Zinc in PDB 8tar: Apc/C-CDH1-UBE2C-Ubiquitin-Cyclinb-Ntd

The binding sites of Zinc atom in the Apc/C-CDH1-UBE2C-Ubiquitin-Cyclinb-Ntd (pdb code 8tar). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Apc/C-CDH1-UBE2C-Ubiquitin-Cyclinb-Ntd, PDB code: 8tar:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Apc/C-CDH1-UBE2C-Ubiquitin-Cyclinb-Ntd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Apc/C-CDH1-UBE2C-Ubiquitin-Cyclinb-Ntd within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:270.2 occ:1.00 H C:HIS56 3.4 233.1 1.0 H C:CYS26 3.6 228.9 1.0 HA C:CYS34 3.8 236.8 1.0 H C:MET28 4.2 230.0 1.0 O C:CYS23 4.2 231.2 1.0 N C:HIS56 4.2 233.1 1.0 N C:CYS26 4.3 228.9 1.0 O C:CYS33 4.4 236.7 1.0 CA C:CYS34 4.5 236.8 1.0 N C:CYS34 4.5 236.8 1.0 CA C:CYS23 4.5 231.2 1.0 C C:CYS23 4.6 231.2 1.0 C C:CYS33 4.7 236.7 1.0 HA C:PHE55 4.7 228.5 1.0 H C:CYS34 4.7 236.8 1.0 CA C:HIS56 4.7 233.1 1.0 CA C:CYS26 4.7 228.9 1.0 H C:ILE25 4.8 227.6 1.0 H C:ARG27 4.8 225.6 1.0 N C:MET28 4.9 230.0 1.0 HA C:CYS23 5.0 231.2 1.0

Zinc binding site 2 out of 4 in the Apc/C-CDH1-UBE2C-Ubiquitin-Cyclinb-Ntd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Apc/C-CDH1-UBE2C-Ubiquitin-Cyclinb-Ntd within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn102 b:294.9 occ:1.00 O C:CYS44 3.3 235.4 1.0 H C:CYS34 3.3 236.8 1.0 HA C:CYS33 3.5 236.7 1.0 CA C:CYS33 3.7 236.7 1.0 N C:CYS34 4.0 236.8 1.0 C C:CYS44 4.1 235.4 1.0 CA C:CYS44 4.3 235.4 1.0 HA C:PRO40 4.4 231.1 1.0 C C:CYS33 4.4 236.7 1.0 H C:CYS37 4.7 242.8 1.0 CA C:CYS37 4.9 242.8 1.0 HA C:CYS44 4.9 235.4 1.0 N C:CYS33 5.0 236.7 1.0

Zinc binding site 3 out of 4 in the Apc/C-CDH1-UBE2C-Ubiquitin-Cyclinb-Ntd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Apc/C-CDH1-UBE2C-Ubiquitin-Cyclinb-Ntd within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn103 b:275.7 occ:1.00 O C:CYS51 2.1 228.4 1.0 C C:CYS51 3.3 228.4 1.0 O C:SER52 4.0 230.6 1.0 C C:SER52 4.0 230.6 1.0 CA C:SER52 4.2 230.6 1.0 N C:SER52 4.2 230.6 1.0 HA C:CYS51 4.2 228.4 1.0 CA C:CYS51 4.3 228.4 1.0 N C:HIS53 4.6 230.9 1.0

Zinc binding site 4 out of 4 in the Apc/C-CDH1-UBE2C-Ubiquitin-Cyclinb-Ntd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Apc/C-CDH1-UBE2C-Ubiquitin-Cyclinb-Ntd within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn901 b:281.0 occ:1.00 H N:CYS233 3.3 224.4 1.0 H N:CYS224 3.5 232.9 1.0 H N:TRP232 3.6 222.3 1.0 HA N:CYS231 3.7 232.3 1.0 O N:ALA222 3.8 226.2 1.0 N N:CYS233 3.9 224.4 1.0 H N:SER225 4.0 232.9 1.0 CA N:CYS231 4.0 232.3 1.0 N N:TRP232 4.1 222.3 1.0 CA N:CYS233 4.2 224.4 1.0 N N:CYS224 4.2 232.9 1.0 HA N:CYS233 4.4 224.4 1.0 C N:CYS231 4.4 232.3 1.0 CA N:CYS224 4.4 232.9 1.0 CA N:CYS221 4.7 237.8 1.0 N N:SER225 4.8 232.9 1.0 C N:TRP232 4.8 222.3 1.0 C N:CYS221 4.9 237.8 1.0 C N:ALA222 4.9 226.2 1.0

T.Bodrug, K.A.Welsh, D.L.Bolhuis, E.Paulakonis, R.C.Martinez-Chacin, B.Liu, N.Pinkin, T.Bonacci, L.Cui, P.Xu, O.Roscow, S.J.Amann, I.Grishkovskaya, M.J.Emanuele, J.S.Harrison, J.P.Steimel, K.M.Hahn, W.Zhang, E.D.Zhong, D.Haselbach, N.G.Brown. Time-Resolved Cryo-Em (Tr-Em) Analysis of Substrate Polyubiquitination By the Ring E3 Anaphase-Promoting Complex/Cyclosome (Apc/C) Nat.Struct.Mol.Biol. 2023.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-023-01105-5