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Magnesium in PDB 5f8j: Enterovirus 71 Polymerase Elongation Complex (C1S4 Form)

Enzymatic activity of Enterovirus 71 Polymerase Elongation Complex (C1S4 Form)

All present enzymatic activity of Enterovirus 71 Polymerase Elongation Complex (C1S4 Form):
2.7.7.48;

Protein crystallography data

The structure of Enterovirus 71 Polymerase Elongation Complex (C1S4 Form), PDB code: 5f8j 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) 46.43 / 2.68
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.430, 76.572, 149.267, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 22.8

Other elements in 5f8j:

The structure of Enterovirus 71 Polymerase Elongation Complex (C1S4 Form) also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Enterovirus 71 Polymerase Elongation Complex (C1S4 Form) (pdb code 5f8j). 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 (C1S4 Form), PDB code: 5f8j:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5f8j

Go back to Magnesium Binding Sites List in 5f8j
Magnesium binding site 1 out of 2 in the Enterovirus 71 Polymerase Elongation Complex (C1S4 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 (C1S4 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:45.5
occ:0.88
O A:HOH1173 2.0 50.1 1.0
O2 A:POP1007 2.1 34.5 0.7
O A:TYR234 2.3 48.2 1.0
OP1 C:C702 2.3 58.1 1.0
OD2 A:ASP329 2.5 44.9 1.0
OD2 A:ASP233 3.0 51.4 1.0
P1 A:POP1007 3.2 29.8 0.7
O3 A:POP1007 3.2 48.2 0.7
C A:TYR234 3.4 43.9 1.0
CG A:ASP329 3.6 47.2 1.0
P C:C702 3.6 56.4 1.0
CG A:ASP233 3.6 48.5 1.0
OD1 A:ASP233 3.7 47.1 1.0
OD1 A:ASP329 4.0 46.9 1.0
MG A:MG1002 4.0 42.4 0.8
N A:TYR234 4.0 46.7 1.0
O5' C:C702 4.0 58.3 1.0
O A:POP1007 4.1 46.8 0.7
C5' C:C702 4.2 57.4 1.0
CA A:TYR234 4.2 39.9 1.0
N A:SER235 4.3 47.5 1.0
O1 A:POP1007 4.3 41.1 0.7
OP2 C:C702 4.4 54.7 1.0
N A:GLY236 4.4 36.1 1.0
CA A:SER235 4.4 40.6 1.0
CB A:TYR234 4.6 41.2 1.0
O C:HOH806 4.7 46.7 1.0
O3' C:A701 4.7 56.8 1.0
NZ A:LYS360 4.7 55.0 1.0
N A:TYR237 4.8 41.8 1.0
CB A:ASP329 4.8 40.1 1.0
C A:SER235 4.9 40.9 1.0
CB A:TYR237 4.9 37.9 1.0
CB A:ASP233 4.9 46.1 1.0
CE A:LYS360 4.9 57.9 1.0

Magnesium binding site 2 out of 2 in 5f8j

Go back to Magnesium Binding Sites List in 5f8j
Magnesium binding site 2 out of 2 in the Enterovirus 71 Polymerase Elongation Complex (C1S4 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 (C1S4 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:42.4
occ:0.78
O C:HOH806 2.1 46.7 1.0
OD1 A:ASP330 2.2 56.9 1.0
OD1 A:ASP233 2.3 47.1 1.0
OP1 C:C702 2.3 58.1 1.0
O3' C:A701 2.4 56.8 1.0
OD1 A:ASP329 2.4 46.9 1.0
P C:C702 2.9 56.4 1.0
CG A:ASP233 3.2 48.5 1.0
CG A:ASP329 3.3 47.2 1.0
CG A:ASP330 3.4 47.7 1.0
C3' C:A701 3.6 43.4 1.0
OD2 A:ASP233 3.6 51.4 1.0
OD2 A:ASP329 3.6 44.9 1.0
OP2 C:C702 3.7 54.7 1.0
C4' C:A701 3.8 43.5 1.0
C5' C:A701 3.9 42.4 1.0
MG A:MG1001 4.0 45.5 0.9
N A:ASP330 4.1 42.5 1.0
O5' C:C702 4.2 58.3 1.0
OD2 A:ASP330 4.2 53.6 1.0
CB A:ASP330 4.4 44.7 1.0
CA A:ASP330 4.4 39.8 1.0
C5' C:C702 4.5 57.4 1.0
C A:ASP329 4.5 40.5 1.0
O A:HOH1173 4.5 50.1 1.0
CB A:ASP233 4.6 46.1 1.0
OP1 C:A701 4.6 44.5 1.0
O5' C:A701 4.7 43.9 1.0
CB A:ASP329 4.7 40.1 1.0
O2' C:A701 4.7 45.6 1.0
C2' C:A701 4.7 42.4 1.0
O C:HOH803 4.8 43.0 1.0
CA A:ASP329 5.0 40.4 1.0

Reference:

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
Page generated: Mon Dec 14 20:17:29 2020

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