Magnesium in PDB 3ly5: DDX18 Dead-Domain

The structure of DDX18 Dead-Domain, PDB code: 3ly5 was solved by P.Schutz, T.Karlberg, C.H.Arrowsmith, H.Berglund, C.Bountra, R.Collins, A.M.Edwards, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, A.Johansson, I.Johansson, A.Kallas, P.Kraulis, T.Kotenyova, A.Kotzsch, N.Markova, M.Moche, T.K.Nielsen, P.Nordlund, T.Nyman, C.Persson, A.K.Roos, M.I.Siponen, L.Svensson, A.G.Thorsell, L.Tresaugues, S.Van Den Berg, E.Wahlberg, J.Weigelt, M.Welin, M.Wisniewska, H.M.Schuler, Structuralgenomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.42 / 2.80
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	41.340, 41.340, 230.541, 90.00, 90.00, 120.00
R / Rfree (%)	24.6 / 27.4

The binding sites of Magnesium atom in the DDX18 Dead-Domain (pdb code 3ly5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the DDX18 Dead-Domain, PDB code: 3ly5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the DDX18 Dead-Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of DDX18 Dead-Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg388 b:55.3 occ:1.00 OE2 A:GLU346 2.8 39.6 1.0 O A:GLY342 3.3 42.3 1.0 CD A:GLU346 3.8 40.5 1.0 O B:HOH47 3.8 27.4 1.0 NH2 B:ARG261 4.0 45.5 1.0 OE1 A:GLU346 4.0 40.0 1.0 C A:GLY342 4.5 42.4 1.0 CA B:SER289 4.7 49.7 1.0 CB B:SER289 4.7 49.7 1.0 CZ B:ARG261 5.0 45.2 1.0

Magnesium binding site 2 out of 2 in the DDX18 Dead-Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of DDX18 Dead-Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg389 b:48.8 occ:1.00 O A:ALA223 2.4 42.2 1.0 NZ A:LYS229 2.7 37.0 1.0 OE2 A:GLU334 2.7 48.5 1.0 N A:ALA365 3.0 47.8 1.0 C A:SER364 3.4 47.4 1.0 C A:ALA223 3.5 42.3 1.0 CA A:SER364 3.6 47.1 1.0 N A:SER364 3.8 46.9 1.0 CA A:ALA365 3.8 48.2 1.0 CB A:ALA365 3.8 48.1 1.0 CD A:GLU334 3.9 47.8 1.0 C A:PHE363 4.0 46.6 1.0 CE A:LYS229 4.0 36.8 1.0 CA A:GLU334 4.0 46.0 1.0 O A:PHE363 4.0 46.5 1.0 CA A:LYS224 4.3 42.6 1.0 O A:SER364 4.3 47.4 1.0 N A:LYS224 4.3 42.4 1.0 N A:GLU334 4.3 45.9 1.0 CA A:ALA223 4.5 42.3 1.0 CD A:LYS229 4.5 37.0 1.0 CB A:GLU334 4.6 46.1 1.0 N A:ALA223 4.6 42.3 1.0 CB A:PHE363 4.6 46.3 1.0 CG A:GLU334 4.6 46.9 1.0 CB A:ALA223 4.7 42.4 1.0 OD1 A:ASP336 4.8 46.1 1.0 C A:LYS224 4.8 42.6 1.0 OE1 A:GLU334 4.9 47.8 1.0 CA A:PHE363 4.9 46.4 1.0 OD1 A:ASP333 4.9 46.6 1.0

P.Schutz, T.Karlberg, S.Van Den Berg, R.Collins, L.Lehtio, M.Hogbom, L.Holmberg-Schiavone, W.Tempel, H.W.Park, M.Hammarstrom, M.Moche, A.G.Thorsell, H.Schuler. Comparative Structural Analysis of Human Dead-Box Rna Helicases. Plos One V. 5 12791 2010.
ISSN: ESSN 1932-6203
PubMed: 20941364
DOI: 10.1371/JOURNAL.PONE.0012791