Zinc in PDB 6vbw: Cryo-Em Structure of Cascade-Tniq-Dsdna Ternary Complex

The binding sites of Zinc atom in the Cryo-Em Structure of Cascade-Tniq-Dsdna Ternary Complex (pdb code 6vbw). 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 Cascade-Tniq-Dsdna Ternary Complex, PDB code: 6vbw:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Cryo-Em Structure of Cascade-Tniq-Dsdna Ternary 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 Cascade-Tniq-Dsdna Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn401 b:97.4 occ:1.00 N I:CYS131 2.2 80.8 1.0 SG I:CYS131 2.5 80.8 1.0 SG I:CYS128 2.5 80.4 1.0 CB I:CYS131 2.9 80.8 1.0 ND1 I:HIS153 3.0 75.4 1.0 C I:LEU130 3.0 76.5 1.0 CA I:CYS131 3.0 80.8 1.0 CE1 I:HIS153 3.0 75.4 1.0 CB I:CYS128 3.2 80.4 1.0 CB I:LEU130 3.4 76.5 1.0 CA I:LEU130 3.5 76.5 1.0 N I:LEU130 3.6 76.5 1.0 O I:CYS128 3.8 80.4 1.0 O I:LEU130 3.9 76.5 1.0 SG I:CYS150 3.9 79.2 1.0 NE2 I:HIS153 4.0 75.4 1.0 CG I:HIS153 4.1 75.4 1.0 C I:CYS128 4.1 80.4 1.0 CA I:CYS128 4.3 80.4 1.0 C I:CYS131 4.4 80.8 1.0 CD2 I:HIS153 4.6 75.4 1.0 C I:PRO129 4.7 76.9 1.0 N I:LEU132 4.7 75.0 1.0 CG I:LEU130 4.8 76.5 1.0 N I:PRO129 4.9 76.9 1.0 CB I:HIS153 4.9 75.4 1.0

Zinc binding site 2 out of 4 in the Cryo-Em Structure of Cascade-Tniq-Dsdna Ternary 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 Cascade-Tniq-Dsdna Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn402 b:0.0 occ:1.00 SG I:CYS161 2.5 82.7 1.0 SG I:CYS181 2.6 82.9 1.0 CB I:CYS161 3.1 82.7 1.0 SG I:CYS178 3.4 81.1 1.0 CB I:CYS178 3.7 81.1 1.0 CB I:CYS181 3.7 82.9 1.0 N I:CYS181 4.1 82.9 1.0 CB I:CYS163 4.1 79.2 1.0 N I:CYS163 4.2 79.2 1.0 N I:SER162 4.3 76.0 1.0 SG I:CYS163 4.3 79.2 1.0 CA I:CYS161 4.5 82.7 1.0 CA I:CYS181 4.6 82.9 1.0 C I:CYS161 4.6 82.7 1.0 CA I:CYS163 4.8 79.2 1.0 CB I:LYS165 4.8 80.8 1.0 N I:LYS180 4.9 79.8 1.0 O I:LYS165 4.9 80.8 1.0 CB I:LYS180 5.0 79.8 1.0

Zinc binding site 3 out of 4 in the Cryo-Em Structure of Cascade-Tniq-Dsdna Ternary 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 Cascade-Tniq-Dsdna Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn401 b:0.1 occ:1.00 SG J:CYS131 2.5 93.0 1.0 CE1 J:HIS153 3.2 84.3 1.0 ND2 J:ASN135 3.4 92.3 1.0 CE1 J:HIS151 3.5 88.4 1.0 CB J:CYS131 3.8 93.0 1.0 ND1 J:HIS153 4.0 84.3 1.0 NE2 J:HIS151 4.1 88.4 1.0 NE2 J:HIS153 4.1 84.3 1.0 ND1 J:HIS151 4.3 88.4 1.0 SG J:CYS150 4.4 86.5 1.0 CG J:ASN135 4.6 92.3 1.0 CA J:CYS131 4.8 93.0 1.0

Zinc binding site 4 out of 4 in the Cryo-Em Structure of Cascade-Tniq-Dsdna Ternary Complex


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 Cascade-Tniq-Dsdna Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn402 b:0.9 occ:1.00 O J:GLU183 2.4 94.1 1.0 CB J:GLU183 2.6 94.1 1.0 C J:GLU183 2.6 94.1 1.0 O J:PRO184 2.8 92.8 1.0 CA J:GLU183 2.9 94.1 1.0 SG J:CYS161 3.2 84.9 1.0 C J:PRO184 3.2 92.8 1.0 N J:PRO184 3.4 92.8 1.0 N J:GLU183 3.4 94.1 1.0 SG J:CYS181 3.5 96.4 1.0 CA J:PRO184 3.8 92.8 1.0 CG J:GLU183 3.9 94.1 1.0 N J:ILE185 3.9 88.0 1.0 CA J:ILE185 4.1 88.0 1.0 CB J:CYS178 4.5 96.4 1.0 CG1 J:ILE185 4.6 88.0 1.0 CD J:PRO184 4.6 92.8 1.0 C J:LYS182 4.7 93.1 1.0 CB J:CYS161 4.9 84.9 1.0 CB J:ILE185 5.0 88.0 1.0

N.Jia, W.Xie, M.J.De La Cruz, E.T.Eng, D.J.Patel. Structure-Function Insights Into the Initial Step of Dna Integration By A Crispr-Cas-Transposon Complex. Cell Res. 2020.
ISSN: ISSN 1001-0602
PubMed: 31925391
DOI: 10.1038/S41422-019-0272-2