Sodium 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:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Sodium atom in the Rna Methyltransferase of Sudan Ebola Virus (pdb code 6yu8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 11 binding sites of Sodium where determined in the Rna Methyltransferase of Sudan Ebola Virus, PDB code: 6yu8:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 11 in the Rna Methyltransferase of Sudan Ebola Virus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Rna Methyltransferase of Sudan Ebola Virus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2106 b:44.8 occ:1.00 O A:HOH2478 2.7 61.9 1.0 O A:HOH2219 2.9 31.9 1.0 ND2 A:ASN1973 3.0 30.6 1.0 CA A:TRP1970 3.4 24.1 1.0 N A:TRP1970 3.8 24.1 1.0 CD1 A:TRP1970 3.9 26.6 1.0 O A:CYS1969 4.0 24.9 1.0 CG A:ASN1973 4.0 30.7 1.0 CB A:TRP1970 4.0 24.1 1.0 C A:CYS1969 4.0 25.0 1.0 CB A:ASN1973 4.1 27.2 1.0 CG A:TRP1970 4.2 25.2 1.0 CE1 A:TYR1974 4.3 31.1 1.0 O A:HOH2405 4.4 52.5 1.0 C A:TRP1970 4.6 23.7 1.0 O A:HOH2411 4.7 47.9 1.0 CD1 A:TYR1974 4.7 29.1 1.0 O A:HOH2248 4.7 73.3 1.0 O A:TRP1970 4.8 24.1 1.0 O A:ASP1966 4.8 24.4 1.0 NE1 A:TRP1970 4.9 26.7 1.0 O A:HOH2257 4.9 38.6 1.0 CB A:CYS1969 5.0 28.1 1.0

Sodium binding site 2 out of 11 in the Rna Methyltransferase of Sudan Ebola Virus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Rna Methyltransferase of Sudan Ebola Virus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2107 b:42.1 occ:1.00 OE2 A:GLU1858 2.5 32.1 1.0 CL A:CL2112 2.7 61.4 1.0 O A:HOH2267 2.9 26.4 1.0 N A:ARG1873 3.1 29.3 1.0 CD A:GLU1858 3.3 31.8 1.0 OE1 A:GLU1858 3.3 32.4 1.0 O A:HOH2318 3.5 31.0 1.0 CA A:PRO1872 3.5 28.4 1.0 C A:PRO1872 3.8 29.1 1.0 CB A:ARG1873 3.8 33.4 1.0 CB A:PRO1872 3.9 29.1 1.0 O A:HOH2256 3.9 37.5 1.0 CA A:ARG1873 4.1 31.0 1.0 O A:HOH2210 4.2 37.9 1.0 O A:HOH2231 4.5 28.4 1.0 O A:HOH2240 4.6 37.7 1.0 NH1 A:ARG1873 4.6 52.0 1.0 CZ A:ARG1873 4.7 52.5 1.0 CG A:GLU1858 4.7 28.7 1.0 NH2 A:ARG1873 4.7 52.6 1.0 N A:MET1874 4.9 31.4 1.0 N A:PRO1872 4.9 28.5 1.0 O A:PRO1872 5.0 28.8 1.0

Sodium binding site 3 out of 11 in the Rna Methyltransferase of Sudan Ebola Virus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Rna Methyltransferase of Sudan Ebola Virus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2108 b:34.4 occ:1.00 O A:THR1899 2.7 28.8 1.0 OD1 A:ASN1853 2.9 25.1 1.0 N A:ILE1901 3.1 24.0 1.0 CA A:ASP1900 3.6 25.8 1.0 CG2 A:ILE1901 3.6 24.9 1.0 CG A:ASN1853 3.7 25.6 1.0 CG1 A:ILE1901 3.7 25.6 1.0 ND2 A:ASN1853 3.7 26.0 1.0 C A:THR1899 3.8 27.9 1.0 CD2 A:LEU1855 3.8 28.9 1.0 C A:ASP1900 3.8 25.2 1.0 CB A:ILE1901 4.0 24.6 1.0 CG A:LEU1855 4.0 27.7 1.0 CA A:ILE1901 4.1 24.6 1.0 CA A:ALA1831 4.1 25.3 1.0 N A:ASP1900 4.2 26.5 1.0 CB A:ALA1831 4.2 25.9 1.0 N A:ALA1831 4.3 24.9 1.0 OD1 A:ASP1900 4.5 26.3 1.0 CD1 A:ILE1901 4.6 26.4 1.0 N A:LEU1855 4.7 24.1 1.0 CB A:ASP1900 4.9 26.0 1.0 CD1 A:LEU1855 4.9 28.1 1.0 C A:THR1854 4.9 24.1 1.0

Sodium binding site 4 out of 11 in the Rna Methyltransferase of Sudan Ebola Virus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Rna Methyltransferase of Sudan Ebola Virus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2109 b:69.3 occ:1.00 CL A:CL2113 2.4 63.9 1.0 OH A:TYR1983 4.0 46.1 1.0 O A:PHE1763 4.1 44.7 1.0 O A:GLY1980 4.2 30.4 1.0 CZ A:TYR1983 4.6 42.2 1.0 CA A:SER1981 4.6 29.1 1.0 OG A:SER1981 4.8 38.1 1.0 CB A:SER1981 4.9 31.9 1.0 CA A:LYS1764 5.0 53.8 1.0

Sodium binding site 5 out of 11 in the Rna Methyltransferase of Sudan Ebola Virus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Rna Methyltransferase of Sudan Ebola Virus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2110 b:48.9 occ:1.00 O A:HIS1947 2.7 36.0 1.0 O A:PRO1915 2.8 34.9 1.0 CG2 A:ILE1948 3.5 36.8 1.0 CB A:ALA1918 3.5 30.6 1.0 N A:ALA1918 3.5 31.9 1.0 C A:ASN1916 3.5 35.7 1.0 CA A:ASN1916 3.5 35.7 1.0 C A:PRO1915 3.8 35.0 1.0 CA A:ILE1948 3.8 35.2 1.0 C A:HIS1947 3.8 34.2 1.0 O A:ASN1916 3.9 36.4 1.0 N A:ASP1917 3.9 34.9 1.0 CA A:ALA1918 4.1 30.4 1.0 CB A:ILE1948 4.1 36.5 1.0 N A:ASN1916 4.1 34.7 1.0 N A:ILE1948 4.3 34.2 1.0 CG2 A:ILE1943 4.3 27.3 1.0 CD2 A:HIS1947 4.4 33.1 1.0 CG2 A:VAL1828 4.5 27.6 1.0 C A:ASP1917 4.5 33.4 1.0 O A:HOH2205 4.6 41.8 1.0 CA A:ASP1917 4.7 34.7 1.0 CB A:ASN1916 4.8 38.0 1.0 CG2 A:ILE1914 4.8 30.9 1.0 O A:ALA1918 4.9 29.4 1.0

Sodium binding site 6 out of 11 in the Rna Methyltransferase of Sudan Ebola Virus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Rna Methyltransferase of Sudan Ebola Virus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2111 b:63.9 occ:1.00 O A:HOH2348 2.5 43.4 1.0 O A:HOH2245 3.2 53.1 1.0 O A:HOH2492 3.2 73.6 1.0 OD2 A:ASP1917 3.2 45.1 1.0 CB A:SER1826 3.8 29.5 1.0 CG A:ASP1917 3.9 42.3 1.0 O A:HOH2230 4.0 56.3 1.0 O A:HOH2476 4.2 55.0 1.0 CB A:GLU1825 4.2 33.5 1.0 O A:HOH2484 4.2 81.0 1.0 OD1 A:ASP1917 4.4 40.6 1.0 O A:HOH2263 4.4 52.3 1.0 NZ A:LYS1849 4.4 42.3 1.0 CE A:LYS1849 4.5 41.3 1.0 OG A:SER1826 4.5 31.9 1.0 O A:ASP1917 4.6 33.6 1.0 O A:GLU1825 4.7 30.9 1.0 CB A:ASP1917 4.7 37.1 1.0 C A:GLU1825 4.7 30.4 1.0 N A:SER1826 4.8 29.5 1.0 CA A:SER1826 4.8 28.3 1.0 O A:HOH2303 4.9 68.2 1.0

Sodium binding site 7 out of 11 in the Rna Methyltransferase of Sudan Ebola Virus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Rna Methyltransferase of Sudan Ebola Virus within 5.0Å range: probe atom residue distance (Å) B Occ B:Na205 b:38.5 occ:1.00 O A:THR2010 2.7 30.4 1.0 CL B:CL210 2.7 50.5 1.0 N B:THR104 3.0 30.8 1.0 CA B:ARG103 3.4 30.3 1.0 O A:HOH2250 3.5 43.8 1.0 OG1 B:THR104 3.5 34.2 1.0 CD B:ARG103 3.6 32.2 1.0 CB A:THR2010 3.7 32.0 1.0 C B:ARG103 3.7 30.8 1.0 C A:THR2010 3.8 30.8 1.0 CB B:ARG103 3.9 30.2 1.0 OG1 A:THR2010 4.0 33.3 1.0 CA B:THR104 4.1 31.6 1.0 CB B:THR104 4.1 33.6 1.0 CG2 B:THR104 4.2 34.9 1.0 CA A:THR2010 4.3 30.3 1.0 CG B:ARG103 4.4 30.6 1.0 O A:HOH2420 4.5 30.0 1.0 O B:PRO102 4.6 31.6 1.0 N B:ALA105 4.7 31.0 1.0 N B:ARG103 4.7 30.6 1.0 NE B:ARG103 4.8 32.5 1.0 CG2 A:THR2010 4.8 32.3 1.0 O B:HOH307 4.9 32.5 1.0 N A:THR2011 4.9 30.6 1.0 O B:ARG103 4.9 31.4 1.0 C B:THR104 4.9 31.6 1.0

Sodium binding site 8 out of 11 in the Rna Methyltransferase of Sudan Ebola Virus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Rna Methyltransferase of Sudan Ebola Virus within 5.0Å range: probe atom residue distance (Å) B Occ B:Na206 b:48.3 occ:1.00 O B:HOH313 2.8 34.6 1.0 O B:HOH352 2.9 39.9 1.0 OG1 B:THR69 3.3 35.9 1.0 ND2 B:ASN84 3.3 38.0 1.0 O B:HOH390 3.5 34.0 1.0 O1 B:GOL202 4.1 41.9 1.0 CB B:THR69 4.4 34.6 1.0 CG B:ASN84 4.6 37.9 1.0 CG B:GLN82 4.8 34.6 1.0 O B:ARG67 4.9 34.9 1.0

Sodium binding site 9 out of 11 in the Rna Methyltransferase of Sudan Ebola Virus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Rna Methyltransferase of Sudan Ebola Virus within 5.0Å range: probe atom residue distance (Å) B Occ B:Na207 b:66.7 occ:1.00 O A:HOH2420 2.1 30.0 1.0 O B:HOH307 3.0 32.5 1.0 NE B:ARG103 3.9 32.5 1.0 O B:HOH375 4.0 45.0 1.0 CD B:ARG103 4.2 32.2 1.0 OE2 B:GLU108 4.4 40.8 1.0 O B:HOH303 4.4 39.0 1.0 CL B:CL210 4.6 50.5 1.0 CZ B:ARG103 4.7 33.3 1.0 OE1 A:GLN2012 4.7 36.2 1.0 NE2 A:GLN2012 4.8 33.0 1.0 NH2 B:ARG103 4.9 35.0 1.0

Sodium binding site 10 out of 11 in the Rna Methyltransferase of Sudan Ebola Virus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Rna Methyltransferase of Sudan Ebola Virus within 5.0Å range: probe atom residue distance (Å) B Occ B:Na208 b:52.6 occ:1.00 O B:HOH393 2.6 80.7 1.0 NE2 B:GLN82 3.3 36.0 1.0 O B:HOH342 3.4 44.1 1.0 CB B:SER17 3.8 39.6 1.0 C B:LEU18 4.0 38.7 1.0 N B:LEU18 4.1 39.0 1.0 OE1 B:GLN82 4.1 37.0 1.0 C B:SER17 4.1 39.3 1.0 CD B:GLN82 4.2 36.8 1.0 N B:ARG19 4.2 37.5 1.0 O B:LEU18 4.2 39.1 1.0 CA B:LEU18 4.2 39.3 1.0 CB B:ARG19 4.3 38.0 1.0 O B:SER17 4.3 39.9 1.0 CA B:SER17 4.6 39.1 1.0 CA B:ARG19 4.7 37.1 1.0 OG B:SER17 4.8 41.0 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