Magnesium in PDB 4tyw: Dead-Box Helicase MSS116 Bound to Ssrna and Adp-Bef

All present enzymatic activity of Dead-Box Helicase MSS116 Bound to Ssrna and Adp-Bef:
3.6.4.13;

The structure of Dead-Box Helicase MSS116 Bound to Ssrna and Adp-Bef, PDB code: 4tyw was solved by A.L.Mallam, D.J.Sidote, A.M.Lambowitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.24 / 2.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	89.829, 126.260, 55.545, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 25.4

The structure of Dead-Box Helicase MSS116 Bound to Ssrna and Adp-Bef also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Magnesium atom in the Dead-Box Helicase MSS116 Bound to Ssrna and Adp-Bef (pdb code 4tyw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Dead-Box Helicase MSS116 Bound to Ssrna and Adp-Bef, PDB code: 4tyw:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dead-Box Helicase MSS116 Bound to Ssrna and Adp-Bef


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dead-Box Helicase MSS116 Bound to Ssrna and Adp-Bef within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:38.2 occ:1.00 O A:HOH802 2.1 36.1 1.0 O A:HOH799 2.1 35.2 1.0 O A:HOH801 2.1 35.6 1.0 O A:HOH800 2.1 40.5 1.0 O2B A:ADP604 2.1 35.2 1.0 F1 A:BEF603 2.1 39.1 1.0 HA2 A:GLY439 3.2 39.6 1.0 BE A:BEF603 3.3 42.0 1.0 PB A:ADP604 3.3 40.9 1.0 HE2 A:LYS158 3.5 49.6 1.0 O1B A:ADP604 3.7 45.3 1.0 HB2 A:LYS158 3.7 46.5 1.0 OD2 A:ASP267 3.8 35.8 1.0 OE2 A:GLU268 3.8 39.1 1.0 OD1 A:ASP267 3.9 33.6 1.0 OG1 A:THR159 4.0 37.3 1.0 F2 A:BEF603 4.0 42.0 1.0 CA A:GLY439 4.1 33.0 1.0 O2A A:ADP604 4.1 38.5 1.0 HG1 A:THR159 4.2 44.8 1.0 HA3 A:GLY439 4.2 39.6 1.0 HD11 A:LEU192 4.2 41.4 1.0 O3B A:ADP604 4.2 38.8 1.0 F3 A:BEF603 4.2 39.9 1.0 CG A:ASP267 4.3 36.5 1.0 HH22 A:ARG469 4.4 45.8 1.0 O A:GLY439 4.4 35.5 1.0 CE A:LYS158 4.4 41.4 1.0 O3A A:ADP604 4.5 42.8 1.0 PA A:ADP604 4.6 40.4 1.0 H A:THR159 4.6 45.8 1.0 CB A:LYS158 4.6 38.7 1.0 O1A A:ADP604 4.6 37.3 1.0 HZ3 A:LYS158 4.7 51.0 1.0 HB3 A:LYS158 4.7 46.5 1.0 O A:HOH711 4.7 34.6 1.0 HE3 A:LYS158 4.7 49.6 1.0 C A:GLY439 4.8 35.3 1.0 HD21 A:LEU192 4.8 40.1 1.0 H A:LYS158 4.9 48.1 1.0 CD A:GLU268 4.9 39.3 1.0 N A:THR159 4.9 38.2 1.0 NZ A:LYS158 4.9 42.5 1.0 HZ2 A:LYS158 4.9 51.0 1.0 HG2 A:GLU268 5.0 43.9 1.0 H A:GLY439 5.0 42.0 1.0

Magnesium binding site 2 out of 2 in the Dead-Box Helicase MSS116 Bound to Ssrna and Adp-Bef


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dead-Box Helicase MSS116 Bound to Ssrna and Adp-Bef within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:46.7 occ:1.00 H A:VAL445 2.4 49.2 1.0 O A:PHE442 2.4 38.2 1.0 O A:ARG466 2.7 40.9 1.0 O A:HOH765 2.8 42.1 1.0 HB A:VAL445 2.8 48.3 1.0 HA A:THR467 2.9 49.5 1.0 HD3 A:ARG469 2.9 47.9 1.0 HG23 A:VAL445 2.9 43.9 1.0 N A:VAL445 3.2 41.0 1.0 H A:ASN444 3.4 46.8 1.0 HB2 A:ARG469 3.4 49.2 1.0 CB A:VAL445 3.5 40.3 1.0 HG3 A:ARG469 3.5 48.5 1.0 CG2 A:VAL445 3.5 36.6 1.0 C A:PHE442 3.6 39.0 1.0 N A:ASN444 3.6 39.0 1.0 CD A:ARG469 3.6 39.9 1.0 HG21 A:VAL445 3.7 43.9 1.0 O A:HOH713 3.8 32.8 1.0 C A:ARG466 3.8 38.9 1.0 CA A:THR467 3.8 41.2 1.0 HD2 A:ARG469 3.8 47.9 1.0 HA A:PRO443 3.9 48.1 1.0 CA A:VAL445 3.9 37.3 1.0 CG A:ARG469 3.9 40.4 1.0 H A:ARG469 4.0 53.9 1.0 C A:PRO443 4.0 39.8 1.0 O A:HOH749 4.0 40.4 1.0 CB A:ARG469 4.1 41.0 1.0 H A:PHE442 4.1 41.9 1.0 HB2 A:PHE442 4.2 46.5 1.0 C A:ASN444 4.2 39.3 1.0 CA A:PRO443 4.2 40.1 1.0 N A:THR467 4.3 40.9 1.0 CA A:ASN444 4.3 38.3 1.0 HG1 A:THR467 4.3 59.3 1.0 HA A:ASN444 4.3 46.0 1.0 N A:PRO443 4.4 38.6 1.0 HG22 A:VAL445 4.4 43.9 1.0 O A:VAL445 4.4 39.1 1.0 O A:HOH810 4.4 42.2 1.0 H A:ALA468 4.4 54.7 1.0 C A:THR467 4.4 44.4 1.0 CA A:PHE442 4.6 38.7 1.0 N A:PHE442 4.6 34.9 1.0 N A:ALA468 4.6 45.6 1.0 N A:ARG469 4.6 44.9 1.0 O A:PRO443 4.6 36.5 1.0 C A:VAL445 4.7 39.5 1.0 HA A:VAL445 4.7 44.8 1.0 HB3 A:ARG469 4.8 49.2 1.0 CB A:THR467 4.8 45.5 1.0 CB A:PHE442 4.8 38.8 1.0 CG1 A:VAL445 4.8 34.9 1.0 HG2 A:ARG469 4.8 48.5 1.0 HB A:THR467 4.9 54.7 1.0 NE A:ARG469 4.9 38.1 1.0 OG1 A:THR467 4.9 49.4 1.0 HG11 A:VAL445 5.0 41.9 1.0 HE A:ARG469 5.0 45.8 1.0

A.L.Mallam, D.J.Sidote, A.M.Lambowitz. Molecular Insights Into Rna and Dna Helicase Evolution From the Determinants of Specificity For A Dead-Box Rna Helicase. Elife V. 4 2014.
ISSN: ESSN 2050-084X
PubMed: 25497230
DOI: 10.7554/ELIFE.04630