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Magnesium in PDB 3ol7: Poliovirus Polymerase Elongation Complex with Ctp

Enzymatic activity of Poliovirus Polymerase Elongation Complex with Ctp

All present enzymatic activity of Poliovirus Polymerase Elongation Complex with Ctp:
2.7.7.48;

Protein crystallography data

The structure of Poliovirus Polymerase Elongation Complex with Ctp, PDB code: 3ol7 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) 48.08 / 2.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 60.724, 60.769, 192.969, 83.01, 82.93, 77.12
R / Rfree (%) 22.6 / 29

Other elements in 3ol7:

The structure of Poliovirus Polymerase Elongation Complex with Ctp also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Poliovirus Polymerase Elongation Complex with Ctp (pdb code 3ol7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Poliovirus Polymerase Elongation Complex with Ctp, PDB code: 3ol7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3ol7

Go back to Magnesium Binding Sites List in 3ol7
Magnesium binding site 1 out of 6 in the Poliovirus Polymerase Elongation Complex with Ctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Poliovirus Polymerase Elongation Complex with Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3005

b:60.0
occ:1.00
 OP1 C:C702 2.5 64.0 1.0
O1 A:POP5004 2.5 46.2 0.8
O A:TYR234 2.5 62.5 1.0
OD2 A:ASP328 2.6 77.8 1.0
O2 A:POP5004 2.6 0.7 0.8
OD1 A:ASP233 3.1 66.8 1.0
P1 A:POP5004 3.1 87.6 0.8
CG A:ASP328 3.4 51.3 1.0
O5' C:C702 3.6 62.7 1.0
P C:C702 3.6 48.5 1.0
C5' C:C702 3.7 58.6 1.0
C A:TYR234 3.7 63.5 1.0
OD1 A:ASP328 3.8 40.5 1.0
O A:POP5004 3.9 63.0 0.8
O A:HOH588 3.9 69.1 1.0
CG A:ASP233 4.2 82.1 1.0
N A:TYR234 4.3 68.5 1.0
O5 A:POP5004 4.3 0.9 0.8
MG A:MG3006 4.3 81.6 1.0
O3 A:POP5004 4.4 76.2 0.8
O A:HOH579 4.4 73.1 1.0
CB A:ASP328 4.4 32.1 1.0
N A:TYR237 4.5 52.8 1.0
CA A:TYR234 4.5 60.6 1.0
CB A:TYR237 4.5 46.7 1.0
O3' C:A701 4.6 59.4 1.0
N A:GLY236 4.6 48.9 1.0
N A:THR235 4.7 54.4 1.0
OP2 C:C702 4.7 52.3 1.0
P2 A:POP5004 4.8 97.5 0.8
OD2 A:ASP233 4.8 84.8 1.0
CA A:THR235 4.8 53.3 1.0
CB A:TYR234 4.8 50.5 1.0
C A:THR235 4.9 50.0 1.0
NZ A:LYS359 4.9 81.3 1.0

Magnesium binding site 2 out of 6 in 3ol7

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Magnesium binding site 2 out of 6 in the Poliovirus Polymerase Elongation Complex with Ctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Poliovirus Polymerase Elongation Complex with Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3006

b:81.6
occ:1.00
 O3' C:A701 2.6 59.4 1.0
OP1 C:C702 2.6 64.0 1.0
OD2 A:ASP233 2.8 84.8 1.0
OD1 A:ASP328 2.9 40.5 1.0
P C:C702 3.2 48.5 1.0
OD2 A:ASP328 3.2 77.8 1.0
CG A:ASP328 3.3 51.3 1.0
OD2 A:ASP329 3.4 61.4 1.0
C5' C:A701 3.5 38.0 1.0
CG A:ASP233 3.5 82.1 1.0
CB A:ASP329 3.6 26.4 1.0
CG A:ASP329 3.6 80.0 1.0
C4' C:A701 3.6 45.5 1.0
C3' C:A701 3.6 44.0 1.0
OD1 A:ASP233 3.7 66.8 1.0
N A:ASP329 3.7 36.5 1.0
CA A:ASP329 3.9 33.5 1.0
OP2 C:C702 4.1 52.3 1.0
O C:HOH138 4.3 45.8 1.0
O A:HOH579 4.3 73.1 1.0
OP1 C:A701 4.3 57.0 1.0
MG A:MG3005 4.3 60.0 1.0
O5' C:A701 4.4 61.0 1.0
OD1 A:ASP329 4.4 94.4 1.0
O5' C:C702 4.4 62.7 1.0
C A:ASP328 4.7 39.9 1.0
C5' C:C702 4.7 58.6 1.0
O2' C:A701 4.7 44.2 1.0
CB A:ASP328 4.7 32.1 1.0
C2' C:A701 4.8 39.2 1.0
CB A:ASP233 4.9 74.0 1.0

Magnesium binding site 3 out of 6 in 3ol7

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Magnesium binding site 3 out of 6 in the Poliovirus Polymerase Elongation Complex with Ctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Poliovirus Polymerase Elongation Complex with Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg3002

b:83.3
occ:1.00
 OP1 G:C702 2.5 63.8 1.0
OD2 E:ASP233 2.5 81.6 1.0
O3' G:A701 2.9 58.9 1.0
P G:C702 3.2 51.0 1.0
CG E:ASP233 3.3 78.8 1.0
OD1 E:ASP328 3.3 42.3 1.0
OD1 E:ASP233 3.4 67.5 1.0
OD2 E:ASP328 3.4 78.5 1.0
OD2 E:ASP329 3.5 57.1 1.0
C5' G:A701 3.6 37.6 1.0
CG E:ASP328 3.7 53.0 1.0
O E:HOH523 3.8 77.8 1.0
O E:HOH562 3.9 65.0 1.0
CG E:ASP329 3.9 77.8 1.0
C3' G:A701 3.9 41.6 1.0
C4' G:A701 3.9 44.4 1.0
OP2 G:C702 3.9 55.6 1.0
OP1 G:A701 4.0 56.3 1.0
O G:HOH381 4.0 41.3 1.0
CB E:ASP329 4.1 25.8 1.0
MG E:MG3003 4.2 59.5 1.0
N E:ASP329 4.3 35.6 1.0
O5' G:A701 4.3 61.7 1.0
CA E:ASP329 4.4 33.7 1.0
O E:HOH556 4.4 73.6 1.0
O5' G:C702 4.5 64.7 1.0
OD1 E:ASP329 4.6 97.1 1.0
CB E:ASP233 4.7 70.3 1.0
P G:A701 4.8 51.4 1.0
C5' G:C702 4.9 53.2 1.0

Magnesium binding site 4 out of 6 in 3ol7

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Magnesium binding site 4 out of 6 in the Poliovirus Polymerase Elongation Complex with Ctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Poliovirus Polymerase Elongation Complex with Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg3003

b:59.5
occ:1.00
 O4 E:POP5003 2.4 36.7 0.7
OP1 G:C702 2.5 63.8 1.0
O E:TYR234 2.5 65.6 1.0
OD2 E:ASP328 2.7 78.5 1.0
O6 E:POP5003 2.8 0.6 0.7
OD1 E:ASP233 3.0 67.5 1.0
P2 E:POP5003 3.0 80.1 0.7
CG E:ASP328 3.5 53.0 1.0
O E:POP5003 3.5 55.7 0.7
P G:C702 3.6 51.0 1.0
O5' G:C702 3.7 64.7 1.0
C E:TYR234 3.7 62.1 1.0
C5' G:C702 3.9 53.2 1.0
OD1 E:ASP328 4.0 42.3 1.0
CG E:ASP233 4.2 78.8 1.0
MG E:MG3002 4.2 83.3 1.0
O1 E:POP5003 4.2 0.3 0.7
N E:TYR234 4.3 68.7 1.0
O5 E:POP5003 4.4 55.0 0.7
CA E:TYR234 4.6 59.0 1.0
N E:GLY236 4.6 50.2 1.0
P1 E:POP5003 4.6 0.9 0.7
N E:TYR237 4.6 54.0 1.0
O3' G:A701 4.6 58.9 1.0
CB E:ASP328 4.6 37.5 1.0
O E:HOH562 4.7 65.0 1.0
N E:THR235 4.7 56.1 1.0
CB E:TYR237 4.7 46.1 1.0
OP2 G:C702 4.7 55.6 1.0
OD2 E:ASP233 4.7 81.6 1.0
NZ E:LYS359 4.7 78.8 1.0
CA E:THR235 4.8 56.1 1.0
C E:THR235 4.9 51.6 1.0
CB E:TYR234 5.0 51.2 1.0

Magnesium binding site 5 out of 6 in 3ol7

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Magnesium binding site 5 out of 6 in the Poliovirus Polymerase Elongation Complex with Ctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Poliovirus Polymerase Elongation Complex with Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg3004

b:83.4
occ:1.00
 O I:TYR234 2.6 0.8 1.0
OD2 I:ASP328 2.6 76.2 1.0
O K:POP5002 2.7 0.0 0.8
O3 K:POP5002 2.8 0.9 0.8
OP1 K:C702 3.0 67.9 1.0
OD1 I:ASP233 3.2 92.2 1.0
P1 K:POP5002 3.3 0.2 0.8
C I:TYR234 3.6 92.3 1.0
CG I:ASP328 3.7 61.5 1.0
P2 K:POP5002 3.7 94.5 0.8
O4 K:POP5002 3.9 68.9 0.8
C5' K:C702 4.0 64.4 1.0
O5 K:POP5002 4.0 95.2 0.8
O5' K:C702 4.0 51.2 1.0
P K:C702 4.1 52.6 1.0
O2 K:POP5002 4.1 1.0 0.8
N I:TYR234 4.2 0.6 1.0
OD1 I:ASP328 4.2 64.2 1.0
N I:GLY236 4.3 71.8 1.0
CA I:TYR234 4.3 98.9 1.0
N I:TYR237 4.3 95.5 1.0
CG I:ASP233 4.3 0.6 1.0
CB I:TYR237 4.4 73.0 1.0
N I:THR235 4.5 74.3 1.0
O I:HOH515 4.5 57.8 1.0
O1 K:POP5002 4.5 93.2 0.8
CB I:TYR234 4.6 86.0 1.0
CA I:THR235 4.6 79.0 1.0
C I:THR235 4.7 81.9 1.0
CB I:ASP328 4.8 46.5 1.0
OD2 I:ASP233 4.8 91.7 1.0
CA I:GLY236 4.9 74.2 1.0

Magnesium binding site 6 out of 6 in 3ol7

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Magnesium binding site 6 out of 6 in the Poliovirus Polymerase Elongation Complex with Ctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Poliovirus Polymerase Elongation Complex with Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg3001

b:74.8
occ:1.00
 O6 M:POP5001 2.5 0.0 0.7
OD2 M:ASP328 2.5 77.1 1.0
O M:TYR234 2.6 0.7 1.0
OP1 O:C702 2.8 66.7 1.0
OD1 M:ASP233 2.9 92.8 1.0
P2 M:POP5001 3.4 99.2 0.7
O M:POP5001 3.5 65.3 0.7
C M:TYR234 3.6 91.5 1.0
CG M:ASP328 3.6 61.8 1.0
O5 M:POP5001 3.8 88.4 0.7
P O:C702 4.0 58.5 1.0
O5' O:C702 4.0 52.1 1.0
C5' O:C702 4.0 62.9 1.0
CG M:ASP233 4.1 0.5 1.0
N M:TYR234 4.1 0.1 1.0
OD1 M:ASP328 4.1 64.3 1.0
CA M:TYR234 4.2 97.2 1.0
N M:GLY236 4.5 70.5 1.0
OD2 M:ASP233 4.5 92.7 1.0
N M:THR235 4.5 73.5 1.0
CB M:TYR234 4.6 85.5 1.0
N M:TYR237 4.6 95.0 1.0
CB M:TYR237 4.6 73.5 1.0
O O:HOH427 4.6 71.7 1.0
CB M:ASP328 4.7 49.6 1.0
O4 M:POP5001 4.7 0.1 0.7
CA M:THR235 4.8 78.7 1.0
C M:THR235 4.9 84.6 1.0

Reference:

P.Gong, O.B.Peersen. Structural Basis For Active Site Closure By the Poliovirus Rna-Dependent Rna Polymerase. Proc.Natl.Acad.Sci.Usa V. 107 22505 2010.
ISSN: ISSN 0027-8424
PubMed: 21148772
DOI: 10.1073/PNAS.1007626107
Page generated: Thu Aug 15 08:25:48 2024

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