Magnesium in PDB 5nju: Flavivirus NS5 Domain

The structure of Flavivirus NS5 Domain, PDB code: 5nju was solved by S.K.Talapatra, C.Chatrin, F.Kozielski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.05 / 2.10
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.390, 67.390, 272.549, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 22.9

The binding sites of Magnesium atom in the Flavivirus NS5 Domain (pdb code 5nju). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Flavivirus NS5 Domain, PDB code: 5nju:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Flavivirus NS5 Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Flavivirus NS5 Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:13.6 occ:1.00 O A:HOH1123 3.1 21.3 1.0 O A:HOH1189 3.2 14.4 1.0 N A:VAL257 3.2 19.1 1.0 NH2 A:ARG37 3.3 22.9 1.0 CG A:ARG37 3.5 24.9 1.0 CG2 A:VAL257 3.7 16.0 1.0 CB A:VAL257 3.7 22.1 1.0 CG2 A:VAL35 3.7 21.3 1.0 CD A:ARG37 3.8 25.2 1.0 CB A:VAL35 3.8 20.2 1.0 CA A:ASP256 4.0 19.5 1.0 CA A:VAL257 4.1 18.5 1.0 CG1 A:VAL35 4.1 17.5 1.0 C A:ASP256 4.1 21.6 1.0 CB A:ASP256 4.3 20.4 1.0 CZ A:ARG37 4.3 21.5 1.0 CB A:ALA54 4.3 13.3 1.0 CG A:ASP256 4.4 25.1 1.0 OD1 A:ASP256 4.5 22.9 1.0 NE A:ARG37 4.5 19.0 1.0 O A:HOH1152 4.6 26.0 1.0 O A:VAL257 4.6 20.6 1.0 CB A:ALA60 4.7 12.7 1.0 C A:VAL257 4.9 22.4 1.0 CB A:ARG37 4.9 26.9 1.0 O A:SER56 4.9 16.9 1.0 OD2 A:ASP256 5.0 28.7 1.0

Magnesium binding site 2 out of 2 in the Flavivirus NS5 Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Flavivirus NS5 Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:17.9 occ:1.00 N B:LEU206 3.0 20.8 1.0 OG B:SER232 3.1 22.3 1.0 N B:ASN228 3.2 27.7 1.0 CE1 A:HIS134 3.3 24.9 1.0 C B:ASN228 3.4 31.0 1.0 NE2 B:GLN199 3.5 30.1 1.0 O B:ASN228 3.6 27.1 1.0 CA B:GLY205 3.6 24.6 1.0 N B:THR229 3.7 29.4 1.0 CA B:THR229 3.7 27.8 1.0 O B:LYS226 3.8 27.5 1.0 CA B:ASN228 3.8 25.0 1.0 NE2 A:HIS134 3.8 32.3 1.0 CB B:SER232 3.8 23.2 1.0 C B:GLY205 3.8 18.8 1.0 CB B:LEU206 3.9 20.0 1.0 CA B:LEU206 4.0 19.1 1.0 CG B:LEU206 4.0 26.1 1.0 O B:LEU206 4.0 19.0 1.0 C B:SER227 4.2 23.5 1.0 CA B:SER227 4.3 22.0 1.0 CD B:GLN199 4.3 28.3 1.0 CB B:ASN228 4.3 29.9 1.0 OE1 B:GLN199 4.5 37.3 1.0 OG1 B:THR229 4.5 27.6 1.0 ND1 A:HIS134 4.5 29.6 1.0 C B:LEU206 4.5 24.6 1.0 CD1 B:LEU206 4.5 25.9 1.0 C B:THR229 4.6 21.3 1.0 O B:THR229 4.7 25.6 1.0 CB B:THR229 4.7 29.4 1.0 C B:LYS226 4.8 29.1 1.0

C.Chatrin, S.K.Talapatra, B.Canard, F.Kozielski. The Structure of the Binary Methyltransferase-Sah Complex From Zika Virus Reveals A Novel Conformation For the Mechanism of Mrna Capping. Oncotarget V. 9 3160 2018.
ISSN: ESSN 1949-2553
PubMed: 29423037
DOI: 10.18632/ONCOTARGET.23223