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Arsenic in PDB 1ra7: Poliovirus Polymerase with Gtp

Enzymatic activity of Poliovirus Polymerase with Gtp

All present enzymatic activity of Poliovirus Polymerase with Gtp:
2.7.7.48;

Protein crystallography data

The structure of Poliovirus Polymerase with Gtp, PDB code: 1ra7 was solved by A.A.Thompson, O.B.Peersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.35
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 128.049, 128.049, 112.759, 90.00, 90.00, 120.00
R / Rfree (%) 22.2 / 25.9

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Poliovirus Polymerase with Gtp (pdb code 1ra7). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 4 binding sites of Arsenic where determined in the Poliovirus Polymerase with Gtp, PDB code: 1ra7:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in 1ra7

Go back to Arsenic Binding Sites List in 1ra7
Arsenic binding site 1 out of 4 in the Poliovirus Polymerase with Gtp


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Poliovirus Polymerase with Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As96

b:81.4
occ:1.00
AS A:CAS96 0.0 81.4 1.0
CE2 A:CAS96 2.2 79.7 1.0
CE1 A:CAS96 2.2 80.6 1.0
SG A:CAS96 2.3 80.5 1.0
CB A:CAS96 3.2 75.6 1.0
OD2 A:ASP99 4.2 73.1 1.0
CA A:CAS96 4.6 74.3 1.0
CG A:ASP99 4.6 72.4 1.0
CB A:GLU98 4.8 74.6 1.0

Arsenic binding site 2 out of 4 in 1ra7

Go back to Arsenic Binding Sites List in 1ra7
Arsenic binding site 2 out of 4 in the Poliovirus Polymerase with Gtp


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Poliovirus Polymerase with Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As212

b:52.0
occ:1.00
AS A:CAS212 0.0 52.0 1.0
CE2 A:CAS212 2.2 45.6 1.0
CE1 A:CAS212 2.2 50.0 1.0
SG A:CAS212 2.3 34.5 1.0
CB A:CAS212 3.3 32.4 1.0
O A:ALA209 3.4 28.8 1.0
CD1 A:LEU374 3.5 44.8 1.0
O A:CAS212 3.6 24.3 1.0
CA A:CAS212 3.8 26.6 1.0
N A:CAS212 3.9 28.4 1.0
C A:CAS212 3.9 25.5 1.0
CE2 A:TYR326 4.1 40.5 1.0
CD2 A:TYR326 4.2 38.9 1.0
C A:ALA209 4.4 30.4 1.0
CG A:PRO214 4.4 26.1 1.0
CD A:PRO214 4.6 23.0 1.0
CB A:ALA209 4.7 27.7 1.0
N A:ASP213 4.8 23.9 1.0
O A:HOH538 4.9 41.4 1.0
N A:GLY211 4.9 31.2 1.0
C A:GLY211 4.9 31.5 1.0
CG A:LEU374 5.0 41.8 1.0
CZ A:TYR326 5.0 40.1 1.0

Arsenic binding site 3 out of 4 in 1ra7

Go back to Arsenic Binding Sites List in 1ra7
Arsenic binding site 3 out of 4 in the Poliovirus Polymerase with Gtp


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Poliovirus Polymerase with Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As281

b:43.7
occ:1.00
AS A:CAS281 0.0 43.7 1.0
CE2 A:CAS281 2.2 38.4 1.0
SG A:CAS281 2.2 38.0 1.0
CE1 A:CAS281 2.2 39.4 1.0
CB A:CAS281 3.1 40.4 1.0
O A:SER271 3.7 35.9 1.0
CA A:CAS281 3.7 39.7 1.0
C A:SER271 4.0 37.4 1.0
CA A:HIS272 4.0 40.0 1.0
CB A:HIS272 4.1 40.0 1.0
N A:HIS272 4.1 38.8 1.0
CZ2 A:TRP5 4.4 30.1 1.0
CG A:HIS272 4.5 39.2 1.0
C A:CAS281 4.7 37.0 1.0
CD2 A:HIS272 4.7 37.5 1.0
N A:VAL282 4.7 35.8 1.0
N A:CAS281 4.9 40.2 1.0
CA A:SER271 4.9 39.6 1.0
O A:TYR280 4.9 40.8 1.0
CH2 A:TRP5 5.0 32.0 1.0

Arsenic binding site 4 out of 4 in 1ra7

Go back to Arsenic Binding Sites List in 1ra7
Arsenic binding site 4 out of 4 in the Poliovirus Polymerase with Gtp


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Poliovirus Polymerase with Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As290

b:60.3
occ:1.00
AS A:CAS290 0.0 60.3 1.0
CE2 A:CAS290 2.2 58.8 1.0
CE1 A:CAS290 2.2 60.2 1.0
SG A:CAS290 2.3 56.5 1.0
CB A:CAS290 3.2 51.9 1.0
SD A:MET187 3.6 52.6 1.0
CD2 A:LEU268 3.6 34.6 1.0
CA A:CAS290 4.3 50.6 1.0
CG A:LEU268 4.4 37.0 1.0
CB A:SER179 4.5 49.2 1.0
CD2 A:LEU154 4.5 47.1 1.0
CE A:MET187 4.5 51.0 1.0
CD2 A:TYR267 4.5 62.5 1.0
OG A:SER179 4.5 49.2 1.0
CB A:ASP183 5.0 53.1 1.0

Reference:

A.A.Thompson, O.B.Peersen. Structural Basis For Proteolysis-Dependent Activation of the Poliovirus Rna-Dependent Rna Polymerase. Embo J. V. 23 3462 2004.
ISSN: ISSN 0261-4189
PubMed: 15306852
DOI: 10.1038/SJ.EMBOJ.7600357
Page generated: Tue Oct 27 16:47:19 2020

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