Manganese in PDB 2jly: Dengue Virus 4 NS3 Helicase in Complex with Ssrna and Adp- Phosphate

All present enzymatic activity of Dengue Virus 4 NS3 Helicase in Complex with Ssrna and Adp- Phosphate:
3.4.21.91;

The structure of Dengue Virus 4 NS3 Helicase in Complex with Ssrna and Adp- Phosphate, PDB code: 2jly was solved by D.H.Luo, T.Xu, R.P.Watson, D.S.Becker, A.Sampath, W.Jahnke, S.S.Yeong, C.H.Wang, S.P.Lim, S.G.Vasudevan, J.Lescar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.99 / 2.4
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	131.748, 105.591, 72.671, 90.00, 117.68, 90.00
R / Rfree (%)	19.911 / 25.494

The binding sites of Manganese atom in the Dengue Virus 4 NS3 Helicase in Complex with Ssrna and Adp- Phosphate (pdb code 2jly). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Dengue Virus 4 NS3 Helicase in Complex with Ssrna and Adp- Phosphate, PDB code: 2jly:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Dengue Virus 4 NS3 Helicase in Complex with Ssrna and Adp- Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Dengue Virus 4 NS3 Helicase in Complex with Ssrna and Adp- Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1621 b:28.1 occ:1.00 O A:HOH2189 2.0 13.9 1.0 O A:HOH2186 2.1 19.1 1.0 O A:HOH2187 2.1 17.5 1.0 O1B A:ADP1619 2.1 31.6 1.0 OG1 A:THR200 2.1 32.5 1.0 O A:HOH2188 2.2 20.3 1.0 CB A:THR200 3.3 32.2 1.0 PB A:ADP1619 3.3 31.0 1.0 O2B A:ADP1619 3.5 30.3 1.0 OE2 A:GLU285 3.6 35.5 1.0 OD2 A:ASP284 3.9 31.5 1.0 O1 A:PO41620 3.9 48.3 0.8 CA A:GLY414 4.0 32.9 1.0 N A:THR200 4.0 32.1 1.0 O2A A:ADP1619 4.1 32.9 1.0 O3B A:ADP1619 4.2 30.1 1.0 CA A:THR200 4.2 32.2 1.0 OD1 A:ASP284 4.3 31.8 1.0 CG2 A:THR200 4.3 32.0 1.0 O3A A:ADP1619 4.4 31.7 1.0 O A:HOH2185 4.5 11.2 1.0 CG A:ASP284 4.5 31.3 1.0 O A:GLY414 4.6 32.8 1.0 CB A:LYS199 4.6 31.4 1.0 PA A:ADP1619 4.7 33.1 1.0 CD A:GLU285 4.7 34.2 1.0 N A:GLY414 4.7 32.9 1.0 CE A:LYS199 4.8 29.0 1.0 C A:GLY414 4.8 32.7 1.0 O4 A:PO41620 4.9 46.5 0.8 P A:PO41620 4.9 47.1 0.8 NH1 A:ARG463 4.9 21.0 1.0 O1A A:ADP1619 5.0 33.8 1.0

Manganese binding site 2 out of 2 in the Dengue Virus 4 NS3 Helicase in Complex with Ssrna and Adp- Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Dengue Virus 4 NS3 Helicase in Complex with Ssrna and Adp- Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1621 b:24.2 occ:1.00 O B:HOH2182 2.1 16.9 1.0 O B:HOH2181 2.1 19.2 1.0 OG1 B:THR200 2.1 32.6 1.0 O B:HOH2180 2.1 15.3 1.0 O B:HOH2179 2.2 23.0 1.0 O1B B:ADP1619 2.2 30.4 1.0 CB B:THR200 3.2 32.1 1.0 PB B:ADP1619 3.4 30.1 1.0 O2B B:ADP1619 3.5 30.5 1.0 OE2 B:GLU285 3.6 35.4 1.0 OD2 B:ASP284 3.9 31.3 1.0 N B:THR200 4.0 32.0 1.0 CA B:GLY414 4.0 32.9 1.0 O2A B:ADP1619 4.1 29.9 1.0 O4 B:PO41620 4.1 48.6 0.8 OD1 B:ASP284 4.2 31.8 1.0 CA B:THR200 4.2 32.3 1.0 CG2 B:THR200 4.3 31.9 1.0 O3A B:ADP1619 4.4 29.6 1.0 CG B:ASP284 4.5 31.3 1.0 O3B B:ADP1619 4.5 28.2 1.0 O B:HOH2178 4.5 10.2 1.0 CB B:LYS199 4.6 31.4 1.0 PA B:ADP1619 4.6 29.4 1.0 CD B:GLU285 4.7 34.0 1.0 O B:GLY414 4.7 32.8 1.0 CE B:LYS199 4.7 28.7 1.0 N B:GLY414 4.8 32.9 1.0 O1A B:ADP1619 4.8 28.7 1.0 C B:GLY414 4.9 32.9 1.0 O2 B:PO41620 4.9 47.5 0.8 P B:PO41620 4.9 47.4 0.8 O1 B:PO41620 5.0 47.0 0.8 C B:LYS199 5.0 31.7 1.0 NH1 B:ARG463 5.0 20.8 1.0

D.Luo, T.Xu, R.P.Watson, D.Scherer-Becker, A.Sampath, W.Jahnke, S.S.Yeong, C.H.Wang, S.P.Lim, A.Strongin, S.G.Vasudevan, J.Lescar. Insights Into Rna Unwinding and Atp Hydrolysis By the Flavivirus NS3 Protein. Embo J. V. 27 3209 2008.
ISSN: ISSN 0261-4189
PubMed: 19008861
DOI: 10.1038/EMBOJ.2008.232