Magnesium 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:

Potassium

(K)

3 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the TDP2 Uba Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 2, PDB code: 6q01:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 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 Magnesium with other atoms in the Mg 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:Mg101 b:15.3 occ:0.43 K A:K104 1.5 35.5 0.5 O A:HOH223 1.7 12.0 0.5 OD1 A:ASP32 2.0 20.1 0.5 O A:HOH322 2.1 21.0 0.4 O A:HOH223 2.1 14.8 0.4 O A:HOH258 2.1 30.2 0.4 CG A:ASP32 3.2 17.8 0.5 HA A:ASP32 3.7 13.6 0.5 HA A:ASP32 3.7 7.8 0.5 OD2 A:ASP32 3.8 22.7 0.5 OD1 A:ASP32 3.8 19.1 0.5 CB A:ASP32 4.0 11.8 0.5 O A:HOH342 4.2 40.3 0.6 CG A:ASP32 4.2 17.2 0.5 CA A:ASP32 4.2 11.2 0.5 CA A:ASP32 4.3 16.2 0.5 CB A:ASP32 4.3 20.5 0.5 O A:ALA28 4.4 9.6 1.0 H A:ASP32 4.4 10.5 0.5 O A:HOH215 4.4 23.5 0.4 H A:ASP32 4.4 12.3 0.5 N A:ASP32 4.5 11.2 1.0 HB3 A:GLN31 4.6 7.8 1.0 O A:HOH240 4.6 28.9 0.6 HG2 A:GLN31 4.7 10.5 1.0 HB3 A:ASP32 4.8 6.9 0.5 HB3 A:ALA28 4.9 9.6 1.0 O A:HOH272 5.0 36.0 0.6 OE1 A:GLN31 5.0 12.9 1.0 O A:HOH224 5.0 18.3 1.0 HB2 A:ASP32 5.0 23.9 0.5

Magnesium binding site 2 out of 2 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 Magnesium with other atoms in the Mg 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 A:Mg102 b:11.0 occ:1.00 OE2 A:GLU16 2.0 10.7 1.0 O A:HOH349 2.1 15.2 1.0 O A:HOH254 2.1 12.1 1.0 O A:HOH309 2.1 12.5 1.0 O A:HOH282 2.1 15.3 1.0 CD A:GLU16 3.1 10.4 1.0 HG3 A:GLU16 3.2 11.8 1.0 H1 A:MET1 3.2 13.6 1.0 CG A:GLU16 3.6 10.1 1.0 HG2 A:GLU16 3.6 13.1 1.0 N A:MET1 4.0 10.4 1.0 OE2 A:GLU18 4.2 18.3 1.0 H2 A:MET1 4.2 11.7 1.0 OE1 A:GLU16 4.2 12.2 1.0 O A:HOH226 4.3 22.7 0.7 O A:HOH358 4.4 15.5 1.0 O A:HOH343 4.9 30.8 1.0 O A:HOH277 4.9 35.4 1.0

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.