Chlorine 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:

Sodium	(Na)	2 atoms
Zinc	(Zn)	2 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total only one binding site of Chlorine was 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:

Chlorine binding site 1 out of 1 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 Chlorine with other atoms in the Cl 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 E:Cl101 b:59.0 occ:1.00 NH2 E:ARG72 2.6 32.2 1.0 O E:PRO38 3.0 15.8 1.0 NZ E:LYS27 3.4 18.2 1.0 CZ E:ARG72 3.6 32.9 1.0 C E:PRO38 3.7 19.0 1.0 OD2 E:ASP52 3.8 34.1 1.0 NH1 E:ARG72 4.0 31.9 1.0 CA E:ASP39 4.0 18.9 1.0 CD E:LYS27 4.0 14.1 1.0 O E:GLN41 4.1 14.1 1.0 OD1 E:ASP39 4.1 26.0 1.0 N E:ASP39 4.2 20.2 1.0 CE E:LYS27 4.2 14.7 1.0 OD1 E:ASP52 4.4 19.7 1.0 CG E:ASP52 4.5 21.0 1.0 C E:ASP39 4.6 17.3 1.0 NE E:ARG72 4.7 32.6 1.0 CB E:PRO38 4.7 10.0 1.0 CA E:PRO38 4.7 12.2 1.0 O E:ASP39 4.8 17.0 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