Magnesium in PDB 3sfu: Crystal Structure of Murine Norovirus Rna Dependent Rna Polymerase in Complex with Ribavirin

The structure of Crystal Structure of Murine Norovirus Rna Dependent Rna Polymerase in Complex with Ribavirin, PDB code: 3sfu was solved by K.H.Kim, I.Alam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.85 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	119.952, 196.084, 109.206, 90.00, 114.12, 90.00
R / Rfree (%)	18.1 / 22.9

The binding sites of Magnesium atom in the Crystal Structure of Murine Norovirus Rna Dependent Rna Polymerase in Complex with Ribavirin (pdb code 3sfu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Murine Norovirus Rna Dependent Rna Polymerase in Complex with Ribavirin, PDB code: 3sfu:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Murine Norovirus Rna Dependent Rna Polymerase in Complex with Ribavirin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Murine Norovirus Rna Dependent Rna Polymerase in Complex with Ribavirin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg610 b:29.5 occ:1.00 O A:GLU348 2.7 23.2 1.0 OD2 A:ASP347 2.7 25.3 1.0 OD2 A:ASP243 2.8 19.6 1.0 O A:SER392 2.8 19.7 1.0 O A:HOH802 2.9 13.2 1.0 CG A:ASP243 3.2 23.2 1.0 OD1 A:ASP243 3.5 22.2 1.0 N A:GLU348 3.7 25.1 1.0 C A:GLU348 3.7 24.3 1.0 C A:SER392 3.9 22.2 1.0 O A:HOH860 3.9 38.8 1.0 CG A:ASP347 4.0 23.1 1.0 CB A:ASP243 4.2 19.8 1.0 O A:HOH767 4.2 24.7 1.0 CA A:GLU348 4.2 24.1 1.0 CA A:PHE393 4.3 20.5 1.0 O A:HOH748 4.3 33.5 1.0 CG2 A:VAL349 4.4 15.3 1.0 N A:PHE393 4.5 18.7 1.0 OG A:SER392 4.5 36.7 1.0 CD1 A:PHE393 4.5 15.0 1.0 OD1 A:ASP347 4.6 33.5 1.0 C A:ASP347 4.6 21.1 1.0 N A:VAL349 4.7 19.7 1.0 CA A:ASP347 4.8 22.4 1.0 CB A:PHE393 4.9 14.8 1.0 CA A:SER392 4.9 24.1 1.0 N A:SER392 5.0 19.7 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Murine Norovirus Rna Dependent Rna Polymerase in Complex with Ribavirin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Murine Norovirus Rna Dependent Rna Polymerase in Complex with Ribavirin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg609 b:45.8 occ:1.00 OD1 B:ASP347 2.6 31.0 1.0 OD1 B:ASP243 2.7 39.2 1.0 O B:GLU348 2.8 28.1 1.0 O B:SER392 2.9 31.8 1.0 CG B:ASP243 3.3 40.5 1.0 O B:HOH774 3.3 44.1 1.0 C B:SER392 3.7 31.7 1.0 N B:GLU348 3.7 26.1 1.0 OD2 B:ASP243 3.8 40.4 1.0 C B:GLU348 3.8 29.3 1.0 CG B:ASP347 3.9 31.1 1.0 CA B:PHE393 4.1 24.4 1.0 CB B:ASP243 4.2 30.8 1.0 N B:PHE393 4.3 23.7 1.0 CA B:GLU348 4.3 29.3 1.0 CD1 B:PHE393 4.3 22.0 1.0 O B:HOH827 4.4 42.3 1.0 CG2 B:VAL349 4.4 21.0 1.0 OD2 B:ASP347 4.6 38.7 1.0 C B:ASP347 4.6 26.6 1.0 CA B:SER392 4.7 39.4 1.0 CB B:PHE393 4.8 19.0 1.0 CA B:ASP347 4.8 26.4 1.0 CB B:SER392 4.8 46.3 1.0 N B:VAL349 4.8 23.1 1.0 CB B:ASP347 4.9 27.8 1.0 N B:SER392 5.0 32.5 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Murine Norovirus Rna Dependent Rna Polymerase in Complex with Ribavirin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Murine Norovirus Rna Dependent Rna Polymerase in Complex with Ribavirin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg604 b:40.9 occ:1.00 OD2 C:ASP347 2.6 28.3 1.0 O C:GLU348 2.7 22.7 1.0 OD2 C:ASP243 2.7 22.9 1.0 O C:HOH767 2.8 20.3 1.0 O C:SER392 2.9 28.4 1.0 CG C:ASP243 3.2 24.1 1.0 OD1 C:ASP243 3.4 19.5 1.0 C C:GLU348 3.7 24.6 1.0 N C:GLU348 3.7 20.4 1.0 CG C:ASP347 3.8 24.4 1.0 C C:SER392 4.0 29.9 1.0 O C:HOH829 4.0 29.4 1.0 O C:HOH727 4.0 44.7 1.0 O C:HOH799 4.1 26.4 1.0 CB C:ASP243 4.2 20.7 1.0 CA C:GLU348 4.3 21.8 1.0 CD1 C:PHE393 4.3 20.3 1.0 CA C:PHE393 4.4 22.3 1.0 OD1 C:ASP347 4.4 30.3 1.0 CG2 C:VAL349 4.5 21.2 1.0 N C:PHE393 4.6 20.8 1.0 C C:ASP347 4.7 23.2 1.0 N C:VAL349 4.7 21.9 1.0 CA C:ASP347 4.8 23.5 1.0 OG C:SER392 4.8 41.8 1.0 CB C:ASP347 4.9 17.6 1.0 CB C:PHE393 5.0 19.0 1.0

I.Alam, J.H.Lee, K.J.Cho, K.R.Han, J.M.Yang, M.S.Chung, K.H.Kim. Crystal Structures of Murine Norovirus-1 Rna-Dependent Rna Polymerase in Complex with 2-Thiouridine or Ribavirin. Virology V. 426 143 2012.
ISSN: ISSN 0042-6822
PubMed: 22341781
DOI: 10.1016/J.VIROL.2012.01.016