Magnesium in PDB 3dkp: Human Dead-Box Rna-Helicase DDX52, Conserved Domain I in Complex with Adp

The structure of Human Dead-Box Rna-Helicase DDX52, Conserved Domain I in Complex with Adp, PDB code: 3dkp was solved by L.Lehtio, T.Karlberg, J.Andersson, C.H.Arrowsmith, H.Berglund, R.Collins, L.G.Dahlgren, A.M.Edwards, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, A.Johansson, I.Johansson, T.Kotenyova, M.Moche, M.E.Nilsson, P.Nordlund, T.Nyman, K.Olesen, C.Persson, J.Sagemark, A.G.Thorsell, L.Tresaugues, S.Van Den Berg, M.Welin, M.Wisniewska, M.Wikstrom, H.Schueler, Structuralgenomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.56 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.630, 38.360, 73.840, 90.00, 90.37, 90.00
R / Rfree (%)	18.2 / 23.6

The binding sites of Magnesium atom in the Human Dead-Box Rna-Helicase DDX52, Conserved Domain I in Complex with Adp (pdb code 3dkp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Human Dead-Box Rna-Helicase DDX52, Conserved Domain I in Complex with Adp, PDB code: 3dkp:

Magnesium binding site 1 out of 1 in the Human Dead-Box Rna-Helicase DDX52, Conserved Domain I in Complex with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dead-Box Rna-Helicase DDX52, Conserved Domain I in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:7.5 occ:1.00 O A:HOH564 2.0 11.7 1.0 O A:HOH562 2.0 9.8 1.0 O1B A:ADP402 2.0 3.3 1.0 O A:HOH563 2.1 7.9 1.0 O A:HOH422 2.2 9.4 1.0 O A:HOH561 2.2 3.5 1.0 PB A:ADP402 3.2 2.0 1.0 O3B A:ADP402 3.6 5.9 1.0 O A:HOH499 3.9 27.8 1.0 OD2 A:ASP318 4.0 14.0 1.0 O2A A:ADP402 4.0 2.0 1.0 OG1 A:THR216 4.1 3.3 1.0 O A:HOH412 4.2 5.2 1.0 OD1 A:ASP318 4.2 11.5 1.0 OE2 A:GLU319 4.3 15.8 1.0 O2B A:ADP402 4.3 2.0 1.0 O3A A:ADP402 4.3 3.6 1.0 O A:HOH410 4.4 4.7 1.0 O A:HOH455 4.4 8.6 1.0 O1A A:ADP402 4.5 5.0 1.0 PA A:ADP402 4.5 2.0 1.0 CG A:ASP318 4.6 10.5 1.0 O A:HOH435 4.7 11.9 1.0 O A:HOH469 4.8 18.3 1.0 CE A:LYS215 4.8 2.8 1.0 NZ A:LYS215 4.8 2.0 1.0 CD A:GLU319 4.8 14.4 1.0 O A:HOH492 4.9 19.9 1.0 CB A:LYS215 4.9 2.0 1.0 N A:THR216 5.0 2.0 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