Zinc in PDB 8a67: Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Matured Synthetic Nanobody NBSL3.3Q (3RD Generation)

The structure of Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Matured Synthetic Nanobody NBSL3.3Q (3RD Generation), PDB code: 8a67 was solved by S.M.Lange, Y.Kulathu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.59 / 1.86
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	57.081, 58.243, 61.662, 78.88, 67.94, 80.16
R / Rfree (%)	18.7 / 24.5

The structure of Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Matured Synthetic Nanobody NBSL3.3Q (3RD Generation) also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Sodium	(Na)	2 atoms

The binding sites of Zinc atom in the Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Matured Synthetic Nanobody NBSL3.3Q (3RD Generation) (pdb code 8a67). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Matured Synthetic Nanobody NBSL3.3Q (3RD Generation), PDB code: 8a67:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Matured Synthetic Nanobody NBSL3.3Q (3RD Generation)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Matured Synthetic Nanobody NBSL3.3Q (3RD Generation) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:8.0 occ:0.78 NE2 D:HIS124 2.3 14.4 1.0 NE2 D:HIS128 2.3 14.0 1.0 ND1 D:HIS126 2.3 7.8 1.0 CD2 D:HIS128 3.1 14.5 1.0 CE1 D:HIS126 3.1 11.2 1.0 CE1 D:HIS124 3.1 14.6 1.0 CD2 D:HIS124 3.3 14.0 1.0 CE1 D:HIS128 3.4 13.1 1.0 CG D:HIS126 3.4 11.9 1.0 CB D:HIS126 3.8 11.8 1.0 CA D:HIS126 3.9 11.0 1.0 NE2 D:HIS126 4.3 12.7 1.0 ND1 D:HIS124 4.3 15.9 1.0 CG D:HIS128 4.3 15.5 1.0 ND1 D:HIS128 4.4 16.4 1.0 CG D:HIS124 4.4 17.1 1.0 CD2 D:HIS126 4.5 14.3 1.0 O D:HIS125 4.6 14.7 1.0 N D:HIS126 4.8 11.8 1.0 C D:HIS126 4.8 16.0 1.0

Zinc binding site 2 out of 2 in the Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Matured Synthetic Nanobody NBSL3.3Q (3RD Generation)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Matured Synthetic Nanobody NBSL3.3Q (3RD Generation) within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn202 b:7.5 occ:0.79 NE2 H:HIS124 2.3 17.1 1.0 NE2 H:HIS128 2.3 15.9 1.0 ND1 H:HIS126 2.3 11.4 1.0 O2 H:IPA201 2.6 23.0 1.0 C1 H:IPA201 2.8 14.9 1.0 CE1 H:HIS126 2.9 13.4 1.0 C2 H:IPA201 3.0 17.4 1.0 CD2 H:HIS124 3.1 12.9 1.0 CD2 H:HIS128 3.3 15.5 1.0 CE1 H:HIS128 3.3 15.9 1.0 CE1 H:HIS124 3.4 15.1 1.0 CG H:HIS126 3.5 13.2 1.0 CB H:HIS126 4.1 13.4 1.0 CA H:HIS126 4.1 17.2 1.0 NE2 H:HIS126 4.2 15.3 1.0 CG H:HIS124 4.3 16.8 1.0 ND1 H:HIS128 4.4 21.3 1.0 CG H:HIS128 4.4 18.1 1.0 ND1 H:HIS124 4.4 16.7 1.0 CD2 H:HIS126 4.5 16.7 1.0 C3 H:IPA201 4.5 23.7 1.0 O H:HIS125 4.8 17.3 1.0

S.M.Lange, M.R.Mcfarland, F.Lamoliatte, D.Kwasna, L.Shen, I.Wallace, I.Cole, L.A.Armstrong, A.Knebel, C.Johnson, V.De Cesare, Y.Kulathu. Comprehensive Approach to Study Branched Ubiquitin Chains Reveals Roles For K48-K63 Branches in Vcp/P97-Related Processes Biorxiv 2023.
ISSN: ISSN 2692-8205
DOI: 10.1101/2023.01.10.523363