Magnesium in PDB 4v0r: Dengue Virus Full Length NS5 Complexed with Gtp and Sah

The structure of Dengue Virus Full Length NS5 Complexed with Gtp and Sah, PDB code: 4v0r was solved by Y.Zhao, S.Soh, J.Zheng, W.W.Phoo, K.Swaminathan, T.C.Cornvik, S.P.Lim, P.-Y.Shi, J.Lescar, S.G.Vasudevan, D.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.88 / 2.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	94.860, 150.970, 69.280, 90.00, 90.00, 90.00
R / Rfree (%)	18.75 / 23.68

The structure of Dengue Virus Full Length NS5 Complexed with Gtp 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 Gtp and Sah (pdb code 4v0r). 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 Gtp and Sah, PDB code: 4v0r:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dengue Virus Full Length NS5 Complexed with Gtp 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 Gtp and Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1885 b:37.4 occ:1.00 O A:HOH2309 1.8 27.6 1.0 O A:HOH2314 1.9 41.5 1.0 O A:HOH2308 1.9 30.4 1.0 OD1 A:ASP664 2.0 42.8 1.0 O A:HOH2371 2.3 37.1 1.0 OD1 A:ASP533 2.4 40.2 1.0 CG A:ASP664 3.0 33.6 1.0 CG A:ASP533 3.3 41.2 1.0 OD2 A:ASP664 3.4 37.9 1.0 OD2 A:ASP533 3.6 46.1 1.0 O A:PRO707 4.1 25.6 1.0 O A:ALA531 4.2 22.9 1.0 CB A:ASP664 4.3 22.5 1.0 O A:CYS665 4.4 20.6 1.0 N A:CYS665 4.5 16.3 1.0 CA A:ASP664 4.5 18.2 1.0 CB A:ASP533 4.6 32.1 1.0 CB A:ALA531 4.7 11.9 1.0 C A:PRO707 4.7 22.3 1.0 C A:ALA531 4.7 19.3 1.0 CA A:ASP533 4.8 26.3 1.0 CA A:PHE708 4.8 31.4 1.0 N A:ASP533 4.9 21.4 1.0

Magnesium binding site 2 out of 2 in the Dengue Virus Full Length NS5 Complexed with Gtp 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 Gtp and Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1886 b:76.4 occ:1.00 O2B A:GTP1884 1.8 94.2 1.0 O2G A:GTP1884 1.9 90.6 1.0 PG A:GTP1884 2.7 89.2 1.0 O3B A:GTP1884 2.7 0.2 1.0 PB A:GTP1884 2.7 91.5 1.0 O A:HOH2007 3.1 60.8 1.0 O A:HOH2004 3.3 64.7 1.0 O1G A:GTP1884 3.3 86.2 1.0 O1A A:GTP1884 3.6 54.9 1.0 O1B A:GTP1884 3.8 88.4 1.0 O3A A:GTP1884 3.8 0.4 1.0 O3G A:GTP1884 4.1 88.5 1.0 NZ A:LYS29 4.1 55.6 1.0 NH2 A:ARG22 4.3 76.6 1.0 PA A:GTP1884 4.4 51.6 1.0 CE2 A:PHE25 4.7 60.2 1.0 NH1 A:ARG22 4.7 77.4 1.0 NH1 A:ARG211 4.8 55.5 1.0 N7 A:GTP1884 4.9 55.9 1.0

Y.Zhao, S.Soh, J.Zheng, W.W.Phoo, K.Swaminathan, T.C.Cornvik, S.P.Lim, P.-Y.Shi, J.Lescar, S.G.Vasudevan, D.Luo. Crystal Structure of the Dengue Virus NS5 Protein Reveals A Novel Inter-Domain Interface Essential For Protein Flexibility and Virus Replication Plos Pathog. 2015.
ISSN: ESSN 1553-7374
DOI: 10.1371/JOURNAL.PPAT.1004682