Magnesium in PDB 8pd6: Crystal Structure of the TRIM58 Pry-Spry Domain in Complex with Trim- 473

All present enzymatic activity of Crystal Structure of the TRIM58 Pry-Spry Domain in Complex with Trim- 473:
2.3.2.27;

The structure of Crystal Structure of the TRIM58 Pry-Spry Domain in Complex with Trim- 473, PDB code: 8pd6 was solved by M.Renatus, K.Hoegenauer, M.Schroeder, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.01 / 1.30
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	55.284, 55.284, 202.763, 90, 90, 120
R / Rfree (%)	13.9 / 17.8

The structure of Crystal Structure of the TRIM58 Pry-Spry Domain in Complex with Trim- 473 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of the TRIM58 Pry-Spry Domain in Complex with Trim- 473 (pdb code 8pd6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the TRIM58 Pry-Spry Domain in Complex with Trim- 473, PDB code: 8pd6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the TRIM58 Pry-Spry Domain in Complex with Trim- 473


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the TRIM58 Pry-Spry Domain in Complex with Trim- 473 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:25.3 occ:1.00 O A:HOH686 2.1 25.7 1.0 OE2 A:GLU354 2.1 22.6 1.0 O A:HOH639 2.1 25.0 1.0 CD A:GLU354 3.1 18.6 1.0 OE1 A:GLU354 3.4 22.8 1.0 O A:HOH603 3.6 35.1 1.0 CG A:GLU354 4.4 18.4 1.0 NH1 A:ARG409 4.7 20.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the TRIM58 Pry-Spry Domain in Complex with Trim- 473


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the TRIM58 Pry-Spry Domain in Complex with Trim- 473 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:13.3 occ:1.00 OE1 A:GLN364 2.8 16.7 1.0 OG1 A:THR366 3.1 14.7 1.0 N A:LEU443 3.2 10.7 1.0 O A:LEU443 3.5 12.5 1.0 N A:THR366 3.6 10.0 1.0 CG2 A:THR366 3.6 14.4 1.0 N A:ASP365 3.6 9.7 1.0 CA A:GLY442 3.8 11.6 1.0 CB A:THR366 3.9 13.4 1.0 CB A:GLN364 3.9 10.6 1.0 CD A:GLN364 3.9 13.6 1.0 C A:GLY442 4.0 11.3 1.0 CA A:LEU443 4.1 11.9 1.0 C A:LEU443 4.2 10.4 1.0 CA A:GLN364 4.2 9.9 1.0 C A:GLN364 4.2 9.8 1.0 CB A:ASP365 4.2 10.3 1.0 CB A:LEU443 4.2 11.8 1.0 CA A:ASP365 4.2 9.9 1.0 CA A:THR366 4.3 11.6 1.0 C A:ASP365 4.4 10.3 1.0 CG A:GLN364 4.5 12.4 1.0 NE2 A:GLN364 5.0 19.0 1.0

K.Hoegenauer, S.An, J.Axford, C.Benander, C.Bergsdorf, J.Botsch, S.Chau, C.Fernandez, S.Gleim, U.Hassiepen, J.Hunziker, E.Joly, A.Keller, S.Lopez Romero, R.Maher, A.S.Mangold, C.Mickanin, M.Mihalic, P.Neuner, A.W.Patterson, F.Perruccio, S.Roggo, J.Scesa, M.Schroder, D.Shkoza, B.Thai, A.Vulpetti, M.Renatus, J.S.Reece-Hoyes. Discovery of Ligands For TRIM58, A Novel Tissue-Selective E3 Ligase Acs Med.Chem.Lett. 2023.
ISSN: ISSN 1948-5875
DOI: 10.1021/ACSMEDCHEMLETT.3C00259