Magnesium in PDB 5dto: Dengue Virus Full Length NS5 Complexed with Viral Cap 0-Rna and Sah

The structure of Dengue Virus Full Length NS5 Complexed with Viral Cap 0-Rna and Sah, PDB code: 5dto was solved by Y.Zhao, T.S.Soh, S.P.Lim, K.Y.Chung, K.Swaminathan, S.G.Vasudevan, P.-Y.Shi, J.Lescar, D.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.33 / 2.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	94.660, 151.394, 69.432, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 24.4

The structure of Dengue Virus Full Length NS5 Complexed with Viral Cap 0-Rna and Sah also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Dengue Virus Full Length NS5 Complexed with Viral Cap 0-Rna and Sah (pdb code 5dto). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Dengue Virus Full Length NS5 Complexed with Viral Cap 0-Rna and Sah, PDB code: 5dto:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dengue Virus Full Length NS5 Complexed with Viral Cap 0-Rna and Sah


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dengue Virus Full Length NS5 Complexed with Viral Cap 0-Rna and Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1004 b:24.7 occ:1.00 OD1 A:ASP664 2.2 37.2 1.0 O A:HOH1160 2.2 22.6 1.0 O A:HOH1144 2.3 18.0 1.0 O A:HOH1145 2.4 25.5 1.0 OD1 A:ASP533 2.6 38.3 1.0 O A:HOH1301 2.9 38.1 1.0 CG A:ASP664 3.0 29.9 1.0 OD2 A:ASP664 3.1 27.6 1.0 CG A:ASP533 3.4 35.6 1.0 OD2 A:ASP533 3.6 46.5 1.0 O A:PRO707 3.8 29.5 1.0 C A:PRO707 4.2 28.1 1.0 CA A:PHE708 4.4 28.5 1.0 CB A:ASP664 4.4 18.2 1.0 N A:PHE708 4.5 28.5 1.0 CB A:PRO707 4.7 28.3 1.0 O A:ALA531 4.7 29.0 1.0 O A:CYS665 4.8 28.4 1.0 N A:CYS709 4.8 31.1 1.0 CA A:ASP664 4.9 17.7 1.0 CB A:ALA531 4.9 19.7 1.0 CB A:ASP533 4.9 20.1 1.0 CG A:PRO707 4.9 28.0 1.0 N A:CYS665 5.0 24.9 1.0

Magnesium binding site 2 out of 2 in the Dengue Virus Full Length NS5 Complexed with Viral Cap 0-Rna and Sah


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dengue Virus Full Length NS5 Complexed with Viral Cap 0-Rna and Sah within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:68.9 occ:1.00 O1A B:M7G0 2.0 73.6 1.0 O B:HOH201 2.0 65.3 1.0 O B:HOH205 2.0 53.4 1.0 O B:HOH207 2.0 69.4 1.0 O2B B:M7G0 2.0 72.9 1.0 OP1 B:A1 2.1 71.9 1.0 PB B:M7G0 3.1 71.9 1.0 P B:A1 3.1 70.9 1.0 PA B:M7G0 3.3 73.2 1.0 O1B B:M7G0 3.4 70.9 1.0 O5' B:A1 3.5 71.1 1.0 O B:HOH204 3.5 54.9 1.0 O3A B:M7G0 3.6 72.4 1.0 N7 B:A1 4.0 73.2 1.0 O2A B:M7G0 4.1 74.6 1.0 C8 B:A1 4.1 72.3 1.0 OG A:SER150 4.1 52.8 1.0 N7 B:G2 4.1 75.5 1.0 O5' B:M7G0 4.4 72.5 1.0 O3B B:M7G0 4.4 71.8 1.0 O4 B:U3 4.4 78.3 1.0 OP2 B:A1 4.5 70.0 1.0 O6 B:G2 4.5 77.6 1.0 C5' B:A1 4.9 70.4 1.0 C5 B:A1 4.9 74.0 1.0 OP2 B:G2 4.9 73.1 1.0 CB A:SER150 4.9 51.1 1.0 N9 B:A1 4.9 72.4 1.0

Y.Zhao, T.S.Soh, S.P.Lim, K.Y.Chung, K.Swaminathan, S.G.Vasudevan, P.-Y.Shi, J.Lescar, D.Luo. Molecular Basis For Specific Viral Rna Recognition and 2'-O-Ribose Methylation By the Dengue Virus Nonstructural Protein 5 (NS5) Proc.Natl.Acad.Sci.Usa V. 112 14834 2015.
ISSN: ESSN 1091-6490
PubMed: 26578813
DOI: 10.1073/PNAS.1514978112