Sodium 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
Zinc	(Zn)	2 atoms

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium 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 Sodium with other atoms in the Na 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:Na102 b:41.6 occ:1.00 OE2 E:GLU18 2.3 38.7 1.0 CD E:GLU18 3.5 30.8 1.0 OE1 E:GLU16 4.0 36.3 1.0 OE1 E:GLU18 4.3 34.5 1.0 CG E:GLU18 4.5 18.2 1.0 N E:MET1 4.7 16.9 1.0 CG E:GLU16 4.8 21.2 1.0 CD E:GLU16 4.8 32.0 1.0 O E:VAL17 4.8 13.9 1.0

Sodium 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 Sodium with other atoms in the Na 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 F:Na102 b:39.3 occ:1.00 OE2 F:GLU34 2.3 43.5 1.0 CD F:GLU34 3.3 44.2 1.0 O F:LYS33 3.4 34.4 1.0 CG2 F:ILE13 3.7 21.3 1.0 CG F:GLU34 3.7 32.9 1.0 CB F:LYS33 4.0 22.6 1.0 C F:LYS33 4.0 30.6 1.0 CB F:ILE13 4.1 18.0 1.0 CD F:LYS33 4.1 20.6 1.0 CG F:LYS33 4.1 23.9 1.0 O F:HOH218 4.4 20.5 1.0 OE1 F:GLU34 4.5 46.8 1.0 CA F:LYS33 4.6 23.0 1.0 CD1 F:ILE13 4.6 20.7 1.0 N F:GLU34 4.7 26.2 1.0 CE F:LYS33 4.8 22.2 1.0 CA F:GLU34 4.8 26.5 1.0 CB F:GLU34 4.8 31.4 1.0 CG1 F:ILE13 5.0 19.2 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