Chlorine 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:

Sodium

(Na)

2 atoms

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

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl601 b:49.9 occ:1.00 N A:LEU365 3.9 15.8 1.0 O A:LEU365 4.0 30.1 1.0 CG A:ARG347 4.1 34.4 1.0 CD A:ARG347 4.3 37.5 1.0 CB A:LEU365 4.4 24.0 1.0 OD1 A:ASP359 4.4 30.7 1.0 O A:ARG347 4.5 31.8 1.0 CA A:LEU365 4.6 20.0 1.0 NH2 B:ARG72 4.6 45.0 1.0 C A:LEU365 4.7 15.1 1.0 CA A:PRO364 4.7 12.0 1.0 C A:PRO364 4.8 18.2 1.0 CB A:ARG347 4.9 24.0 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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 A:Cl602 b:67.0 occ:1.00 N A:LYS251 3.0 69.8 1.0 CA A:LYS251 3.5 57.4 1.0 O A:SER491 3.9 39.5 1.0 C A:TRP250 4.1 67.9 1.0 CA A:TRP250 4.2 58.8 1.0 CG A:LYS251 4.3 69.3 1.0 CD A:LYS251 4.4 76.5 1.0 O A:GLN249 4.4 52.9 1.0 CB A:LYS251 4.5 56.5 1.0 CG A:GLU492 4.6 44.2 1.0 N A:GLU252 4.6 66.0 1.0 C A:LYS251 4.7 61.2 1.0 CD1 A:TRP250 4.7 44.5 1.0 CA A:GLU492 4.7 51.5 1.0 CG A:TRP250 4.8 40.1 1.0 C A:SER491 4.9 38.0 1.0 NE1 A:TRP250 5.0 40.6 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