Sodium in PDB 7npi: Crystal Structure of MINDY2 (C266A) in Complex with LYS48-Linked Penta-Ubiquitin (K48-UB5)

All present enzymatic activity of Crystal Structure of MINDY2 (C266A) in Complex with LYS48-Linked Penta-Ubiquitin (K48-UB5):
3.4.19.12;

The structure of Crystal Structure of MINDY2 (C266A) in Complex with LYS48-Linked Penta-Ubiquitin (K48-UB5), PDB code: 7npi was solved by S.M.Lange, L.A.Armstrong, Y.Kulathu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	126.63 / 2.81
Space group	C 1 2 1 1
Cell size a, b, c (Å), α, β, γ (°)	162.061, 203.071, 265.035, 90, 107.14, 90
R / Rfree (%)	22.8 / 28.8

The structure of Crystal Structure of MINDY2 (C266A) in Complex with LYS48-Linked Penta-Ubiquitin (K48-UB5) also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of MINDY2 (C266A) in Complex with LYS48-Linked Penta-Ubiquitin (K48-UB5) (pdb code 7npi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of MINDY2 (C266A) in Complex with LYS48-Linked Penta-Ubiquitin (K48-UB5), PDB code: 7npi:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of MINDY2 (C266A) in Complex with LYS48-Linked Penta-Ubiquitin (K48-UB5)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of MINDY2 (C266A) in Complex with LYS48-Linked Penta-Ubiquitin (K48-UB5) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:30.0 occ:1.00 OG1 A:THR453 3.0 47.3 1.0 CA A:GLY438 3.7 62.0 1.0 CZ2 A:TRP250 4.0 41.8 1.0 O A:LYS454 4.1 40.8 1.0 CB A:THR453 4.1 29.6 1.0 CG2 A:THR453 4.2 30.7 1.0 C A:GLY438 4.4 51.1 1.0 CD2 A:TYR455 4.4 52.0 1.0 O A:GLY438 4.5 53.3 1.0 N A:GLY438 4.5 55.5 1.0 CZ A:PHE493 4.5 33.7 1.0 C A:LYS454 4.7 35.0 1.0 CE1 A:PHE493 4.7 47.1 1.0 CB A:TYR455 4.8 57.4 1.0 CH2 A:TRP250 4.8 45.4 1.0 CE2 A:TRP250 4.8 32.7 1.0 N A:LYS454 4.9 37.8 1.0 NE1 A:TRP250 4.9 40.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of MINDY2 (C266A) in Complex with LYS48-Linked Penta-Ubiquitin (K48-UB5)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of MINDY2 (C266A) in Complex with LYS48-Linked Penta-Ubiquitin (K48-UB5) within 5.0Å range: probe atom residue distance (Å) B Occ S:Na601 b:22.5 occ:1.00 OG1 S:THR453 2.8 47.6 1.0 CA S:GLY438 3.8 72.8 1.0 CZ2 S:TRP250 3.9 81.0 1.0 O S:LYS454 3.9 65.4 1.0 CB S:THR453 3.9 45.3 1.0 CG2 S:THR453 4.1 41.5 1.0 CZ S:PHE493 4.2 52.4 1.0 CD1 S:TYR455 4.2 74.3 1.0 CE2 S:PHE493 4.4 68.5 1.0 CB S:TYR455 4.4 69.1 1.0 C S:GLY438 4.4 60.8 1.0 C S:LYS454 4.5 57.7 1.0 N S:GLY438 4.5 66.4 1.0 CE2 S:TRP250 4.7 67.9 1.0 CH2 S:TRP250 4.7 72.2 1.0 O S:GLY438 4.7 64.8 1.0 N S:LYS454 4.8 58.3 1.0 NE1 S:TRP250 4.8 64.1 1.0 CG S:TYR455 4.8 67.2 1.0 CA S:TYR455 4.8 64.6 1.0 N S:TYR455 5.0 68.6 1.0

S.A.Abdul Rehman, L.A.Armstrong, S.M.Lange, Y.A.Kristariyanto, T.W.Grawert, A.Knebel, D.I.Svergun, Y.Kulathu. Mechanism of Activation and Regulation of Deubiquitinase Activity in MINDY1 and MINDY2 To Be Published.
DOI: 10.1016/J.MOLCEL.2021.08.024