Magnesium in PDB 5d98: Influenza C Virus Rna-Dependent Rna Polymerase - Space Group P43212

All present enzymatic activity of Influenza C Virus Rna-Dependent Rna Polymerase - Space Group P43212:
2.7.7.48;

The structure of Influenza C Virus Rna-Dependent Rna Polymerase - Space Group P43212, PDB code: 5d98 was solved by N.Hengrung, K.El Omari, I.Serna Martin, F.T.Vreede, S.Cusack, R.P.Rambo, C.Vonrhein, G.Bricogne, D.I.Stuart, J.M.Grimes, E.Fodor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.01 / 3.90
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	185.660, 185.660, 598.220, 90.00, 90.00, 90.00
R / Rfree (%)	28.6 / 32.6

The binding sites of Magnesium atom in the Influenza C Virus Rna-Dependent Rna Polymerase - Space Group P43212 (pdb code 5d98). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Influenza C Virus Rna-Dependent Rna Polymerase - Space Group P43212, PDB code: 5d98:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Influenza C Virus Rna-Dependent Rna Polymerase - Space Group P43212


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Influenza C Virus Rna-Dependent Rna Polymerase - Space Group P43212 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg800 b:0.6 occ:1.00 MG A:MG801 2.9 0.2 1.0 OD2 A:ASP93 3.0 0.6 1.0 OE1 A:GLU104 3.0 0.5 1.0 OD1 A:ASP93 3.1 0.9 1.0 NE2 A:HIS41 3.2 0.5 1.0 CG A:ASP93 3.5 0.5 1.0 CE1 A:HIS41 3.5 0.6 1.0 O A:ILE105 3.5 0.0 1.0 CD A:GLU104 3.7 0.6 1.0 OE2 A:GLU65 3.9 0.3 1.0 CG A:GLU104 3.9 0.8 1.0 CD2 A:HIS41 4.1 0.2 1.0 CE A:LYS119 4.1 0.7 1.0 NZ A:LYS119 4.4 0.5 1.0 ND1 A:HIS41 4.5 0.7 1.0 C A:ILE105 4.6 0.7 1.0 OE2 A:GLU104 4.7 0.5 1.0 CG A:HIS41 4.8 0.6 1.0 N A:ILE105 4.8 0.2 1.0 CB A:ASP93 5.0 0.1 1.0

Magnesium binding site 2 out of 4 in the Influenza C Virus Rna-Dependent Rna Polymerase - Space Group P43212


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Influenza C Virus Rna-Dependent Rna Polymerase - Space Group P43212 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:0.2 occ:1.00 OE2 A:GLU65 1.9 0.3 1.0 OD1 A:ASP93 2.1 0.9 1.0 MG A:MG800 2.9 0.6 1.0 CD A:GLU65 3.1 0.8 1.0 CG A:ASP93 3.3 0.5 1.0 OE1 A:GLU65 3.8 0.1 1.0 OE1 A:GLU104 3.8 0.5 1.0 O A:LEU91 3.9 0.2 1.0 OD2 A:ASP93 4.0 0.6 1.0 CG A:GLU65 4.1 0.5 1.0 CE1 A:HIS41 4.4 0.6 1.0 N A:ASP93 4.4 0.5 1.0 CB A:GLU65 4.5 0.8 1.0 CB A:ASP93 4.5 0.1 1.0 CA A:ASP93 4.5 0.4 1.0 C A:CYS92 4.5 0.3 1.0 CG A:GLU104 4.7 0.8 1.0 CD A:GLU104 4.8 0.6 1.0 O A:CYS92 4.8 0.2 1.0 NE2 A:HIS41 4.9 0.5 1.0 C A:LEU91 5.0 0.3 1.0 CA A:CYS92 5.0 0.8 1.0

Magnesium binding site 3 out of 4 in the Influenza C Virus Rna-Dependent Rna Polymerase - Space Group P43212


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Influenza C Virus Rna-Dependent Rna Polymerase - Space Group P43212 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg800 b:0.5 occ:1.00 OD2 D:ASP93 2.5 0.8 1.0 OD1 D:ASP93 2.8 0.1 1.0 OE1 D:GLU104 2.8 0.8 1.0 CG D:ASP93 3.0 1.0 1.0 NE2 D:HIS41 3.1 0.4 1.0 O D:ILE105 3.3 0.9 1.0 CD D:GLU104 3.3 0.2 1.0 CG D:GLU104 3.4 0.2 1.0 CE1 D:HIS41 3.5 0.5 1.0 MG D:MG801 3.6 0.6 1.0 OE2 D:GLU65 4.1 0.6 1.0 CE D:LYS119 4.2 0.3 1.0 CD2 D:HIS41 4.2 0.6 1.0 N D:ILE105 4.3 0.8 1.0 C D:ILE105 4.3 0.0 1.0 OE2 D:GLU104 4.4 0.4 1.0 CB D:ASP93 4.5 0.7 1.0 NZ D:LYS119 4.6 0.5 1.0 ND1 D:HIS41 4.6 0.7 1.0 CB D:GLU104 4.7 0.7 1.0 CA D:ILE105 4.9 0.8 1.0 C D:GLU104 5.0 0.1 1.0 CG D:HIS41 5.0 0.0 1.0

Magnesium binding site 4 out of 4 in the Influenza C Virus Rna-Dependent Rna Polymerase - Space Group P43212


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Influenza C Virus Rna-Dependent Rna Polymerase - Space Group P43212 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg801 b:0.6 occ:1.00 OE2 D:GLU65 2.4 0.6 1.0 OD1 D:ASP93 2.9 0.1 1.0 O D:LEU91 3.3 0.6 1.0 CD D:GLU65 3.4 0.1 1.0 MG D:MG800 3.6 0.5 1.0 OE1 D:GLU104 3.8 0.8 1.0 OE1 D:GLU65 3.9 0.6 1.0 CG D:ASP93 4.1 1.0 1.0 C D:LEU91 4.5 0.8 1.0 C D:CYS92 4.6 0.5 1.0 CG D:GLU65 4.6 0.8 1.0 O D:CYS92 4.7 0.3 1.0 OD2 D:ASP93 4.7 0.8 1.0 N D:ASP93 4.8 0.2 1.0 CD D:GLU104 4.8 0.2 1.0 CA D:CYS92 4.9 0.2 1.0 CB D:GLU65 4.9 0.3 1.0 CG D:GLU104 5.0 0.2 1.0 CA D:ASP93 5.0 1.0 1.0

N.Hengrung, K.El Omari, I.Serna Martin, F.T.Vreede, S.Cusack, R.P.Rambo, C.Vonrhein, G.Bricogne, D.I.Stuart, J.M.Grimes, E.Fodor. Crystal Structure of the Rna-Dependent Rna Polymerase From Influenza C Virus. Nature V. 527 114 2015.
ISSN: ESSN 1476-4687
PubMed: 26503046
DOI: 10.1038/NATURE15525