Magnesium in PDB 3o8d: Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv

All present enzymatic activity of Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv:
3.4.21.98; 3.6.1.15; 3.6.4.13;

The structure of Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv, PDB code: 3o8d was solved by T.C.Appleby, J.R.Somoza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.02 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.749, 110.416, 144.374, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 23.3

The structure of Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Magnesium atom in the Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv (pdb code 3o8d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv, PDB code: 3o8d:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg850 b:18.4 occ:1.00 O1B A:ADP875 2.0 15.7 1.0 F1 A:BEF885 2.1 18.4 1.0 O A:HOH633 2.2 16.4 1.0 OG A:SER211 2.2 15.9 1.0 O A:HOH2 2.3 15.8 1.0 OE2 A:GLU291 2.3 15.6 1.0 PB A:ADP875 3.2 16.7 1.0 CD A:GLU291 3.2 18.6 1.0 BE A:BEF885 3.2 17.6 1.0 CB A:SER211 3.3 15.7 1.0 OE1 A:GLU291 3.4 17.2 1.0 O3B A:ADP875 3.5 16.8 1.0 OD2 A:ASP290 4.0 20.6 1.0 O2A A:ADP875 4.0 20.6 1.0 N A:SER211 4.0 14.4 1.0 OD1 A:ASP290 4.1 17.1 1.0 F3 A:BEF885 4.1 15.5 1.0 CA A:SER211 4.2 15.5 1.0 O3A A:ADP875 4.2 16.9 1.0 O2B A:ADP875 4.3 15.5 1.0 F2 A:BEF885 4.4 18.9 1.0 O A:HOH1 4.4 16.3 1.0 CG A:ASP290 4.4 20.6 1.0 CA A:GLY417 4.5 18.3 1.0 PA A:ADP875 4.5 19.7 1.0 CG A:GLU291 4.6 17.5 1.0 O A:GLY417 4.7 20.4 1.0 CB A:LYS210 4.7 17.2 1.0 CE A:LYS210 4.7 17.3 1.0 O A:HOH638 4.7 16.2 1.0 NH2 A:ARG467 4.8 17.8 1.0 C A:LYS210 4.8 16.2 1.0 O1A A:ADP875 4.8 20.2 1.0 ND2 A:ASN229 4.9 22.8 1.0

Magnesium binding site 2 out of 2 in the Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg850 b:20.4 occ:1.00 F1 B:BEF885 2.1 18.0 1.0 O1B B:ADP875 2.1 16.8 1.0 OG B:SER211 2.1 19.3 1.0 O B:HOH644 2.2 21.4 1.0 O B:HOH637 2.3 16.7 1.0 OE2 B:GLU291 2.4 22.1 1.0 CB B:SER211 3.1 20.7 1.0 PB B:ADP875 3.2 20.0 1.0 BE B:BEF885 3.2 20.0 1.0 CD B:GLU291 3.3 28.1 1.0 O3B B:ADP875 3.5 20.0 1.0 OE1 B:GLU291 3.5 24.2 1.0 OD2 B:ASP290 3.9 21.7 1.0 O2A B:ADP875 4.0 19.8 1.0 N B:SER211 4.1 17.1 1.0 F3 B:BEF885 4.1 24.4 1.0 OD1 B:ASP290 4.1 20.6 1.0 CA B:SER211 4.2 21.1 1.0 O B:HOH632 4.2 17.1 1.0 O2B B:ADP875 4.3 19.8 1.0 O3A B:ADP875 4.3 21.0 1.0 F2 B:BEF885 4.3 19.3 1.0 CG B:ASP290 4.4 22.7 1.0 CA B:GLY417 4.4 20.2 1.0 PA B:ADP875 4.5 19.5 1.0 O B:GLY417 4.7 21.0 1.0 CG B:GLU291 4.7 17.3 1.0 ND2 B:ASN229 4.7 24.7 1.0 CE B:LYS210 4.7 19.5 1.0 O B:HOH662 4.8 19.7 1.0 NH2 B:ARG467 4.8 21.0 1.0 CB B:LYS210 4.8 22.1 1.0 O1A B:ADP875 4.8 17.4 1.0 C B:LYS210 4.9 17.6 1.0 NZ B:LYS210 5.0 18.3 1.0

T.C.Appleby, R.Anderson, O.Fedorova, A.M.Pyle, R.Wang, X.Liu, K.M.Brendza, J.R.Somoza. Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv. J.Mol.Biol. V. 405 1139 2011.
ISSN: ISSN 0022-2836
PubMed: 21145896
DOI: 10.1016/J.JMB.2010.11.034