Magnesium in PDB 7w2p: Tudor Domain of Smn in Complex with A Small Molecule

The structure of Tudor Domain of Smn in Complex with A Small Molecule, PDB code: 7w2p was solved by W.Li, C.H.Arrowsmith, A.M.Edwards, Y.Liu, J.Min, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.44 / 1.15
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	35.893, 35.893, 92, 90, 90, 90
R / Rfree (%)	12.8 / 15

The structure of Tudor Domain of Smn in Complex with A Small Molecule also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Magnesium atom in the Tudor Domain of Smn in Complex with A Small Molecule (pdb code 7w2p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Tudor Domain of Smn in Complex with A Small Molecule, PDB code: 7w2p:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Tudor Domain of Smn in Complex with A Small Molecule


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tudor Domain of Smn in Complex with A Small Molecule within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:13.3 occ:1.00 O A:HOH333 2.0 21.3 1.0 O A:HOH331 2.0 20.1 1.0 O A:HOH337 2.0 19.8 1.0 O A:HOH311 2.0 12.4 1.0 O A:HOH303 2.1 13.8 1.0 O A:HOH330 2.1 19.4 1.0 OE2 A:GLU121 4.0 15.3 1.0 O A:LYS119 4.2 10.7 1.0 CB A:ALA86 4.5 29.2 1.0 O A:PHE118 4.5 12.3 1.0 CA A:LYS119 4.7 10.1 0.3 CA A:LYS119 4.8 11.1 0.7 C A:LYS119 4.9 9.3 1.0 CD A:GLU121 5.0 12.5 1.0

Magnesium binding site 2 out of 2 in the Tudor Domain of Smn in Complex with A Small Molecule


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tudor Domain of Smn in Complex with A Small Molecule within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:17.9 occ:0.70 O A:HOH338 2.0 26.1 0.7 O A:HOH335 2.0 20.9 0.7 O A:HOH304 2.0 21.0 1.0 O A:HOH323 2.1 21.9 1.0 O A:HOH336 2.1 24.9 0.7 O A:HOH334 2.1 27.3 0.7 OD2 A:ASP117 4.1 13.2 1.0 OD1 A:ASP117 4.5 11.3 1.0 CB A:LYS119 4.6 13.9 0.7 CG A:ASP117 4.7 11.3 1.0 CG A:LYS119 4.8 20.1 0.7 CB A:LYS119 5.0 10.5 0.3

Y.Liu, A.Iqbal, W.Li, Z.Ni, Y.Wang, J.Ramprasad, K.J.Abraham, M.Zhang, D.Y.Zhao, S.Qin, P.Loppnau, H.Jiang, X.Guo, P.J.Brown, X.Zhen, G.Xu, K.Mekhail, X.Ji, M.T.Bedford, J.F.Greenblatt, J.Min. A Small Molecule Antagonist of Smn Disrupts the Interaction Between Smn and Rnap II. Nat Commun V. 13 5453 2022.
ISSN: ESSN 2041-1723
PubMed: 36114190
DOI: 10.1038/S41467-022-33229-5