Zinc in PDB 8u13: Cryo-Em Structure of the Human Nucleosome Core Particle Ubiquitylated at Histone H2A Lysine 15 in Complex with RNF168-UBCH5C (Class 1)

All present enzymatic activity of Cryo-Em Structure of the Human Nucleosome Core Particle Ubiquitylated at Histone H2A Lysine 15 in Complex with RNF168-UBCH5C (Class 1):
2.3.2.27;

The binding sites of Zinc atom in the Cryo-Em Structure of the Human Nucleosome Core Particle Ubiquitylated at Histone H2A Lysine 15 in Complex with RNF168-UBCH5C (Class 1) (pdb code 8u13). 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 Structure of the Human Nucleosome Core Particle Ubiquitylated at Histone H2A Lysine 15 in Complex with RNF168-UBCH5C (Class 1), PDB code: 8u13:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of the Human Nucleosome Core Particle Ubiquitylated at Histone H2A Lysine 15 in Complex with RNF168-UBCH5C (Class 1)


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 Human Nucleosome Core Particle Ubiquitylated at Histone H2A Lysine 15 in Complex with RNF168-UBCH5C (Class 1) within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn301 b:471.1 occ:1.00 ND1 K:HIS33 2.1 412.3 1.0 SG K:CYS51 2.3 417.1 1.0 SG K:CYS54 2.3 421.6 1.0 SG K:CYS31 2.3 394.4 1.0 CE1 K:HIS33 2.8 412.3 1.0 CG K:HIS33 2.9 412.3 1.0 CB K:CYS31 3.3 394.4 1.0 CB K:CYS51 3.4 417.1 1.0 CB K:HIS33 3.4 412.3 1.0 CB K:CYS54 3.6 421.6 1.0 NE2 K:HIS33 3.7 412.3 1.0 N K:CYS54 3.8 421.6 1.0 CD2 K:HIS33 3.8 412.3 1.0 CA K:CYS54 4.2 421.6 1.0 CB K:PHE53 4.4 423.1 1.0 NE K:ARG56 4.5 371.0 1.0 CD1 K:LEU29 4.5 384.4 1.0 CB K:ARG56 4.7 371.0 1.0 CA K:CYS31 4.7 394.4 1.0 NH2 K:ARG56 4.7 371.0 1.0 CA K:HIS33 4.8 412.3 1.0 C K:PHE53 4.8 423.1 1.0 O K:CYS31 4.8 394.4 1.0 CA K:CYS51 4.8 417.1 1.0 C K:CYS54 4.8 421.6 1.0 N K:PHE53 4.9 423.1 1.0 N K:HIS33 4.9 412.3 1.0 CD2 K:PHE53 4.9 423.1 1.0 CA K:PHE53 4.9 423.1 1.0 C K:CYS31 5.0 394.4 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of the Human Nucleosome Core Particle Ubiquitylated at Histone H2A Lysine 15 in Complex with RNF168-UBCH5C (Class 1)


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 Human Nucleosome Core Particle Ubiquitylated at Histone H2A Lysine 15 in Complex with RNF168-UBCH5C (Class 1) within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn302 b:530.7 occ:1.00 CB K:CYS39 2.3 418.5 1.0 SG K:CYS16 2.3 424.3 1.0 SG K:CYS19 2.3 433.9 1.0 SG K:CYS39 2.3 418.5 1.0 SG K:CYS36 2.3 418.6 1.0 CB K:CYS16 3.2 424.3 1.0 CB K:CYS19 3.7 433.9 1.0 CA K:CYS39 3.8 418.5 1.0 CB K:CYS36 3.9 418.6 1.0 N K:CYS36 4.1 418.6 1.0 N K:CYS19 4.1 433.9 1.0 N K:CYS39 4.4 418.5 1.0 CA K:CYS36 4.5 418.6 1.0 CA K:CYS19 4.6 433.9 1.0 CD1 K:ILE18 4.6 414.5 1.0 CA K:CYS16 4.6 424.3 1.0 C K:CYS39 4.7 418.5 1.0 O K:CYS36 4.7 418.6 1.0 CB K:LEU35 4.7 409.9 1.0 CB K:ILE18 4.8 414.5 1.0

Q.Hu, M.V.Botuyan, D.Zhao, G.Cui, G.Mer. Cryo-Em Structure of the Human Nucleosome Core Particle Ubiquitylated at Histone H2A Lysine 15 in Complex with RNF168-UBCH5C (Class 1) To Be Published.