Zinc in PDB 6tm5: Cryo-Em Structure of the Anaphase-Promoting Complex/Cyclosome, in Complex with the NEK2A Substrate at 3.9 Angstrom Resolution

All present enzymatic activity of Cryo-Em Structure of the Anaphase-Promoting Complex/Cyclosome, in Complex with the NEK2A Substrate at 3.9 Angstrom Resolution:
2.7.11.1;

The binding sites of Zinc atom in the Cryo-Em Structure of the Anaphase-Promoting Complex/Cyclosome, in Complex with the NEK2A Substrate at 3.9 Angstrom Resolution (pdb code 6tm5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Cryo-Em Structure of the Anaphase-Promoting Complex/Cyclosome, in Complex with the NEK2A Substrate at 3.9 Angstrom Resolution, PDB code: 6tm5:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Cryo-Em Structure of the Anaphase-Promoting Complex/Cyclosome, in Complex with the NEK2A Substrate at 3.9 Angstrom Resolution


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 Anaphase-Promoting Complex/Cyclosome, in Complex with the NEK2A Substrate at 3.9 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:0.7 occ:1.00 ND1 B:HIS56 2.2 0.5 1.0 CB B:CYS23 2.3 0.4 1.0 CE1 B:HIS56 2.3 0.5 1.0 O B:MET28 2.4 0.4 1.0 SG B:CYS23 2.6 0.4 1.0 C B:MET28 3.3 0.4 1.0 N B:MET28 3.5 0.4 1.0 CG B:HIS56 3.6 0.5 1.0 CB B:MET28 3.6 0.4 1.0 NE2 B:HIS56 3.7 0.5 1.0 CA B:MET28 3.7 0.4 1.0 CA B:CYS23 3.8 0.4 1.0 CD2 B:HIS56 4.2 0.5 1.0 CB B:CYS34 4.3 0.5 1.0 N B:CYS23 4.4 0.4 1.0 CB B:HIS56 4.4 0.5 1.0 N B:ARG27 4.5 0.7 1.0 CB B:CYS26 4.5 0.3 1.0 N B:CYS26 4.6 0.3 1.0 N B:ALA29 4.6 0.5 1.0 C B:ARG27 4.6 0.7 1.0 C B:CYS26 4.6 0.3 1.0 C B:CYS23 4.6 0.4 1.0 SG B:CYS59 4.7 0.5 1.0 N B:HIS56 4.8 0.5 1.0 N B:PHE30 4.8 0.3 1.0 CA B:CYS26 4.8 0.3 1.0 CA B:CYS34 4.8 0.5 1.0 C B:ALA29 4.8 0.5 1.0 CG B:MET28 4.9 0.4 1.0 O B:CYS23 5.0 0.4 1.0

Zinc binding site 2 out of 3 in the Cryo-Em Structure of the Anaphase-Promoting Complex/Cyclosome, in Complex with the NEK2A Substrate at 3.9 Angstrom Resolution


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 Anaphase-Promoting Complex/Cyclosome, in Complex with the NEK2A Substrate at 3.9 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:0.2 occ:1.00 SG B:CYS76 2.4 0.7 1.0 SG B:CYS51 2.5 0.6 1.0 CB B:CYS51 2.5 0.6 1.0 CB B:HIS53 2.6 0.3 1.0 ND1 B:HIS53 2.7 0.3 1.0 CG B:HIS53 2.8 0.3 1.0 CB B:CYS76 3.5 0.7 1.0 O B:CYS51 3.7 0.6 1.0 CA B:CYS51 3.7 0.6 1.0 CE1 B:HIS53 3.7 0.3 1.0 CA B:HIS53 3.8 0.3 1.0 N B:HIS53 3.8 0.3 1.0 C B:CYS51 3.9 0.6 1.0 CD2 B:HIS53 3.9 0.3 1.0 CB B:CYS73 3.9 0.5 1.0 SG B:CYS73 4.0 0.5 1.0 NE2 B:HIS53 4.3 0.3 1.0 N B:CYS76 4.5 0.7 1.0 CZ3 B:TRP80 4.6 0.1 1.0 CA B:CYS76 4.6 0.7 1.0 CE2 B:PHE55 4.7 0.8 1.0 N B:SER52 4.7 0.4 1.0 N B:CYS51 4.7 0.6 1.0 C B:HIS53 4.7 0.3 1.0 C B:SER52 4.9 0.4 1.0 CZ B:PHE55 4.9 0.8 1.0 O B:HIS53 5.0 0.3 1.0

Zinc binding site 3 out of 3 in the Cryo-Em Structure of the Anaphase-Promoting Complex/Cyclosome, in Complex with the NEK2A Substrate at 3.9 Angstrom Resolution


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 the Anaphase-Promoting Complex/Cyclosome, in Complex with the NEK2A Substrate at 3.9 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn103 b:0.8 occ:1.00 O B:CYS37 1.9 0.6 1.0 CB B:CYS37 2.5 0.6 1.0 C B:CYS37 2.6 0.6 1.0 CA B:CYS37 2.6 0.6 1.0 N B:CYS37 2.6 0.6 1.0 O B:CYS34 3.0 0.5 1.0 CB B:CYS44 3.7 0.7 1.0 CB B:CYS33 3.7 0.2 1.0 SG B:CYS37 3.7 0.6 1.0 N B:LYS38 3.9 0.9 1.0 C B:ASP36 3.9 0.1 1.0 N B:CYS34 4.0 0.5 1.0 SG B:CYS34 4.0 0.5 1.0 SG B:CYS44 4.0 0.7 1.0 ND1 B:HIS58 4.1 0.6 1.0 C B:CYS34 4.1 0.5 1.0 CE1 B:HIS58 4.3 0.6 1.0 O B:VAL39 4.4 0.4 1.0 C B:CYS33 4.4 0.2 1.0 CA B:CYS33 4.4 0.2 1.0 N B:VAL39 4.5 0.4 1.0 CA B:CYS34 4.5 0.5 1.0 N B:ASP36 4.6 0.1 1.0 CA B:ASP36 4.6 0.1 1.0 CB B:ASP36 4.7 0.1 1.0 CA B:LYS38 4.7 0.9 1.0 SG B:CYS33 4.8 0.2 1.0 O B:ASP36 4.8 0.1 1.0 C B:LYS38 4.8 0.9 1.0 CB B:CYS34 4.9 0.5 1.0

C.Alfieri, D.Barford. A Unique Binding Mode of NEK2A to the Apc/C Allows Its Ubiquitination During Prometaphase To Be Published.