Magnesium in PDB 7w9s: Crystal Structure of the Enterovirus 71 Polymerase Elongation Complex (C1S3 Form)

All present enzymatic activity of Crystal Structure of the Enterovirus 71 Polymerase Elongation Complex (C1S3 Form):
2.7.7.48; 3.4.22.28; 3.4.22.29; 3.6.1.15;

The structure of Crystal Structure of the Enterovirus 71 Polymerase Elongation Complex (C1S3 Form), PDB code: 7w9s was solved by M.Wang, P.Gong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.94 / 2.53
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.992, 77.663, 150.831, 90, 90, 90
R / Rfree (%)	20 / 24.1

The structure of Crystal Structure of the Enterovirus 71 Polymerase Elongation Complex (C1S3 Form) also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of the Enterovirus 71 Polymerase Elongation Complex (C1S3 Form) (pdb code 7w9s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Enterovirus 71 Polymerase Elongation Complex (C1S3 Form), PDB code: 7w9s:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Enterovirus 71 Polymerase Elongation Complex (C1S3 Form)


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 the Enterovirus 71 Polymerase Elongation Complex (C1S3 Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg506 b:66.0 occ:1.00 OD2 A:ASP330 2.1 71.0 1.0 OD1 A:ASP329 2.4 63.0 1.0 OD1 A:ASP233 2.4 66.2 1.0 O1A A:CTP501 2.5 68.0 1.0 O3' C:A701 2.6 63.4 1.0 CG A:ASP329 3.2 63.2 1.0 CG A:ASP330 3.3 73.6 1.0 OD2 A:ASP329 3.4 64.3 1.0 CG A:ASP233 3.4 65.2 1.0 PA A:CTP501 3.5 70.4 1.0 OD2 A:ASP233 3.6 67.7 1.0 O5' A:CTP501 3.6 63.2 1.0 MG A:MG507 3.7 65.1 1.0 C3' C:A701 3.8 63.2 1.0 OD1 A:ASP330 3.9 83.4 1.0 O2A A:CTP501 3.9 75.9 1.0 C5' A:CTP501 4.1 64.3 1.0 N A:ASP330 4.2 58.0 1.0 CB A:ASP330 4.5 62.4 1.0 C5' C:A701 4.5 56.4 1.0 NZ A:LYS360 4.5 70.1 1.0 C4' C:A701 4.5 62.8 1.0 CA A:ASP330 4.6 60.2 1.0 CB A:ASP329 4.6 55.4 1.0 C A:ASP329 4.6 58.1 1.0 O5' C:A701 4.7 60.9 1.0 OP1 C:A701 4.7 63.1 1.0 CB A:ASP233 4.8 66.5 1.0 CA A:ASP329 5.0 56.6 1.0 O3A A:CTP501 5.0 70.5 1.0 O2B A:CTP501 5.0 63.2 1.0 N A:ASP329 5.0 54.8 1.0 C2' C:A701 5.0 62.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Enterovirus 71 Polymerase Elongation Complex (C1S3 Form)


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 the Enterovirus 71 Polymerase Elongation Complex (C1S3 Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg507 b:65.1 occ:1.00 O2B A:CTP501 2.0 63.2 1.0 O A:TYR234 2.1 63.1 1.0 OD2 A:ASP329 2.2 64.3 1.0 OD2 A:ASP233 2.3 67.7 1.0 O1A A:CTP501 2.3 68.0 1.0 O2G A:CTP501 2.6 65.8 1.0 PB A:CTP501 3.2 64.3 1.0 CG A:ASP233 3.2 65.2 1.0 C A:TYR234 3.3 61.5 1.0 CG A:ASP329 3.3 63.2 1.0 PA A:CTP501 3.5 70.4 1.0 OD1 A:ASP233 3.6 66.2 1.0 N A:TYR234 3.7 60.3 1.0 PG A:CTP501 3.7 79.8 1.0 MG A:MG506 3.7 66.0 1.0 O3A A:CTP501 3.7 70.5 1.0 OD1 A:ASP329 3.8 63.0 1.0 O3B A:CTP501 3.9 64.6 1.0 CA A:TYR234 3.9 59.1 1.0 C5' A:CTP501 4.0 64.3 1.0 O5' A:CTP501 4.2 63.2 1.0 CB A:TYR234 4.3 58.8 1.0 O1G A:CTP501 4.3 76.3 1.0 N A:SER235 4.3 63.5 1.0 O1B A:CTP501 4.4 58.3 1.0 NZ A:LYS360 4.5 70.1 1.0 CB A:ASP329 4.5 55.4 1.0 CB A:ASP233 4.5 66.5 1.0 N A:GLY236 4.6 54.2 1.0 CB A:TYR237 4.6 54.1 1.0 CA A:SER235 4.6 60.6 1.0 N A:TYR237 4.7 56.9 1.0 C A:ASP233 4.7 63.1 1.0 O2A A:CTP501 4.7 75.9 1.0 CE A:LYS360 4.8 73.5 1.0 C A:SER235 4.9 60.7 1.0 O3G A:CTP501 5.0 83.0 1.0 CA A:ASP233 5.0 61.5 1.0

R.Li, M.Wang, P.Gong. Crystal Structure of A Pre-Chemistry Viral Rna-Dependent Rna Polymerase Suggests Participation of Two Basic Residues in Catalysis. Nucleic Acids Res. V. 50 12389 2022.
ISSN: ESSN 1362-4962
PubMed: 36477355
DOI: 10.1093/NAR/GKAC1133