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Manganese in PDB 3ol8: Poliovirus Polymerase Elongation Complex with Ctp-Mn

Enzymatic activity of Poliovirus Polymerase Elongation Complex with Ctp-Mn

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

Protein crystallography data

The structure of Poliovirus Polymerase Elongation Complex with Ctp-Mn, PDB code: 3ol8 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) 44.16 / 2.75
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 60.779, 60.863, 193.078, 83.06, 83.04, 76.81
R / Rfree (%) 22.4 / 27.7

Other elements in 3ol8:

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

Zinc (Zn) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Poliovirus Polymerase Elongation Complex with Ctp-Mn (pdb code 3ol8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Poliovirus Polymerase Elongation Complex with Ctp-Mn, PDB code: 3ol8:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 3ol8

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Manganese binding site 1 out of 8 in the Poliovirus Polymerase Elongation Complex with Ctp-Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Poliovirus Polymerase Elongation Complex with Ctp-Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn3007

b:91.1
occ:1.00
 OP1 C:C702 2.5 63.3 1.0
OD2 A:ASP328 2.5 62.3 1.0
O1 A:POP5004 2.6 45.7 0.7
O A:TYR234 2.6 71.8 1.0
OD1 A:ASP233 2.6 73.8 1.0
O2 A:POP5004 2.8 90.6 0.7
O A:HOH551 2.9 96.6 1.0
P1 A:POP5004 3.1 75.7 0.7
CG A:ASP328 3.3 53.7 1.0
OD1 A:ASP328 3.5 46.2 1.0
CG A:ASP233 3.6 73.3 1.0
O A:HOH512 3.7 65.5 1.0
P C:C702 3.7 54.2 1.0
C A:TYR234 3.7 60.3 1.0
MN A:MN3008 3.7 74.1 1.0
O5' C:C702 3.8 66.5 1.0
O A:POP5004 3.9 66.3 0.7
OD2 A:ASP233 4.0 87.6 1.0
N A:TYR234 4.0 67.0 1.0
O5 A:POP5004 4.0 0.3 0.7
C5' C:C702 4.1 62.4 1.0
CA A:TYR234 4.4 58.1 1.0
O3 A:POP5004 4.5 77.4 0.7
CB A:ASP328 4.5 35.1 1.0
P2 A:POP5004 4.5 0.3 0.7
NZ A:LYS359 4.5 99.0 1.0
O3' C:A701 4.6 65.6 1.0
CB A:TYR234 4.7 57.2 1.0
N A:THR235 4.7 65.0 1.0
OP2 C:C702 4.8 55.3 1.0
N A:GLY236 4.8 56.2 1.0
CB A:TYR237 4.8 48.7 1.0
N A:TYR237 4.8 61.4 1.0
CB A:ASP233 4.9 73.1 1.0
CA A:THR235 4.9 56.2 1.0
O4 A:POP5004 5.0 0.4 0.7

Manganese binding site 2 out of 8 in 3ol8

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Manganese binding site 2 out of 8 in the Poliovirus Polymerase Elongation Complex with Ctp-Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Poliovirus Polymerase Elongation Complex with Ctp-Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn3008

b:74.1
occ:1.00
 OD2 A:ASP233 2.3 87.6 1.0
OP1 C:C702 2.4 63.3 1.0
OD1 A:ASP328 2.4 46.2 1.0
O3' C:A701 2.6 65.6 1.0
P C:C702 3.1 54.2 1.0
CG A:ASP328 3.1 53.7 1.0
OD2 A:ASP329 3.2 82.4 1.0
CG A:ASP233 3.3 73.3 1.0
OD2 A:ASP328 3.3 62.3 1.0
CG A:ASP329 3.5 77.5 1.0
N A:ASP329 3.5 50.0 1.0
OD1 A:ASP233 3.6 73.8 1.0
CB A:ASP329 3.7 36.8 1.0
C3' C:A701 3.7 41.6 1.0
MN A:MN3007 3.7 91.1 1.0
C4' C:A701 3.9 47.7 1.0
CA A:ASP329 3.9 40.1 1.0
C5' C:A701 3.9 44.2 1.0
OP2 C:C702 4.1 55.3 1.0
O5' C:C702 4.1 66.5 1.0
OD1 A:ASP329 4.2 94.6 1.0
C5' C:C702 4.3 62.4 1.0
C A:ASP328 4.4 52.7 1.0
CB A:ASP328 4.5 35.1 1.0
CB A:ASP233 4.6 73.1 1.0
O2' C:A701 4.6 49.4 1.0
O5' C:A701 4.7 67.9 1.0
CA A:ASP328 4.7 49.8 1.0
N A:ASP328 4.8 33.2 1.0
OP1 C:A701 4.8 53.3 1.0
O A:HOH491 4.8 53.7 1.0
C2' C:A701 4.8 46.4 1.0
O2 A:POP5004 4.9 90.6 0.7
CA A:ASP233 5.0 65.3 1.0

Manganese binding site 3 out of 8 in 3ol8

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Manganese binding site 3 out of 8 in the Poliovirus Polymerase Elongation Complex with Ctp-Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Poliovirus Polymerase Elongation Complex with Ctp-Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn3005

b:87.3
occ:1.00
 OP1 G:C702 2.5 62.6 1.0
OD2 E:ASP328 2.5 60.8 1.0
O E:TYR234 2.6 72.4 1.0
OD1 E:ASP233 2.6 74.0 1.0
O G:POP5003 2.6 47.2 0.7
O5 G:POP5003 3.0 60.8 0.7
O2 G:POP5003 3.2 58.9 0.7
CG E:ASP328 3.3 50.9 1.0
P2 G:POP5003 3.4 79.2 0.7
OD1 E:ASP328 3.5 42.4 1.0
P1 G:POP5003 3.5 88.6 0.7
CG E:ASP233 3.5 74.9 1.0
C E:TYR234 3.7 60.0 1.0
P G:C702 3.7 55.8 1.0
MN E:MN3006 3.8 74.8 1.0
O5' G:C702 3.9 66.9 1.0
OD2 E:ASP233 3.9 90.3 1.0
N E:TYR234 4.0 73.0 1.0
C5' G:C702 4.2 60.8 1.0
O4 G:POP5003 4.3 81.3 0.7
CA E:TYR234 4.3 57.6 1.0
O3 G:POP5003 4.4 74.4 0.7
NZ E:LYS359 4.5 99.2 1.0
CB E:ASP328 4.5 38.9 1.0
O3' G:A701 4.6 63.9 1.0
O6 G:POP5003 4.7 89.8 0.7
CB E:TYR234 4.7 59.3 1.0
O1 G:POP5003 4.7 56.9 0.7
N E:THR235 4.7 63.1 1.0
CB E:ASP233 4.8 70.3 1.0
OP2 G:C702 4.8 60.8 1.0
N E:GLY236 4.8 60.2 1.0
CB E:TYR237 4.9 47.4 1.0
N E:TYR237 4.9 61.1 1.0
CA E:THR235 4.9 53.5 1.0

Manganese binding site 4 out of 8 in 3ol8

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Manganese binding site 4 out of 8 in the Poliovirus Polymerase Elongation Complex with Ctp-Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Poliovirus Polymerase Elongation Complex with Ctp-Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn3006

b:74.8
occ:1.00
 OD2 E:ASP233 2.3 90.3 1.0
OP1 G:C702 2.4 62.6 1.0
OD1 E:ASP328 2.4 42.4 1.0
O3' G:A701 2.6 63.9 1.0
P G:C702 3.1 55.8 1.0
OD2 E:ASP329 3.1 81.6 1.0
CG E:ASP328 3.2 50.9 1.0
CG E:ASP233 3.3 74.9 1.0
CG E:ASP329 3.4 76.6 1.0
OD2 E:ASP328 3.4 60.8 1.0
N E:ASP329 3.6 46.2 1.0
CB E:ASP329 3.6 36.4 1.0
OD1 E:ASP233 3.7 74.0 1.0
C3' G:A701 3.7 43.2 1.0
MN E:MN3005 3.8 87.3 1.0
C4' G:A701 3.8 48.8 1.0
C5' G:A701 3.9 37.9 1.0
CA E:ASP329 3.9 43.3 1.0
OD1 E:ASP329 4.1 98.2 1.0
OP2 G:C702 4.1 60.8 1.0
O5' G:C702 4.2 66.9 1.0
C5' G:C702 4.4 60.8 1.0
C E:ASP328 4.4 49.9 1.0
CB E:ASP328 4.6 38.9 1.0
O G:HOH121 4.6 61.5 1.0
CB E:ASP233 4.6 70.3 1.0
O5' G:A701 4.6 67.0 1.0
OP1 G:A701 4.7 57.1 1.0
O2' G:A701 4.7 53.8 1.0
C2' G:A701 4.8 48.6 1.0
N E:ASP328 4.8 33.4 1.0
CA E:ASP328 4.8 49.9 1.0

Manganese binding site 5 out of 8 in 3ol8

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Manganese binding site 5 out of 8 in the Poliovirus Polymerase Elongation Complex with Ctp-Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Poliovirus Polymerase Elongation Complex with Ctp-Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn3003

b:0.9
occ:1.00
 OD2 I:ASP328 2.4 69.3 1.0
O I:TYR234 2.4 0.9 1.0
O I:POP5002 2.6 0.2 0.8
OP1 K:C702 2.9 73.9 1.0
OD1 I:ASP233 3.0 96.0 1.0
P1 I:POP5002 3.2 0.2 0.8
O3 I:POP5002 3.2 98.0 0.8
O2 I:POP5002 3.4 0.3 0.8
CG I:ASP328 3.4 58.8 1.0
C I:TYR234 3.6 91.4 1.0
CG I:ASP233 3.9 98.9 1.0
OD1 I:ASP328 3.9 59.9 1.0
P2 I:POP5002 4.0 0.1 0.8
OD2 I:ASP233 4.0 94.6 1.0
N I:TYR234 4.1 99.8 1.0
P K:C702 4.1 64.7 1.0
O5' K:C702 4.2 85.2 1.0
CA I:TYR234 4.3 87.5 1.0
C5' K:C702 4.3 70.4 1.0
MN I:MN3004 4.3 90.8 1.0
O5 I:POP5002 4.3 0.9 0.8
O6 I:POP5002 4.4 1.0 0.8
N I:GLY236 4.5 84.8 1.0
N I:THR235 4.5 92.2 1.0
CB I:TYR237 4.5 74.6 1.0
CB I:ASP328 4.6 46.1 1.0
N I:TYR237 4.6 92.7 1.0
CA I:THR235 4.6 94.5 1.0
O1 I:POP5002 4.6 0.7 0.8
CB I:TYR234 4.6 77.3 1.0
C I:THR235 4.8 90.4 1.0

Manganese binding site 6 out of 8 in 3ol8

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Manganese binding site 6 out of 8 in the Poliovirus Polymerase Elongation Complex with Ctp-Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Poliovirus Polymerase Elongation Complex with Ctp-Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn3004

b:90.8
occ:1.00
 OD2 I:ASP233 2.3 94.6 1.0
OP1 K:C702 2.4 73.9 1.0
OD1 I:ASP328 2.5 59.9 1.0
O3' K:A701 2.6 61.0 1.0
P K:C702 3.0 64.7 1.0
OD2 I:ASP329 3.0 90.0 1.0
CG I:ASP328 3.4 58.8 1.0
CG I:ASP233 3.5 98.9 1.0
N I:ASP329 3.5 44.7 1.0
CG I:ASP329 3.6 74.0 1.0
OD2 I:ASP328 3.6 69.3 1.0
CB I:ASP329 3.7 38.8 1.0
C3' K:A701 3.7 57.1 1.0
CA I:ASP329 3.9 43.3 1.0
C4' K:A701 3.9 64.1 1.0
C5' K:A701 4.0 48.3 1.0
OP2 K:C702 4.0 66.0 1.0
OD1 I:ASP233 4.1 96.0 1.0
O5' K:C702 4.2 85.2 1.0
MN I:MN3003 4.3 0.9 1.0
C5' K:C702 4.4 70.4 1.0
C I:ASP328 4.5 60.7 1.0
OD1 I:ASP329 4.5 95.2 1.0
CB I:ASP233 4.6 96.6 1.0
OP1 K:A701 4.7 75.2 1.0
CB I:ASP328 4.7 46.1 1.0
O5' K:A701 4.7 66.5 1.0
O2' K:A701 4.7 68.7 1.0
C2' K:A701 4.8 55.8 1.0
CA I:ASP328 4.9 56.0 1.0
N I:ASP328 4.9 44.7 1.0

Manganese binding site 7 out of 8 in 3ol8

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Manganese binding site 7 out of 8 in the Poliovirus Polymerase Elongation Complex with Ctp-Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Poliovirus Polymerase Elongation Complex with Ctp-Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mn3001

b:0.0
occ:1.00
 O O:POP5001 2.4 86.7 0.7
O M:TYR234 2.5 0.5 1.0
OD2 M:ASP328 2.5 67.1 1.0
OP1 O:C702 2.9 75.0 1.0
OD1 M:ASP233 3.0 96.0 1.0
O5 O:POP5001 3.1 80.2 0.7
P2 O:POP5001 3.3 93.1 0.7
O3 O:POP5001 3.4 70.4 0.7
CG M:ASP328 3.5 56.8 1.0
P1 O:POP5001 3.5 73.8 0.7
C M:TYR234 3.6 90.4 1.0
CG M:ASP233 3.9 99.3 1.0
OD1 M:ASP328 3.9 58.2 1.0
OD2 M:ASP233 4.1 94.0 1.0
P O:C702 4.1 63.6 1.0
O1 O:POP5001 4.2 73.6 0.7
N M:TYR234 4.2 0.3 1.0
O5' O:C702 4.2 83.1 1.0
O4 O:POP5001 4.2 83.9 0.7
C5' O:C702 4.3 68.8 1.0
CA M:TYR234 4.4 86.4 1.0
MN M:MN3002 4.4 86.2 1.0
N M:GLY236 4.4 89.0 1.0
O6 O:POP5001 4.5 98.8 0.7
N M:THR235 4.5 89.8 1.0
CB M:TYR237 4.6 73.3 1.0
CA M:THR235 4.6 93.1 1.0
N M:TYR237 4.6 90.9 1.0
CB M:ASP328 4.6 44.1 1.0
CB M:TYR234 4.7 78.1 1.0
O2 O:POP5001 4.8 41.4 0.7
C M:THR235 4.8 92.8 1.0

Manganese binding site 8 out of 8 in 3ol8

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Manganese binding site 8 out of 8 in the Poliovirus Polymerase Elongation Complex with Ctp-Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Poliovirus Polymerase Elongation Complex with Ctp-Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mn3002

b:86.2
occ:1.00
 OP1 O:C702 2.4 75.0 1.0
OD2 M:ASP233 2.4 94.0 1.0
O3' O:A701 2.5 61.5 1.0
OD1 M:ASP328 2.5 58.2 1.0
P O:C702 3.0 63.6 1.0
OD2 M:ASP329 3.0 91.1 1.0
CG M:ASP328 3.4 56.8 1.0
N M:ASP329 3.5 48.0 1.0
CG M:ASP329 3.5 73.2 1.0
CG M:ASP233 3.6 99.3 1.0
C3' O:A701 3.6 58.0 1.0
CB M:ASP329 3.6 43.5 1.0
OD2 M:ASP328 3.6 67.1 1.0
C4' O:A701 3.8 63.2 1.0
CA M:ASP329 3.8 44.8 1.0
C5' O:A701 3.9 45.3 1.0
OP2 O:C702 3.9 63.5 1.0
OD1 M:ASP233 4.2 96.0 1.0
O5' O:C702 4.2 83.1 1.0
C5' O:C702 4.3 68.8 1.0
MN M:MN3001 4.4 0.0 1.0
C M:ASP328 4.4 59.1 1.0
OD1 M:ASP329 4.4 94.4 1.0
O2' O:A701 4.5 67.0 1.0
O5' O:A701 4.6 64.6 1.0
CB M:ASP328 4.7 44.1 1.0
C2' O:A701 4.7 54.6 1.0
OP1 O:A701 4.7 72.8 1.0
CB M:ASP233 4.7 96.4 1.0
N M:ASP328 4.9 47.0 1.0
CA M:ASP328 4.9 56.0 1.0
O M:TYR326 4.9 48.5 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: Sat Oct 5 17:24:03 2024

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