Magnesium in PDB 5f8i: Enterovirus 71 Polymerase Elongation Complex (C1S2/3 Form)

All present enzymatic activity of Enterovirus 71 Polymerase Elongation Complex (C1S2/3 Form):
2.7.7.48;

The structure of Enterovirus 71 Polymerase Elongation Complex (C1S2/3 Form), PDB code: 5f8i was solved by B.Shu, P.Gong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.27 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.669, 77.310, 149.656, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 24.4

The structure of Enterovirus 71 Polymerase Elongation Complex (C1S2/3 Form) also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the Enterovirus 71 Polymerase Elongation Complex (C1S2/3 Form) (pdb code 5f8i). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Enterovirus 71 Polymerase Elongation Complex (C1S2/3 Form), PDB code: 5f8i:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Enterovirus 71 Polymerase Elongation Complex (C1S2/3 Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Enterovirus 71 Polymerase Elongation Complex (C1S2/3 Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1004 b:51.3 occ:0.51 O2B A:CTP1001 1.9 58.1 0.7 OD2 A:ASP329 2.1 60.6 1.0 O A:TYR234 2.2 56.8 1.0 O1A A:CTP1001 2.4 55.3 0.7 O A:HOH1197 3.1 46.9 1.0 C A:TYR234 3.2 50.6 1.0 CG A:ASP329 3.2 54.2 1.0 PB A:CTP1001 3.2 50.2 0.7 PA A:CTP1001 3.5 53.3 0.7 O3A A:CTP1001 3.7 57.2 0.7 CB A:TYR234 3.8 56.6 1.0 CA A:TYR234 3.8 56.4 1.0 OD1 A:ASP329 3.9 58.2 1.0 N A:TYR234 3.9 56.1 1.0 O3B A:CTP1001 4.0 50.2 0.7 C5' A:CTP1001 4.0 50.3 0.7 N A:TYR237 4.2 48.4 1.0 N A:SER235 4.2 52.6 1.0 CB A:TYR237 4.2 47.5 1.0 O A:HOH1148 4.2 53.9 1.0 N A:GLY236 4.2 46.1 1.0 CB A:ASP329 4.3 50.7 1.0 O5' A:CTP1001 4.3 51.5 0.7 O1B A:CTP1001 4.4 58.5 0.7 CA A:SER235 4.4 50.1 1.0 C A:SER235 4.6 50.1 1.0 O2A A:CTP1001 4.8 56.5 0.7 CA A:TYR237 4.8 45.0 1.0 CA A:GLY236 5.0 43.9 1.0

Magnesium binding site 2 out of 2 in the Enterovirus 71 Polymerase Elongation Complex (C1S2/3 Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Enterovirus 71 Polymerase Elongation Complex (C1S2/3 Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1005 b:47.8 occ:0.53 O A:HOH1209 1.8 52.1 1.0 O A:HOH1145 1.9 56.3 1.0 OD1 A:ASP330 2.2 51.0 1.0 CG A:ASP330 3.1 48.1 1.0 OD2 A:ASP330 3.3 50.3 1.0 O A:THR373 3.5 44.3 1.0 O A:HOH1118 3.6 68.1 1.0 OG1 A:THR373 3.8 53.2 1.0 CA A:PHE374 3.9 41.2 1.0 C A:THR373 3.9 46.5 1.0 N A:PHE374 4.1 43.3 1.0 N A:LEU375 4.3 46.4 1.0 OD1 A:ASP233 4.4 69.2 1.0 CB A:ASP330 4.5 48.3 1.0 C A:PHE374 4.5 46.0 1.0 CB A:THR373 4.7 49.7 1.0 CD1 A:PHE374 4.8 43.6 1.0 CA A:ASP330 4.8 49.0 1.0 O A:VAL331 4.9 48.3 1.0 CA A:THR373 4.9 46.3 1.0 N A:LYS376 4.9 43.9 1.0 CB A:PHE374 5.0 43.2 1.0

B.Shu, P.Gong. Structural Basis of Viral Rna-Dependent Rna Polymerase Catalysis and Translocation Proc.Natl.Acad.Sci.Usa V. 113 E4005 2016.
ISSN: ESSN 1091-6490
PubMed: 27339134
DOI: 10.1073/PNAS.1602591113