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Arsenic in PDB 2im1: Crystal Structure of Poliovirus Polymerase Complexed with Ctp and MN2+

Enzymatic activity of Crystal Structure of Poliovirus Polymerase Complexed with Ctp and MN2+

All present enzymatic activity of Crystal Structure of Poliovirus Polymerase Complexed with Ctp and MN2+:
2.7.7.48;

Protein crystallography data

The structure of Crystal Structure of Poliovirus Polymerase Complexed with Ctp and MN2+, PDB code: 2im1 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) 28.20 / 2.50
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 128.942, 128.942, 112.979, 90.00, 90.00, 120.00
R / Rfree (%) 23.9 / 26.8

Other elements in 2im1:

The structure of Crystal Structure of Poliovirus Polymerase Complexed with Ctp and MN2+ also contains other interesting chemical elements:

Manganese (Mn) 3 atoms
Sodium (Na) 1 atom

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Crystal Structure of Poliovirus Polymerase Complexed with Ctp and MN2+ (pdb code 2im1). 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 Ctp and MN2+, PDB code: 2im1:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in 2im1

Go back to Arsenic Binding Sites List in 2im1
Arsenic binding site 1 out of 4 in the Crystal Structure of Poliovirus Polymerase Complexed with Ctp and MN2+


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 Ctp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As96

b:86.1
occ:1.00
AS A:CAS96 0.0 86.1 1.0
CE2 A:CAS96 2.2 84.1 1.0
CE1 A:CAS96 2.3 84.6 1.0
SG A:CAS96 2.3 82.5 1.0
CB A:CAS96 3.1 78.3 1.0
OD2 A:ASP99 4.0 72.5 1.0
CA A:CAS96 4.6 76.5 1.0
CG A:ASP99 4.6 72.5 1.0
CB A:GLU98 5.0 78.2 1.0

Arsenic binding site 2 out of 4 in 2im1

Go back to Arsenic Binding Sites List in 2im1
Arsenic binding site 2 out of 4 in the Crystal Structure of Poliovirus Polymerase Complexed with Ctp and MN2+


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 Ctp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As212

b:48.0
occ:1.00
AS A:CAS212 0.0 48.0 1.0
CE1 A:CAS212 2.2 48.5 1.0
CE2 A:CAS212 2.2 43.5 1.0
SG A:CAS212 2.3 34.5 1.0
CB A:CAS212 3.3 32.5 1.0
O A:ALA209 3.4 27.0 1.0
O A:CAS212 3.5 29.7 1.0
CD1 A:LEU374 3.7 38.9 1.0
C A:CAS212 3.9 27.3 1.0
CA A:CAS212 3.9 28.8 1.0
N A:CAS212 3.9 31.0 1.0
C A:ALA209 4.4 26.4 1.0
CG A:PRO214 4.4 25.5 1.0
CD A:PRO214 4.4 23.7 1.0
CE2 A:TYR326 4.6 39.4 1.0
CD2 A:TYR326 4.6 36.9 1.0
CB A:ALA209 4.7 22.8 1.0
N A:ASP213 4.8 24.8 1.0
N A:GLY211 4.9 33.2 1.0
O A:HOH519 5.0 35.8 1.0
C A:GLY211 5.0 32.1 1.0

Arsenic binding site 3 out of 4 in 2im1

Go back to Arsenic Binding Sites List in 2im1
Arsenic binding site 3 out of 4 in the Crystal Structure of Poliovirus Polymerase Complexed with Ctp and MN2+


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 Ctp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As281

b:48.5
occ:1.00
AS A:CAS281 0.0 48.5 1.0
CE2 A:CAS281 2.2 44.8 1.0
CE1 A:CAS281 2.2 45.9 1.0
SG A:CAS281 2.2 41.3 1.0
CB A:CAS281 3.1 43.6 1.0
O A:SER271 3.9 43.6 1.0
CA A:CAS281 3.9 45.0 1.0
C A:SER271 4.1 45.1 1.0
CA A:HIS272 4.1 45.7 1.0
CB A:HIS272 4.2 44.3 1.0
N A:HIS272 4.2 44.8 1.0
CZ2 A:TRP5 4.5 35.9 1.0
CG A:HIS272 4.5 43.2 1.0
CD2 A:HIS272 4.7 42.2 1.0
C A:CAS281 4.8 43.8 1.0
N A:VAL282 4.9 41.2 1.0
CA A:SER271 4.9 45.6 1.0
N A:CAS281 5.0 47.0 1.0

Arsenic binding site 4 out of 4 in 2im1

Go back to Arsenic Binding Sites List in 2im1
Arsenic binding site 4 out of 4 in the Crystal Structure of Poliovirus Polymerase Complexed with Ctp and MN2+


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 Ctp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As290

b:70.7
occ:1.00
AS A:CAS290 0.0 70.7 1.0
CE2 A:CAS290 2.2 67.4 1.0
CE1 A:CAS290 2.3 69.2 1.0
SG A:CAS290 2.3 63.7 1.0
CB A:CAS290 3.1 55.8 1.0
SD A:MET187 3.7 51.2 1.0
CD2 A:LEU268 3.8 33.9 1.0
CB A:SER179 4.1 50.1 1.0
CA A:CAS290 4.2 52.8 1.0
CD2 A:LEU154 4.6 43.2 1.0
CG A:LEU268 4.6 37.7 1.0
OG A:SER179 4.7 48.8 1.0
CB A:ASP183 4.8 57.5 1.0
CD2 A:TYR267 4.9 62.2 1.0
N A:SER291 5.0 49.5 1.0
CE A:MET187 5.0 51.5 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: Tue Oct 27 16:49:01 2020

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