Potassium in PDB 6q01: TDP2 Uba Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 2

The structure of TDP2 Uba Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 2, PDB code: 6q01 was solved by M.J.Schellenberg, J.M.Krahn, R.S.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.96 / 0.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.793, 65.461, 67.677, 90.00, 90.00, 90.00
R / Rfree (%)	10 / 11.4

The structure of TDP2 Uba Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 2 also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Potassium atom in the TDP2 Uba Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 2 (pdb code 6q01). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the TDP2 Uba Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 2, PDB code: 6q01:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the TDP2 Uba Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of TDP2 Uba Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:K104 b:35.5 occ:0.48 O A:HOH258 1.1 30.2 0.4 MG A:MG101 1.5 15.3 0.4 O A:HOH322 2.0 21.0 0.4 OD1 A:ASP32 2.3 20.1 0.5 O A:HOH223 3.0 12.0 0.5 O A:HOH342 3.0 40.3 0.6 OD1 A:ASP32 3.2 19.1 0.5 CG A:ASP32 3.3 17.8 0.5 O A:HOH223 3.4 14.8 0.4 O A:HOH272 3.7 36.0 0.6 OD2 A:ASP32 3.8 22.7 0.5 CG A:ASP32 3.9 17.2 0.5 HA A:ASP32 4.1 13.6 0.5 O A:HOH215 4.1 23.5 0.4 HA A:ASP32 4.1 7.8 0.5 CB A:ASP32 4.1 11.8 0.5 CB A:ASP32 4.4 20.5 0.5 CA A:ASP32 4.7 11.2 0.5 CA A:ASP32 4.7 16.2 0.5 OD2 A:ASP32 4.8 22.0 0.5 O A:HOH240 4.8 28.9 0.6 HB3 A:ASP32 5.0 6.9 0.5

Potassium binding site 2 out of 3 in the TDP2 Uba Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of TDP2 Uba Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ C:K102 b:11.7 occ:0.36 O C:HOH267 1.1 10.4 0.5 O C:HOH211 1.9 8.0 0.5 O C:ALA36 2.6 9.0 1.0 OH C:TYR61 2.8 10.0 1.0 O A:GLY47 2.9 10.8 1.0 O C:HOH267 3.1 23.6 0.5 HA3 A:GLY47 3.3 10.1 1.0 HE1 C:TYR61 3.3 10.4 1.0 HH C:TYR61 3.3 12.2 1.0 C A:GLY47 3.7 9.0 1.0 C C:ALA36 3.8 8.0 1.0 CZ C:TYR61 3.8 8.5 1.0 HE2 A:LYS48 3.8 22.2 1.0 CE1 C:TYR61 3.9 8.8 1.0 CA A:GLY47 3.9 9.0 1.0 HB3 C:SER37 3.9 13.5 1.0 HA2 A:GLY47 4.1 11.2 1.0 O C:SER37 4.1 9.9 1.0 O A:HOH385 4.1 18.2 0.5 CE A:LYS48 4.1 15.5 1.0 HB3 C:CYS38 4.1 11.4 1.0 HB1 C:ALA36 4.2 9.0 1.0 HA C:ALA36 4.3 9.0 1.0 CD A:LYS48 4.4 13.3 1.0 C C:SER37 4.4 8.3 1.0 CA C:ALA36 4.6 8.1 1.0 HE1 C:PHE62 4.7 9.0 1.0 O C:HOH229 4.7 16.5 0.8 HG2 A:LYS48 4.7 19.4 1.0 N C:SER37 4.7 8.2 1.0 CB C:SER37 4.8 10.4 1.0 CA C:SER37 4.9 8.5 1.0 CB C:ALA36 4.9 8.6 1.0 N A:LYS48 4.9 8.3 1.0 O A:HOH385 4.9 17.7 0.5 HA A:LYS48 4.9 7.4 1.0

Potassium binding site 3 out of 3 in the TDP2 Uba Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of TDP2 Uba Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ D:K101 b:13.0 occ:0.27 O D:HOH204 1.7 16.2 0.6 OH D:TYR61 2.7 15.8 1.0 O D:HOH240 2.7 26.8 0.7 O D:ALA36 2.8 10.8 1.0 O D:SER37 2.9 10.3 1.0 HB3 D:SER37 3.4 8.3 1.0 HE1 D:TYR61 3.5 18.3 1.0 C D:SER37 3.7 8.5 1.0 CZ D:TYR61 3.7 12.1 1.0 HB3 D:CYS38 3.8 10.6 1.0 C D:ALA36 4.0 8.1 1.0 CE1 D:TYR61 4.0 11.9 1.0 CB D:SER37 4.2 8.9 1.0 HA3 B:GLY47 4.3 11.8 0.3 CA D:SER37 4.3 8.2 1.0 O D:HOH275 4.4 21.1 0.6 O B:GLY47 4.4 13.0 0.3 O B:HOH194 4.5 26.2 0.4 HA D:CYS38 4.5 6.7 1.0 N D:CYS38 4.5 8.2 1.0 N D:SER37 4.6 8.3 1.0 HB1 D:ALA36 4.6 10.5 1.0 O B:GLY47 4.7 12.1 0.7 CB D:CYS38 4.7 9.0 1.0 HA3 B:GLY47 4.7 10.1 0.7 O B:HOH205 4.7 31.2 0.5 O D:HOH275 4.8 19.5 0.4 CA D:CYS38 4.8 8.5 1.0 OG D:SER37 4.8 11.0 1.0 O B:HOH205 4.9 30.4 0.5 HB2 D:SER37 4.9 9.2 1.0 CE2 D:TYR61 4.9 10.9 1.0 O B:HOH194 4.9 32.5 0.6

M.J.Schellenberg, C.D.Appel, A.A.Riccio, L.R.Butler, J.M.Krahn, R.S.Williams. Ubiquitin Stimulated Reversal of Topoisomerase 2 Dna Protein Crosslinks By TDP2 To Be Published.