Magnesium in PDB 4k4z: Coxsackievirus B3 Polymerase Elongation Complex (R2_MG_FORM)

All present enzymatic activity of Coxsackievirus B3 Polymerase Elongation Complex (R2_MG_FORM):
2.7.7.48;

The structure of Coxsackievirus B3 Polymerase Elongation Complex (R2_MG_FORM), PDB code: 4k4z was solved by P.Gong, O.B.Peersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.58 / 2.17
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	60.641, 60.633, 194.680, 89.98, 89.92, 78.68
R / Rfree (%)	20.4 / 24.4

The binding sites of Magnesium atom in the Coxsackievirus B3 Polymerase Elongation Complex (R2_MG_FORM) (pdb code 4k4z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Coxsackievirus B3 Polymerase Elongation Complex (R2_MG_FORM), PDB code: 4k4z:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Coxsackievirus B3 Polymerase Elongation Complex (R2_MG_FORM)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Coxsackievirus B3 Polymerase Elongation Complex (R2_MG_FORM) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:40.7 occ:1.00 O A:HOH892 2.0 26.7 1.0 OD1 A:ASP330 2.1 29.5 1.0 O A:HOH889 2.2 38.6 1.0 O A:HOH893 2.2 36.9 1.0 O A:HOH891 2.2 29.4 1.0 O A:HOH890 2.3 36.6 1.0 CG A:ASP330 3.2 25.1 1.0 OD2 A:ASP330 3.7 25.9 1.0 OD1 A:ASP233 3.8 39.8 1.0 O C:HOH802 3.8 25.3 1.0 O A:HOH683 4.1 34.3 1.0 O A:THR373 4.1 27.9 1.0 O A:HOH883 4.3 35.5 1.0 N A:VAL331 4.4 22.9 1.0 O A:VAL331 4.4 24.6 1.0 OG1 A:THR373 4.4 35.6 1.0 CB A:ASP330 4.5 22.9 1.0 CA A:ASP330 4.6 23.7 1.0 O A:PHE232 4.6 30.7 1.0 OD1 A:ASP359 4.7 51.6 1.0 C A:THR373 4.8 30.4 1.0 O A:HOH753 4.9 43.7 1.0 O A:HOH634 4.9 35.6 1.0 CG A:ASP233 4.9 38.2 1.0 CA A:PHE374 4.9 26.6 1.0

Magnesium binding site 2 out of 4 in the Coxsackievirus B3 Polymerase Elongation Complex (R2_MG_FORM)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Coxsackievirus B3 Polymerase Elongation Complex (R2_MG_FORM) within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg501 b:36.9 occ:1.00 O E:HOH843 1.9 36.7 1.0 O E:HOH842 1.9 24.6 1.0 OD1 E:ASP330 2.1 27.4 1.0 O E:HOH841 2.2 27.9 1.0 O E:HOH844 2.2 38.5 1.0 O E:HOH845 2.3 37.0 1.0 CG E:ASP330 3.3 25.1 1.0 OD2 E:ASP330 3.8 28.5 1.0 OD1 E:ASP233 3.8 40.1 1.0 O E:HOH604 3.8 27.0 1.0 O E:THR373 4.1 28.8 1.0 O E:HOH714 4.2 35.3 1.0 O E:HOH807 4.3 32.7 1.0 O E:VAL331 4.3 25.9 1.0 OG1 E:THR373 4.3 34.9 1.0 N E:VAL331 4.3 21.1 1.0 O E:HOH701 4.4 42.9 1.0 CB E:ASP330 4.5 22.6 1.0 CA E:ASP330 4.5 22.7 1.0 O E:PHE232 4.7 33.5 1.0 OD1 E:ASP359 4.8 50.0 1.0 C E:THR373 4.8 30.3 1.0 CA E:PHE374 5.0 27.1 1.0 CG E:ASP233 5.0 40.2 1.0 C E:ASP330 5.0 26.0 1.0

Magnesium binding site 3 out of 4 in the Coxsackievirus B3 Polymerase Elongation Complex (R2_MG_FORM)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Coxsackievirus B3 Polymerase Elongation Complex (R2_MG_FORM) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg501 b:36.1 occ:1.00 O I:HOH879 2.0 28.5 1.0 O I:HOH881 2.0 40.6 1.0 OD1 I:ASP330 2.0 29.9 1.0 O I:HOH880 2.2 35.1 1.0 O I:HOH878 2.2 28.2 1.0 O I:HOH877 2.2 34.9 1.0 CG I:ASP330 3.2 25.1 1.0 OD2 I:ASP330 3.7 26.7 1.0 O I:HOH611 3.9 23.4 1.0 OD1 I:ASP233 4.0 41.9 1.0 O I:THR373 4.0 27.9 1.0 O I:HOH655 4.0 34.6 1.0 N I:VAL331 4.2 24.8 1.0 O I:VAL331 4.2 24.9 1.0 CB I:ASP330 4.4 22.4 1.0 OG1 I:THR373 4.4 36.3 1.0 O K:HOH815 4.4 34.2 1.0 CA I:ASP330 4.5 23.4 1.0 O I:PHE232 4.6 33.8 1.0 OD1 I:ASP359 4.8 51.6 1.0 C I:THR373 4.8 31.6 1.0 C I:ASP330 4.9 27.9 1.0 CA I:PHE374 4.9 24.4 1.0 CD1 I:PHE374 5.0 24.2 1.0

Magnesium binding site 4 out of 4 in the Coxsackievirus B3 Polymerase Elongation Complex (R2_MG_FORM)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Coxsackievirus B3 Polymerase Elongation Complex (R2_MG_FORM) within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg501 b:40.2 occ:1.00 O M:HOH902 1.9 33.0 1.0 OD1 M:ASP330 2.0 29.2 1.0 O M:HOH903 2.1 39.9 1.0 O M:HOH901 2.1 32.7 1.0 O M:HOH900 2.2 38.2 1.0 O M:HOH904 2.2 42.4 1.0 CG M:ASP330 3.2 24.9 1.0 OD2 M:ASP330 3.7 28.6 1.0 O M:HOH610 3.8 25.4 1.0 O M:THR373 3.9 31.9 1.0 OD1 M:ASP233 4.0 42.2 1.0 O M:HOH651 4.2 34.2 1.0 O M:VAL331 4.2 26.3 1.0 N M:VAL331 4.2 25.3 1.0 OG1 M:THR373 4.3 38.5 1.0 CB M:ASP330 4.4 22.8 1.0 CA M:ASP330 4.5 23.5 1.0 C M:THR373 4.6 32.9 1.0 O M:PHE232 4.7 33.7 1.0 OD1 M:ASP359 4.7 54.6 1.0 CA M:PHE374 4.8 27.4 1.0 O M:HOH694 4.9 45.4 1.0 C M:ASP330 4.9 27.7 1.0 CD1 M:PHE374 4.9 27.3 1.0

P.Gong, M.G.Kortus, J.C.Nix, R.E.Davis, O.B.Peersen. Structures of Coxsackievirus, Rhinovirus, and Poliovirus Polymerase Elongation Complexes Solved By Engineering Rna Mediated Crystal Contacts. Plos One V. 8 60272 2013.
ISSN: ESSN 1932-6203
PubMed: 23667424
DOI: 10.1371/JOURNAL.PONE.0060272