Magnesium in PDB 6yu8: Rna Methyltransferase of Sudan Ebola Virus

The structure of Rna Methyltransferase of Sudan Ebola Virus, PDB code: 6yu8 was solved by F.Ferron, C.Valle, V.Zamboni, B.Canard, E.Decroly, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	82.62 / 1.84
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	153.761, 153.761, 105.354, 90, 90, 120
R / Rfree (%)	19.5 / 21.5

The structure of Rna Methyltransferase of Sudan Ebola Virus also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Sodium	(Na)	11 atoms

The binding sites of Magnesium atom in the Rna Methyltransferase of Sudan Ebola Virus (pdb code 6yu8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Rna Methyltransferase of Sudan Ebola Virus, PDB code: 6yu8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Rna Methyltransferase of Sudan Ebola Virus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rna Methyltransferase of Sudan Ebola Virus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2114 b:51.4 occ:1.00 O A:HOH2266 2.7 35.1 1.0 OE2 A:GLU1832 2.7 38.6 1.0 OD2 A:ASP1924 2.8 32.4 1.0 CD A:GLU1832 3.2 36.9 1.0 OE1 A:GLU1832 3.2 37.0 1.0 O A:GLU1832 3.2 30.2 1.0 CD2 A:HIS1811 3.5 31.6 1.0 N A:GLY1837 3.6 26.7 1.0 NE2 A:HIS1811 3.6 32.1 1.0 CG A:ASP1924 3.7 30.8 1.0 CB A:ASP1924 3.9 25.7 1.0 C A:GLU1832 4.0 29.3 1.0 CA A:GLY1837 4.0 27.5 1.0 OG A:SER1836 4.0 34.8 1.0 CA A:GLU1832 4.1 28.1 1.0 O A:HOH2387 4.1 49.3 1.0 N A:SER1836 4.3 29.0 1.0 CG A:GLU1832 4.4 32.5 1.0 CB A:GLU1832 4.6 30.0 1.0 C A:SER1836 4.6 27.8 1.0 CG A:HIS1811 4.8 31.3 1.0 O A:HOH2331 4.8 35.9 1.0 CA A:SER1836 4.8 29.1 1.0 O A:HOH2234 4.8 26.3 1.0 C A:GLY1835 4.9 29.1 1.0 OD1 A:ASP1924 4.9 30.0 1.0 N A:GLY1835 4.9 27.2 1.0 O A:HOH2337 4.9 39.5 1.0 O A:HOH2283 4.9 46.4 1.0 CE1 A:HIS1811 5.0 32.2 1.0 CA A:GLY1835 5.0 28.1 1.0

Magnesium binding site 2 out of 2 in the Rna Methyltransferase of Sudan Ebola Virus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rna Methyltransferase of Sudan Ebola Virus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2115 b:40.1 occ:1.00 O A:TYR1821 2.3 36.0 1.0 O A:HOH2339 2.3 41.8 1.0 O A:HOH2409 2.4 47.9 1.0 O A:HOH2202 2.5 45.0 1.0 O A:LEU1818 2.5 33.2 1.0 OH A:TYR1845 2.5 33.9 1.0 CZ A:TYR1845 3.4 31.8 1.0 CE2 A:TYR1845 3.4 31.0 1.0 C A:LEU1818 3.4 34.3 1.0 C A:TYR1821 3.5 36.0 1.0 O A:TRP1819 3.8 42.4 1.0 CA A:TRP1819 3.9 41.5 1.0 C A:TRP1819 4.0 41.7 1.0 N A:TRP1819 4.0 37.4 1.0 N A:TYR1821 4.1 37.9 1.0 CA A:TYR1821 4.3 36.8 1.0 CB A:LEU1818 4.3 31.3 1.0 O A:HOH2416 4.4 75.5 1.0 N A:ASN1822 4.4 35.9 1.0 CA A:ASN1822 4.5 37.2 1.0 OD1 A:ASP1815 4.5 36.6 1.0 CA A:LEU1818 4.5 31.6 1.0 O A:ASP1815 4.6 31.9 1.0 CE A:LYS1844 4.6 43.9 1.0 CE1 A:TYR1845 4.6 30.8 1.0 CD2 A:TYR1845 4.7 30.3 1.0 NZ A:LYS1844 4.8 45.6 1.0 N A:GLU1820 4.8 40.9 1.0 O A:HOH2293 4.8 48.5 1.0 CB A:TYR1821 4.9 37.0 1.0

C.Valle, B.Martin, F.Ferron, V.Roig-Zamboni, A.Desmyter, F.Debart, J.J.Vasseur, B.Canard, B.Coutard, E.Decroly. First Insights Into the Structural Features of Ebola Virus Methyltransferase Activities. Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
PubMed: 33503246
DOI: 10.1093/NAR/GKAA1276