Zinc in PDB 8x7i: Cryo-Em Structures of RNF168/UBCH5C-Ub in Complex with H2AK13UB Nucleosomes Determined By Intein-Based E2-Ub-Ncp Conjugation Strategy

All present enzymatic activity of Cryo-Em Structures of RNF168/UBCH5C-Ub in Complex with H2AK13UB Nucleosomes Determined By Intein-Based E2-Ub-Ncp Conjugation Strategy:
2.3.2.23; 2.3.2.24; 2.3.2.27;

The binding sites of Zinc atom in the Cryo-Em Structures of RNF168/UBCH5C-Ub in Complex with H2AK13UB Nucleosomes Determined By Intein-Based E2-Ub-Ncp Conjugation Strategy (pdb code 8x7i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryo-Em Structures of RNF168/UBCH5C-Ub in Complex with H2AK13UB Nucleosomes Determined By Intein-Based E2-Ub-Ncp Conjugation Strategy, PDB code: 8x7i:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structures of RNF168/UBCH5C-Ub in Complex with H2AK13UB Nucleosomes Determined By Intein-Based E2-Ub-Ncp Conjugation Strategy


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structures of RNF168/UBCH5C-Ub in Complex with H2AK13UB Nucleosomes Determined By Intein-Based E2-Ub-Ncp Conjugation Strategy within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn201 b:257.7 occ:1.00 CE1 L:HIS33 2.0 224.0 1.0 ND1 L:HIS33 2.1 224.0 1.0 SG L:CYS51 2.3 210.1 1.0 SG L:CYS31 2.3 218.0 1.0 SG L:CYS54 2.3 213.5 1.0 NE2 L:HIS33 2.8 224.0 1.0 CG L:HIS33 3.0 224.0 1.0 CB L:CYS31 3.2 218.0 1.0 CD2 L:HIS33 3.4 224.0 1.0 CB L:CYS51 3.5 210.1 1.0 N L:CYS54 3.6 213.5 1.0 CB L:CYS54 3.7 213.5 1.0 CB L:PHE53 3.8 217.7 1.0 CD2 L:PHE53 3.9 217.7 1.0 CB L:HIS33 4.1 224.0 1.0 CA L:CYS54 4.1 213.5 1.0 O L:CYS31 4.3 218.0 1.0 CG L:PHE53 4.3 217.7 1.0 C L:PHE53 4.4 217.7 1.0 CA L:PHE53 4.5 217.7 1.0 CB L:ARG56 4.5 191.9 1.0 CA L:CYS31 4.6 218.0 1.0 N L:PHE53 4.6 217.7 1.0 C L:CYS54 4.7 213.5 1.0 C L:CYS31 4.8 218.0 1.0 CD1 L:LEU29 4.8 216.7 1.0 CA L:CYS51 4.9 210.1 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structures of RNF168/UBCH5C-Ub in Complex with H2AK13UB Nucleosomes Determined By Intein-Based E2-Ub-Ncp Conjugation Strategy


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structures of RNF168/UBCH5C-Ub in Complex with H2AK13UB Nucleosomes Determined By Intein-Based E2-Ub-Ncp Conjugation Strategy within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn202 b:299.0 occ:1.00 SG L:CYS36 2.3 253.7 1.0 SG L:CYS16 2.3 283.0 1.0 SG L:CYS39 2.3 248.3 1.0 SG L:CYS19 2.3 282.5 1.0 CB L:CYS19 2.8 282.5 1.0 CB L:CYS16 2.9 283.0 1.0 CB L:CYS39 3.0 248.3 1.0 N L:CYS19 3.3 282.5 1.0 CA L:CYS19 3.6 282.5 1.0 CB L:CYS36 3.7 253.7 1.0 N L:CYS36 4.2 253.7 1.0 CA L:CYS39 4.2 248.3 1.0 N L:CYS39 4.2 248.3 1.0 CA L:CYS16 4.4 283.0 1.0 C L:CYS19 4.5 282.5 1.0 C L:ILE18 4.5 270.0 1.0 CA L:CYS36 4.5 253.7 1.0 CB L:ILE18 4.6 270.0 1.0 N L:MET20 4.7 282.3 1.0 N L:ILE18 4.7 270.0 1.0 CA L:ILE18 4.9 270.0 1.0 C L:CYS16 5.0 283.0 1.0

H.Ai, Z.Tong, Z.Deng, Q.Shi, S.Tao, J.Liang, M.Sun, X.Wu, Q.Zheng, L.Liang, J.B.Li, S.Gao, C.Tian, L.Liu, M.Pan. Capturing Snapshots of Nucleosomal H2A K13/K15 Ubiquitination Mediated By the Monomeric E3 Ligase RNF168 Biorxiv 2024.
ISSN: ISSN 2692-8205
DOI: 10.1101/2024.01.02.573964