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Arsenic in PDB 2im2: Crystal Structure of Poliovirus Polymerase Complexed with Utp and MG2+

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

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

Protein crystallography data

The structure of Crystal Structure of Poliovirus Polymerase Complexed with Utp and MG2+, PDB code: 2im2 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) 27.00 / 2.35
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 128.981, 128.981, 113.140, 90.00, 90.00, 120.00
R / Rfree (%) 22.9 / 26.7

Other elements in 2im2:

The structure of Crystal Structure of Poliovirus Polymerase Complexed with Utp 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 Utp and MG2+ (pdb code 2im2). 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 Utp and MG2+, PDB code: 2im2:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in 2im2

Go back to Arsenic Binding Sites List in 2im2
Arsenic binding site 1 out of 4 in the Crystal Structure of Poliovirus Polymerase Complexed with Utp 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 Utp and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As96

b:81.3
occ:1.00
 AS A:CAS96 0.0 81.3 1.0
CE2 A:CAS96 2.2 80.4 1.0
CE1 A:CAS96 2.2 81.3 1.0
SG A:CAS96 2.3 79.7 1.0
CB A:CAS96 3.2 75.6 1.0
OD2 A:ASP99 4.3 73.2 1.0
CA A:CAS96 4.6 74.1 1.0
CG A:ASP99 4.7 73.8 1.0
CB A:GLU98 5.0 78.6 1.0

Arsenic binding site 2 out of 4 in 2im2

Go back to Arsenic Binding Sites List in 2im2
Arsenic binding site 2 out of 4 in the Crystal Structure of Poliovirus Polymerase Complexed with Utp 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 Utp and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As212

b:48.6
occ:1.00
 AS A:CAS212 0.0 48.6 1.0
CE2 A:CAS212 2.2 43.5 1.0
CE1 A:CAS212 2.2 47.3 1.0
SG A:CAS212 2.3 32.8 1.0
CB A:CAS212 3.3 30.6 1.0
O A:ALA209 3.4 27.1 1.0
O A:CAS212 3.6 25.6 1.0
CD1 A:LEU374 3.8 35.2 1.0
CA A:CAS212 3.9 26.3 1.0
C A:CAS212 3.9 25.5 1.0
N A:CAS212 3.9 28.4 1.0
CE2 A:TYR326 4.1 36.4 1.0
CD2 A:TYR326 4.3 32.7 1.0
CG A:PRO214 4.3 24.7 1.0
C A:ALA209 4.4 25.9 1.0
CD A:PRO214 4.4 22.9 1.0
N A:ASP213 4.8 24.9 1.0
CB A:ALA209 4.8 22.4 1.0
N A:GLY211 4.9 27.7 1.0
CZ A:TYR326 4.9 35.5 1.0
C A:GLY211 5.0 28.3 1.0

Arsenic binding site 3 out of 4 in 2im2

Go back to Arsenic Binding Sites List in 2im2
Arsenic binding site 3 out of 4 in the Crystal Structure of Poliovirus Polymerase Complexed with Utp 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 Utp and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As281

b:44.4
occ:1.00
 AS A:CAS281 0.0 44.4 1.0
CE2 A:CAS281 2.2 41.8 1.0
CE1 A:CAS281 2.2 40.0 1.0
SG A:CAS281 2.3 36.9 1.0
CB A:CAS281 3.1 40.2 1.0
CA A:CAS281 3.8 41.7 1.0
O A:SER271 3.9 38.8 1.0
C A:SER271 4.1 40.2 1.0
CA A:HIS272 4.2 42.2 1.0
CB A:HIS272 4.2 41.5 1.0
N A:HIS272 4.2 41.3 1.0
CZ2 A:TRP5 4.4 27.6 1.0
CG A:HIS272 4.6 42.0 1.0
C A:CAS281 4.8 39.9 1.0
CD2 A:HIS272 4.8 41.4 1.0
N A:VAL282 4.9 37.0 1.0
CA A:SER271 4.9 40.6 1.0
N A:CAS281 5.0 43.0 1.0

Arsenic binding site 4 out of 4 in 2im2

Go back to Arsenic Binding Sites List in 2im2
Arsenic binding site 4 out of 4 in the Crystal Structure of Poliovirus Polymerase Complexed with Utp 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 Utp and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As290

b:73.6
occ:1.00
 AS A:CAS290 0.0 73.6 1.0
CE2 A:CAS290 2.2 71.9 1.0
CE1 A:CAS290 2.3 73.9 1.0
SG A:CAS290 2.3 67.0 1.0
CB A:CAS290 3.1 59.9 1.0
SD A:MET187 3.8 56.3 1.0
CB A:SER179 4.0 44.7 1.0
CD2 A:LEU268 4.0 31.4 1.0
CA A:CAS290 4.2 56.5 1.0
OG A:SER179 4.5 41.5 1.0
CD2 A:LEU154 4.6 44.4 1.0
CG A:LEU268 4.6 33.9 1.0
CB A:ASP183 4.7 48.8 1.0
N A:SER291 4.8 53.6 1.0
CD2 A:TYR267 4.8 61.4 1.0
C A:CAS290 5.0 55.3 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 11:24:54 2024

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