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

Enzymatic activity of Dengue Virus 4 NS3 Helicase in Complex with Ssrna and Adp- Vanadate

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

Protein crystallography data

The structure of Dengue Virus 4 NS3 Helicase in Complex with Ssrna and Adp- Vanadate, PDB code: 2jlx 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) 20.00 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 132.537, 105.207, 72.352, 90.00, 117.62, 90.00
R / Rfree (%) 19.565 / 24.506

Other elements in 2jlx:

The structure of Dengue Virus 4 NS3 Helicase in Complex with Ssrna and Adp- Vanadate also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Vanadium (V) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Dengue Virus 4 NS3 Helicase in Complex with Ssrna and Adp- Vanadate (pdb code 2jlx). 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- Vanadate, PDB code: 2jlx:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 2jlx

Go back to Manganese Binding Sites List in 2jlx
Manganese binding site 1 out of 2 in the Dengue Virus 4 NS3 Helicase in Complex with Ssrna and Adp- Vanadate


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- Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1621

b:17.4
occ:1.00
O4 A:VO41620 1.7 26.7 1.0
O1B A:ADP1619 1.9 16.3 1.0
O A:HOH2198 2.0 4.2 1.0
OG1 A:THR200 2.2 20.3 1.0
O A:HOH2197 2.3 20.4 1.0
O A:HOH2196 2.4 28.9 1.0
PB A:ADP1619 3.2 15.6 1.0
CB A:THR200 3.2 19.5 1.0
V A:VO41620 3.5 27.4 1.0
O3B A:ADP1619 3.6 17.8 1.0
OE2 A:GLU285 3.7 27.6 1.0
OD2 A:ASP284 3.8 23.5 1.0
O1A A:ADP1619 3.9 22.6 1.0
N A:THR200 3.9 19.4 1.0
CA A:GLY414 4.0 21.1 1.0
O2B A:ADP1619 4.1 15.1 1.0
CA A:THR200 4.2 19.5 1.0
O2 A:VO41620 4.2 26.8 1.0
OD1 A:ASP284 4.3 24.4 1.0
O3A A:ADP1619 4.3 20.4 1.0
CG2 A:THR200 4.3 19.5 1.0
PA A:ADP1619 4.4 20.9 1.0
O3 A:VO41620 4.5 26.6 1.0
CG A:ASP284 4.5 21.2 1.0
O A:GLY414 4.5 20.4 1.0
CD A:GLU285 4.7 24.5 1.0
O2A A:ADP1619 4.7 21.1 1.0
N A:GLY414 4.7 21.7 1.0
CB A:LYS199 4.8 18.8 1.0
O1 A:VO41620 4.8 27.7 1.0
C A:GLY414 4.8 20.8 1.0
CE A:LYS199 5.0 14.7 1.0
C A:LYS199 5.0 19.1 1.0

Manganese binding site 2 out of 2 in 2jlx

Go back to Manganese Binding Sites List in 2jlx
Manganese binding site 2 out of 2 in the Dengue Virus 4 NS3 Helicase in Complex with Ssrna and Adp- Vanadate


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- Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1621

b:17.7
occ:1.00
O3 B:VO41620 1.6 27.7 1.0
O B:HOH2170 2.0 3.4 1.0
O B:HOH2171 2.0 23.7 1.0
OG1 B:THR200 2.1 19.5 1.0
O1B B:ADP1619 2.2 19.9 1.0
O B:HOH2172 2.3 26.8 1.0
CB B:THR200 3.3 19.2 1.0
PB B:ADP1619 3.4 15.4 1.0
V B:VO41620 3.4 28.0 1.0
OE2 B:GLU285 3.6 26.1 1.0
O3B B:ADP1619 3.6 19.0 1.0
OD2 B:ASP284 4.0 24.4 1.0
N B:THR200 4.0 19.3 1.0
O1A B:ADP1619 4.0 22.1 1.0
OD1 B:ASP284 4.0 24.8 1.0
CA B:GLY414 4.1 21.1 1.0
CA B:THR200 4.3 19.4 1.0
O2B B:ADP1619 4.3 17.2 1.0
CG2 B:THR200 4.3 19.2 1.0
O4 B:VO41620 4.4 26.3 1.0
O1 B:VO41620 4.4 26.2 1.0
O3A B:ADP1619 4.4 20.8 1.0
CG B:ASP284 4.4 21.1 1.0
PA B:ADP1619 4.6 21.5 1.0
O B:GLY414 4.6 20.6 1.0
CD B:GLU285 4.7 22.8 1.0
O2 B:VO41620 4.8 25.6 1.0
N B:GLY414 4.8 21.6 1.0
O2A B:ADP1619 4.8 22.4 1.0
CB B:LYS199 4.8 18.6 1.0
C B:GLY414 4.9 20.8 1.0
CE B:LYS199 5.0 15.5 1.0

Reference:

D.H.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
Page generated: Tue Dec 15 04:03:27 2020

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