Magnesium in PDB 6kwq: Crystal Structure of Enterovirus 71 Polymerase Elongation Complex (Native Form)

Enzymatic activity of Crystal Structure of Enterovirus 71 Polymerase Elongation Complex (Native Form)

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

Protein crystallography data

The structure of Crystal Structure of Enterovirus 71 Polymerase Elongation Complex (Native Form), PDB code: 6kwq was solved by W.Shi, P.Gong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.00 / 1.76
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 124.301, 75.544, 74.031, 90.00, 91.46, 90.00
R / Rfree (%) 18.1 / 21.4

Other elements in 6kwq:

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

Zinc (Zn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Enterovirus 71 Polymerase Elongation Complex (Native Form) (pdb code 6kwq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Enterovirus 71 Polymerase Elongation Complex (Native Form), PDB code: 6kwq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6kwq

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Magnesium binding site 1 out of 5 in the Crystal Structure of Enterovirus 71 Polymerase Elongation Complex (Native 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 Enterovirus 71 Polymerase Elongation Complex (Native Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:15.9
occ:0.73
 O A:HOH668 2.0 23.2 1.0
OD1 A:ASP330 2.0 20.7 1.0
O A:HOH793 2.1 19.6 1.0
O A:HOH863 2.1 23.0 1.0
O A:HOH653 2.1 20.8 1.0
O A:HOH770 2.2 27.4 1.0
CG A:ASP330 3.1 18.8 1.0
OD2 A:ASP330 3.7 20.1 1.0
OD1 A:ASP233 3.9 26.6 1.0
O A:THR373 4.0 21.0 1.0
O A:HOH677 4.1 21.2 1.0
O A:VAL331 4.3 19.4 1.0
N A:VAL331 4.3 15.1 1.0
O A:HOH1012 4.3 41.2 1.0
OG1 A:THR373 4.4 23.0 1.0
O A:HOH638 4.4 25.0 1.0
CB A:ASP330 4.4 22.1 1.0
CA A:ASP330 4.5 16.9 1.0
O C:HOH836 4.5 29.2 1.0
OD1 A:ASP359 4.5 33.9 1.0
O A:HOH877 4.6 27.2 1.0
C A:THR373 4.7 16.8 1.0
CA A:PHE374 4.8 18.9 1.0
CG A:ASP233 4.9 29.1 1.0
O A:PHE232 4.9 23.1 1.0
C A:ASP330 4.9 15.9 1.0

Magnesium binding site 2 out of 5 in 6kwq

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Magnesium binding site 2 out of 5 in the Crystal Structure of Enterovirus 71 Polymerase Elongation Complex (Native 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 Enterovirus 71 Polymerase Elongation Complex (Native Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:28.5
occ:0.60
 O A:HOH909 1.9 41.1 1.0
O A:HOH1052 1.9 36.5 1.0
O A:HOH1101 2.2 46.1 1.0
O B:HOH806 2.3 31.8 1.0
O A:HOH937 2.3 37.6 1.0
ND2 A:ASN106 3.5 31.5 1.0
O B:HOH849 3.6 39.2 1.0
O B:HOH868 3.7 26.4 1.0
O A:HIS199 3.7 21.7 1.0
O A:HOH902 4.1 33.8 1.0
O A:HOH979 4.2 44.7 1.0
CA A:ALA200 4.2 24.0 1.0
OP1 B:C604 4.3 25.6 1.0
O A:HOH773 4.4 42.8 1.0
O A:HOH1087 4.4 39.9 1.0
C A:HIS199 4.5 23.9 1.0
O A:HOH925 4.7 31.2 1.0
N A:ALA200 4.7 19.8 1.0
CG A:ASN106 4.7 31.6 1.0
O A:GLY211 4.9 22.4 1.0
CB A:ALA200 4.9 23.3 1.0

Magnesium binding site 3 out of 5 in 6kwq

Go back to Magnesium Binding Sites List in 6kwq
Magnesium binding site 3 out of 5 in the Crystal Structure of Enterovirus 71 Polymerase Elongation Complex (Native Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Enterovirus 71 Polymerase Elongation Complex (Native Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg701

b:33.4
occ:0.66
 O B:HOH827 2.0 38.9 1.0
O B:HOH805 2.1 37.2 1.0
O B:HOH823 2.1 36.6 1.0
O C:HOH819 2.2 49.8 1.0
O B:HOH883 2.3 41.2 1.0
O B:HOH884 2.4 37.0 1.0
O6 B:G607 3.9 37.3 1.0
O B:HOH837 4.0 41.0 1.0
O B:HOH843 4.1 41.3 1.0
O B:HOH855 4.2 35.1 1.0
N7 B:G607 4.2 31.2 1.0
O C:HOH820 4.3 49.7 1.0
O6 B:G608 4.4 40.4 1.0
O4 C:U693 4.4 48.2 1.0
C6 B:G607 4.6 35.5 1.0
C5 B:G607 4.8 32.5 1.0
N4 C:C694 4.9 44.7 1.0

Magnesium binding site 4 out of 5 in 6kwq

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Magnesium binding site 4 out of 5 in the Crystal Structure of Enterovirus 71 Polymerase Elongation Complex (Native Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Enterovirus 71 Polymerase Elongation Complex (Native Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:43.6
occ:0.66
 OP2 B:A598 1.9 38.9 1.0
O B:HOH834 2.0 46.6 1.0
O B:HOH812 2.0 43.1 1.0
O B:HOH815 2.1 44.1 1.0
O B:HOH839 2.1 50.5 1.0
P B:A598 3.2 41.2 1.0
O5' B:A598 3.7 39.8 1.0
OP1 B:A598 4.0 46.2 1.0
N7 B:G599 4.1 31.0 1.0
O6 B:G599 4.3 45.3 1.0
O3' B:C597 4.4 43.7 1.0
C8 B:A598 4.4 34.2 1.0
N7 B:A598 4.5 33.2 1.0
OP1 B:C597 4.6 55.3 1.0
C3' B:C597 4.6 39.1 1.0
O5' B:C597 4.7 48.3 1.0
OP2 B:G599 4.7 40.4 1.0
OP2 B:C597 4.8 50.4 1.0
C5 B:G599 4.9 34.1 1.0
P B:C597 4.9 47.6 1.0
C6 B:G599 5.0 37.5 1.0

Magnesium binding site 5 out of 5 in 6kwq

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Magnesium binding site 5 out of 5 in the Crystal Structure of Enterovirus 71 Polymerase Elongation Complex (Native Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Enterovirus 71 Polymerase Elongation Complex (Native Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg703

b:32.5
occ:0.71
 O B:HOH862 2.0 37.5 1.0
O B:HOH809 2.0 35.6 1.0
O A:HOH1040 2.2 36.5 1.0
O B:HOH829 2.2 34.8 1.0
N7 B:G582 2.2 30.4 1.0
O A:HOH704 2.2 31.6 1.0
C8 B:G582 3.0 29.7 1.0
C5 B:G582 3.4 28.4 1.0
O6 B:G582 3.9 30.9 1.0
C6 B:G582 4.1 32.9 1.0
O B:HOH822 4.1 36.6 1.0
O B:HOH840 4.2 32.9 1.0
OG1 A:THR21 4.2 25.9 1.0
OP2 B:G582 4.3 29.7 1.0
N9 B:G582 4.3 31.7 1.0
O A:HOH1050 4.3 41.4 1.0
O2' B:G581 4.3 32.9 1.0
O B:HOH835 4.3 40.4 1.0
O A:HOH652 4.4 29.3 1.0
C4 B:G582 4.5 30.6 1.0
O A:HOH712 4.7 39.9 1.0
O3' B:G581 4.8 33.2 1.0
O5' B:G582 4.9 35.0 1.0
P B:G582 5.0 36.3 1.0

Reference:

W.Shi, H.Q.Ye, C.L.Deng, R.Li, B.Zhang, P.Gong. A Nucleobase-Binding Pocket in A Viral Rna-Dependent Rna Polymerase Contributes to Elongation Complex Stability. Nucleic Acids Res. 2019.
ISSN: ESSN 1362-4962
PubMed: 31863580
DOI: 10.1093/NAR/GKZ1170
Page generated: Mon Dec 14 23:11:31 2020

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