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Arsenic in PDB 2im3: Crystal Structure of Poliovirus Polymerase Complexed with Utp and MN2+

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

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

Protein crystallography data

The structure of Crystal Structure of Poliovirus Polymerase Complexed with Utp and MN2+, PDB code: 2im3 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) 29.70 / 2.60
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 128.115, 128.115, 112.833, 90.00, 90.00, 120.00
R / Rfree (%) 23.7 / 26.9

Other elements in 2im3:

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

Manganese (Mn) 2 atoms
Sodium (Na) 1 atom

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Crystal Structure of Poliovirus Polymerase Complexed with Utp and MN2+ (pdb code 2im3). 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 MN2+, PDB code: 2im3:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in 2im3

Go back to Arsenic Binding Sites List in 2im3
Arsenic binding site 1 out of 4 in the Crystal Structure of Poliovirus Polymerase Complexed with Utp 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 Utp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As96

b:93.1
occ:1.00
 AS A:CAS96 0.0 93.1 1.0
CE2 A:CAS96 2.2 89.4 1.0
CE1 A:CAS96 2.3 90.4 1.0
SG A:CAS96 2.3 86.5 1.0
CB A:CAS96 3.1 81.5 1.0
OD2 A:ASP99 3.9 66.2 1.0
CA A:CAS96 4.6 79.0 1.0
CG A:ASP99 4.6 66.3 1.0
CB A:GLU98 5.0 77.0 1.0

Arsenic binding site 2 out of 4 in 2im3

Go back to Arsenic Binding Sites List in 2im3
Arsenic binding site 2 out of 4 in the Crystal Structure of Poliovirus Polymerase Complexed with Utp 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 Utp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As212

b:62.6
occ:1.00
 AS A:CAS212 0.0 62.6 1.0
CE2 A:CAS212 2.2 55.7 1.0
CE1 A:CAS212 2.2 60.3 1.0
SG A:CAS212 2.3 45.4 1.0
CB A:CAS212 3.3 37.8 1.0
CD1 A:LEU374 3.4 36.4 1.0
O A:ALA209 3.5 25.2 1.0
O A:CAS212 3.6 34.7 1.0
C A:CAS212 3.9 32.9 1.0
CA A:CAS212 3.9 34.1 1.0
N A:CAS212 3.9 34.0 1.0
CG A:PRO214 4.0 30.4 1.0
CD A:PRO214 4.2 30.8 1.0
CE2 A:TYR326 4.3 41.2 1.0
CD2 A:TYR326 4.4 39.3 1.0
C A:ALA209 4.5 25.1 1.0
N A:ASP213 4.7 31.5 1.0
CB A:ALA209 4.8 22.5 1.0
CG A:LEU374 4.8 38.3 1.0
N A:PRO214 4.9 30.2 1.0

Arsenic binding site 3 out of 4 in 2im3

Go back to Arsenic Binding Sites List in 2im3
Arsenic binding site 3 out of 4 in the Crystal Structure of Poliovirus Polymerase Complexed with Utp 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 Utp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As281

b:48.1
occ:1.00
 AS A:CAS281 0.0 48.1 1.0
CE2 A:CAS281 2.2 45.9 1.0
SG A:CAS281 2.2 40.3 1.0
CE1 A:CAS281 2.3 45.4 1.0
CB A:CAS281 3.1 45.2 1.0
O A:SER271 3.7 43.9 1.0
CA A:CAS281 3.9 45.6 1.0
C A:SER271 4.2 44.3 1.0
CA A:HIS272 4.2 46.2 1.0
CZ2 A:TRP5 4.3 41.8 1.0
CB A:HIS272 4.4 45.9 1.0
N A:HIS272 4.4 44.9 1.0
C A:CAS281 4.7 45.4 1.0
CG A:HIS272 4.8 45.9 1.0
N A:VAL282 4.8 44.3 1.0
CD2 A:HIS272 4.8 45.5 1.0
CH2 A:TRP5 4.9 40.7 1.0
CE2 A:TRP5 4.9 43.1 1.0
N A:CAS281 5.0 47.3 1.0
CD2 A:HIS270 5.0 45.5 1.0

Arsenic binding site 4 out of 4 in 2im3

Go back to Arsenic Binding Sites List in 2im3
Arsenic binding site 4 out of 4 in the Crystal Structure of Poliovirus Polymerase Complexed with Utp 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 Utp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As290

b:0.7
occ:1.00
 AS A:CAS290 0.0 0.7 1.0
CE2 A:CAS290 2.2 0.7 1.0
CE1 A:CAS290 2.2 0.8 1.0
SG A:CAS290 2.3 93.5 1.0
SD A:MET187 3.1 53.0 1.0
CB A:CAS290 3.2 78.6 1.0
CE2 A:TYR267 3.2 67.2 1.0
CD2 A:LEU268 3.7 39.7 1.0
CZ A:TYR267 3.8 68.2 1.0
CB A:SER179 3.9 51.4 1.0
CD2 A:TYR267 3.9 63.8 1.0
OG A:SER179 3.9 52.2 1.0
OH A:TYR267 4.0 70.7 1.0
CA A:CAS290 4.0 69.2 1.0
N A:SER291 4.2 61.1 1.0
CG A:MET187 4.4 50.2 1.0
CE A:MET187 4.5 52.9 1.0
C A:CAS290 4.6 65.3 1.0
CG A:LEU268 4.8 38.8 1.0
CB A:ASP183 4.8 52.9 1.0
O A:SER291 4.9 57.8 1.0
CE1 A:TYR267 4.9 64.9 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 11:27:19 2024

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