Magnesium in PDB 5elx: S. Cerevisiae DBP5 Bound to Rna and Mant-Adp BEF3

All present enzymatic activity of S. Cerevisiae DBP5 Bound to Rna and Mant-Adp BEF3:
3.6.4.13;

The structure of S. Cerevisiae DBP5 Bound to Rna and Mant-Adp BEF3, PDB code: 5elx was solved by M.K.Merchant, Y.Modis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.26 / 1.81
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.082, 91.751, 104.521, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 20.8

The structure of S. Cerevisiae DBP5 Bound to Rna and Mant-Adp BEF3 also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Magnesium atom in the S. Cerevisiae DBP5 Bound to Rna and Mant-Adp BEF3 (pdb code 5elx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the S. Cerevisiae DBP5 Bound to Rna and Mant-Adp BEF3, PDB code: 5elx:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the S. Cerevisiae DBP5 Bound to Rna and Mant-Adp BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of S. Cerevisiae DBP5 Bound to Rna and Mant-Adp BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:7.3 occ:1.00 F3 A:BEF503 2.0 7.9 1.0 O A:HOH626 2.1 8.0 1.0 O3 A:M2A501 2.1 8.7 1.0 O A:HOH620 2.1 8.9 1.0 O A:HOH697 2.1 8.4 1.0 O A:HOH692 2.2 9.1 1.0 BE A:BEF503 3.1 10.1 1.0 P1 A:M2A501 3.2 8.5 1.0 O1 A:M2A501 3.4 8.7 1.0 OG1 A:THR145 3.8 9.8 1.0 OE2 A:GLU240 3.9 8.9 1.0 OD2 A:ASP239 3.9 8.8 1.0 F2 A:BEF503 4.0 10.6 1.0 OD1 A:ASP239 4.1 6.4 1.0 CA A:GLY393 4.1 8.3 1.0 O6 A:M2A501 4.2 5.8 1.0 O4 A:M2A501 4.2 9.2 1.0 F1 A:BEF503 4.3 8.5 1.0 O A:GLY393 4.4 9.8 1.0 O2 A:M2A501 4.4 6.6 1.0 O A:HOH789 4.4 8.6 1.0 CG A:ASP239 4.4 11.7 1.0 CE A:LYS144 4.4 8.8 1.0 P2 A:M2A501 4.4 8.1 1.0 O5 A:M2A501 4.5 8.0 1.0 C A:GLY393 4.8 9.4 1.0 CB A:LYS144 4.8 6.3 1.0 NH2 A:ARG429 4.8 8.5 1.0 O A:HOH686 4.9 9.6 1.0 N A:THR145 4.9 10.8 1.0 CD A:GLU240 4.9 10.1 1.0 O A:HOH754 5.0 11.9 1.0 NZ A:LYS144 5.0 7.9 1.0

Magnesium binding site 2 out of 2 in the S. Cerevisiae DBP5 Bound to Rna and Mant-Adp BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of S. Cerevisiae DBP5 Bound to Rna and Mant-Adp BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg506 b:26.4 occ:1.00 O A:HOH805 1.9 25.9 1.0 O A:HOH694 2.1 20.8 1.0 O A:HOH858 2.2 24.2 1.0 OD2 A:ASP264 2.3 20.4 1.0 CG A:ASP264 3.2 20.2 1.0 OD1 A:ASP264 3.3 16.5 1.0 O A:HOH862 3.7 30.4 1.0 O A:HOH741 4.1 18.5 1.0 O A:HOH856 4.1 19.8 1.0 O A:HOH779 4.3 19.7 1.0 O A:HOH719 4.6 20.2 1.0 CB A:ASP264 4.6 13.9 1.0

E.V.Wong, W.Cao, J.Voros, M.Merchant, Y.Modis, D.D.Hackney, B.Montpetit, E.M.De La Cruz. Pi Release Limits the Intrinsic and Rna-Stimulated Atpase Cycles of Dead-Box Protein 5 (DBP5). J.Mol.Biol. V. 428 492 2016.
ISSN: ESSN 1089-8638
PubMed: 26730886
DOI: 10.1016/J.JMB.2015.12.018