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Arsenic in PDB 2ily: Crystal Structure of Poliovirus Polymerase Complexed with Atp and MG2+

Enzymatic activity of Crystal Structure of Poliovirus Polymerase Complexed with Atp and MG2+

All present enzymatic activity of Crystal Structure of Poliovirus Polymerase Complexed with Atp and MG2+:
2.7.7.48;

Protein crystallography data

The structure of Crystal Structure of Poliovirus Polymerase Complexed with Atp and MG2+, PDB code: 2ily 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) 29.80 / 2.60
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 128.526, 128.526, 112.891, 90.00, 90.00, 120.00
R / Rfree (%) 23 / 25

Other elements in 2ily:

The structure of Crystal Structure of Poliovirus Polymerase Complexed with Atp and MG2+ also contains other interesting chemical elements:

Sodium (Na) 1 atom

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Crystal Structure of Poliovirus Polymerase Complexed with Atp and MG2+ (pdb code 2ily). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 4 binding sites of Arsenic where determined in the Crystal Structure of Poliovirus Polymerase Complexed with Atp and MG2+, PDB code: 2ily:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in 2ily

Go back to Arsenic Binding Sites List in 2ily
Arsenic binding site 1 out of 4 in the Crystal Structure of Poliovirus Polymerase Complexed with Atp and MG2+


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Crystal Structure of Poliovirus Polymerase Complexed with Atp and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As96

b:81.7
occ:1.00
 AS A:CAS96 0.0 81.7 1.0
CE2 A:CAS96 2.2 79.3 1.0
CE1 A:CAS96 2.3 79.3 1.0
SG A:CAS96 2.3 75.0 1.0
CB A:CAS96 3.1 70.2 1.0
OD2 A:ASP99 4.1 66.5 1.0
CG A:ASP99 4.4 65.9 1.0
CA A:CAS96 4.6 67.7 1.0
CB A:ASP99 4.9 64.4 1.0
OD1 A:ASP99 4.9 66.7 1.0
N A:ASP99 5.0 65.9 1.0

Arsenic binding site 2 out of 4 in 2ily

Go back to Arsenic Binding Sites List in 2ily
Arsenic binding site 2 out of 4 in the Crystal Structure of Poliovirus Polymerase Complexed with Atp and MG2+


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Crystal Structure of Poliovirus Polymerase Complexed with Atp and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As212

b:53.0
occ:1.00
 AS A:CAS212 0.0 53.0 1.0
CE2 A:CAS212 2.2 47.5 1.0
CE1 A:CAS212 2.2 50.8 1.0
SG A:CAS212 2.3 41.5 1.0
CB A:CAS212 3.3 35.4 1.0
O A:ALA209 3.4 25.0 1.0
O A:CAS212 3.5 28.7 1.0
CD1 A:LEU374 3.7 31.5 1.0
C A:CAS212 3.8 29.4 1.0
CA A:CAS212 3.9 31.5 1.0
N A:CAS212 4.1 31.8 1.0
CG A:PRO214 4.2 23.6 1.0
CD A:PRO214 4.3 23.5 1.0
CE2 A:TYR326 4.4 33.9 1.0
C A:ALA209 4.5 24.7 1.0
CD2 A:TYR326 4.5 32.6 1.0
N A:ASP213 4.7 27.5 1.0
CB A:ALA209 4.9 24.8 1.0
C A:GLY211 4.9 30.4 1.0
N A:GLY211 4.9 28.8 1.0
N A:PRO214 5.0 23.4 1.0

Arsenic binding site 3 out of 4 in 2ily

Go back to Arsenic Binding Sites List in 2ily
Arsenic binding site 3 out of 4 in the Crystal Structure of Poliovirus Polymerase Complexed with Atp and MG2+


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Crystal Structure of Poliovirus Polymerase Complexed with Atp and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As281

b:42.0
occ:1.00
 AS A:CAS281 0.0 42.0 1.0
CE2 A:CAS281 2.2 39.4 1.0
CE1 A:CAS281 2.2 40.9 1.0
SG A:CAS281 2.3 35.8 1.0
CB A:CAS281 3.1 39.7 1.0
CA A:CAS281 3.9 41.7 1.0
O A:SER271 3.9 44.5 1.0
C A:SER271 4.2 46.0 1.0
CZ2 A:TRP5 4.2 32.0 1.0
CA A:HIS272 4.3 45.2 1.0
N A:HIS272 4.4 45.5 1.0
CB A:HIS272 4.4 45.2 1.0
CG A:HIS272 4.8 45.9 1.0
C A:CAS281 4.8 41.4 1.0
CH2 A:TRP5 4.9 31.7 1.0
CE2 A:TRP5 4.9 32.7 1.0
N A:VAL282 4.9 39.5 1.0
CD2 A:HIS272 4.9 46.1 1.0
N A:CAS281 5.0 43.7 1.0
CD2 A:HIS270 5.0 46.5 1.0

Arsenic binding site 4 out of 4 in 2ily

Go back to Arsenic Binding Sites List in 2ily
Arsenic binding site 4 out of 4 in the Crystal Structure of Poliovirus Polymerase Complexed with Atp and MG2+


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Crystal Structure of Poliovirus Polymerase Complexed with Atp and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As290

b:58.6
occ:1.00
 AS A:CAS290 0.0 58.6 1.0
CE2 A:CAS290 2.2 56.8 1.0
CE1 A:CAS290 2.3 58.1 1.0
SG A:CAS290 2.3 56.2 1.0
CB A:CAS290 3.1 48.0 1.0
CD2 A:LEU268 3.8 36.9 1.0
SD A:MET187 3.8 45.0 1.0
CA A:CAS290 4.2 44.0 1.0
CB A:SER179 4.4 40.0 1.0
CG A:LEU268 4.4 38.0 1.0
CD2 A:LEU154 4.7 41.4 1.0
OG A:SER179 4.7 40.6 1.0
N A:SER291 4.9 40.7 1.0
CD2 A:TYR267 4.9 63.2 1.0

Reference:

A.A.Thompson, R.A.Albertini, O.B.Peersen. Stabilization of Poliovirus Polymerase By Ntp Binding and Fingers-Thumb Interactions. J.Mol.Biol. V. 366 1459 2007.
ISSN: ISSN 0022-2836
PubMed: 17223130
DOI: 10.1016/J.JMB.2006.11.070
Page generated: Wed Jul 10 11:23:59 2024

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