 1.0 CB A:CYS965 3.5 52.2 1.0 N A:CYS1312 4.1 97.9 1.0 N A:CYS1342 4.1 69.9 1.0 N A:CYS1345 4.2 65.6 1.0 CA A:CYS1312 4.3 98.5 1.0 CA A:CYS1345 4.3 61.0 1.0 CA A:CYS1342 4.3 65.6 1.0 N A:CYS965 4.4 60.9 1.0 CA A:CYS965 4.5 54.8 1.0 NH2 A:ARG876 4.6 94.9 1.0 CG A:ARG967 4.8 45.1 1.0 O A:CYS1342 4.9 70.5 1.0 C A:CYS1342 4.9 69.8 1.0

T.Hong, Q.Luo, H.Ma, X.Wang, X.Li, C.Shen, J.Pang, Y.Wang, Y.Chen, C.Zhang, Z.Su, H.Dong, X.Tang. Structural Basis of Negative Regulation of Crispr-CAS7-11 By Tpr-Chat. Signal Transduct Target Ther V. 9 111 2024.
ISSN: ESSN 2059-3635
PubMed: 38735995
DOI: 10.1038/S41392-024-01821-4