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Arsenic in PDB 2ia5: T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium.

Enzymatic activity of T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium.

All present enzymatic activity of T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium.:
2.7.1.78;

Protein crystallography data

The structure of T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium., PDB code: 2ia5 was solved by H.Zhu, P.C.Smith, L.K.Wang, C.D.Lima, S.Shuman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 2.90
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 124.630, 128.050, 357.120, 90.00, 90.00, 90.00
R / Rfree (%) 24 / 28.6

Other elements in 2ia5:

The structure of T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium. also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms

Arsenic Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Arsenic atom in the T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium. (pdb code 2ia5). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 11 binding sites of Arsenic where determined in the T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium., PDB code: 2ia5:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Arsenic binding site 1 out of 11 in 2ia5

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Arsenic binding site 1 out of 11 in the T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium.


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As951

b:1.0
occ:1.00
 SG A:CYS184 3.5 0.4 1.0
CD2 A:TRP231 3.7 75.2 1.0
CG A:TRP231 3.8 72.1 1.0
CE3 A:TRP231 3.9 75.1 1.0
CE2 A:TRP231 4.2 76.8 1.0
CD1 A:LEU181 4.2 96.4 1.0
CG1 A:VAL166 4.3 45.6 1.0
CB A:TRP231 4.3 69.2 1.0
CB A:CYS184 4.3 0.9 1.0
NH1 A:ARG213 4.3 0.9 1.0
CD1 A:TRP231 4.3 75.3 1.0
NE1 A:TRP231 4.5 74.9 1.0
CZ3 A:TRP231 4.6 76.5 1.0
CB A:ALA171 4.6 54.0 1.0
CZ2 A:TRP231 4.8 80.2 1.0
CG2 A:THR228 4.9 68.8 1.0
CH2 A:TRP231 5.0 78.8 1.0

Arsenic binding site 2 out of 11 in 2ia5

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Arsenic binding site 2 out of 11 in the T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium.


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As952

b:95.3
occ:1.00
 CD2 B:TRP231 3.6 62.4 1.0
CG B:TRP231 3.7 59.6 1.0
SG B:CYS184 3.7 81.4 0.5
CE3 B:TRP231 3.9 60.8 1.0
CE2 B:TRP231 4.0 64.4 1.0
CD1 B:TRP231 4.1 63.9 1.0
CB B:TRP231 4.2 56.9 1.0
NE1 B:TRP231 4.3 62.3 1.0
CB B:ALA171 4.5 53.0 1.0
CZ3 B:TRP231 4.5 56.3 1.0
CG1 B:VAL166 4.5 46.7 1.0
CB B:CYS184 4.6 97.3 1.0
CZ2 B:TRP231 4.6 64.5 1.0
CH2 B:TRP231 4.9 60.1 1.0

Arsenic binding site 3 out of 11 in 2ia5

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Arsenic binding site 3 out of 11 in the T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium.


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As953

b:98.7
occ:1.00
 O C:HOH2659 2.6 55.7 1.0
SG C:CYS184 3.2 73.7 0.6
CG C:TRP231 3.8 75.2 1.0
CD2 C:TRP231 3.9 76.0 1.0
CB C:CYS184 3.9 81.3 1.0
CD1 C:TRP231 4.0 74.6 1.0
CE2 C:TRP231 4.2 75.3 1.0
NE1 C:TRP231 4.2 72.8 1.0
CB C:TRP231 4.3 76.3 1.0
CE3 C:TRP231 4.4 73.5 1.0
CA C:CYS184 4.9 88.7 1.0
CZ2 C:TRP231 5.0 73.3 1.0

Arsenic binding site 4 out of 11 in 2ia5

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Arsenic binding site 4 out of 11 in the T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium.


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As954

b:0.9
occ:1.00
 O D:HOH2585 2.9 38.0 1.0
SG D:CYS184 3.5 59.5 0.5
CD2 D:TRP231 4.0 66.0 1.0
NH2 D:ARG213 4.1 0.0 1.0
CG D:TRP231 4.1 67.8 1.0
CB D:CYS184 4.2 71.8 1.0
CE3 D:TRP231 4.2 62.6 1.0
CG1 D:VAL166 4.4 32.7 1.0
CB D:TRP231 4.4 65.1 1.0
CE D:MET227 4.4 0.4 1.0
CZ D:ARG213 4.5 0.7 1.0
CE2 D:TRP231 4.5 65.0 1.0
CD1 D:TRP231 4.6 70.5 1.0
NH1 D:ARG213 4.6 0.3 1.0
CG2 D:THR228 4.7 53.1 1.0
NE1 D:TRP231 4.8 63.0 1.0
CB D:ALA171 4.9 41.3 1.0
CZ3 D:TRP231 4.9 63.6 1.0
O D:HOH2907 5.0 50.2 1.0

Arsenic binding site 5 out of 11 in 2ia5

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Arsenic binding site 5 out of 11 in the T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium.


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 5 of T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:As955

b:0.0
occ:1.00
 SG E:CYS184 3.5 0.8 1.0
CD2 E:TRP231 3.5 86.8 1.0
CG E:TRP231 3.7 88.9 1.0
CE2 E:TRP231 3.8 87.4 1.0
CE3 E:TRP231 3.9 87.2 1.0
CD1 E:TRP231 4.0 88.6 1.0
NE1 E:TRP231 4.1 88.3 1.0
CB E:TRP231 4.3 90.5 1.0
CB E:ALA171 4.4 70.9 1.0
CZ2 E:TRP231 4.5 88.0 1.0
CB E:CYS184 4.5 0.7 1.0
CZ3 E:TRP231 4.5 87.4 1.0
CG1 E:VAL166 4.5 60.9 1.0
CH2 E:TRP231 4.7 88.8 1.0

Arsenic binding site 6 out of 11 in 2ia5

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Arsenic binding site 6 out of 11 in the T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium.


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 6 of T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:As956

b:86.0
occ:1.00
 OH F:TYR179 3.1 0.4 1.0
SG F:CYS184 3.3 83.5 0.6
CD2 F:TRP231 3.7 39.3 1.0
CG F:TRP231 3.9 40.7 1.0
CB F:CYS184 3.9 91.8 1.0
CE3 F:TRP231 4.0 33.2 1.0
CE2 F:TRP231 4.1 41.3 1.0
CZ F:TYR179 4.1 0.4 1.0
CD1 F:TRP231 4.3 44.7 1.0
CB F:TRP231 4.4 41.4 1.0
NE1 F:TRP231 4.4 44.6 1.0
CB F:ALA171 4.4 36.4 1.0
CG1 F:VAL166 4.6 27.3 1.0
CE1 F:TYR179 4.6 0.8 1.0
CZ3 F:TRP231 4.6 33.2 1.0
CZ2 F:TRP231 4.7 43.1 1.0
CH2 F:TRP231 4.9 39.2 1.0

Arsenic binding site 7 out of 11 in 2ia5

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Arsenic binding site 7 out of 11 in the T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium.


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 7 of T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:As957

b:83.2
occ:1.00
 CD2 G:TRP231 3.7 45.8 1.0
CG G:TRP231 3.7 48.4 1.0
CB G:CYS184 4.0 83.4 1.0
CD1 G:TRP231 4.0 45.3 1.0
CE2 G:TRP231 4.1 42.3 1.0
SG G:CYS184 4.1 95.0 1.0
CE3 G:TRP231 4.1 45.1 1.0
NE1 G:TRP231 4.2 39.4 1.0
CB G:TRP231 4.3 49.5 1.0
CZ2 G:TRP231 4.8 41.0 1.0
CZ3 G:TRP231 4.8 41.2 1.0
CB G:ALA171 4.8 27.5 1.0
CG1 G:VAL166 4.9 26.7 1.0

Arsenic binding site 8 out of 11 in 2ia5

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Arsenic binding site 8 out of 11 in the T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium.


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 8 of T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:As958

b:0.1
occ:1.00
 CD2 H:TRP231 3.5 93.8 1.0
CG H:TRP231 3.6 93.7 1.0
SG H:CYS184 3.8 0.4 1.0
CE2 H:TRP231 3.9 93.0 1.0
CE3 H:TRP231 3.9 93.5 1.0
CD1 H:TRP231 4.0 92.0 1.0
NE1 H:TRP231 4.1 90.8 1.0
CB H:TRP231 4.2 93.2 1.0
CB H:CYS184 4.5 0.2 1.0
CG1 H:VAL166 4.5 68.6 1.0
CZ3 H:TRP231 4.5 90.7 1.0
CZ2 H:TRP231 4.5 93.2 1.0
CB H:ALA171 4.6 67.3 1.0
CH2 H:TRP231 4.8 89.5 1.0
NH2 H:ARG213 4.9 95.8 1.0

Arsenic binding site 9 out of 11 in 2ia5

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Arsenic binding site 9 out of 11 in the T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium.


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 9 of T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium. within 5.0Å range:
probe atom residue distance (Å) B Occ
I:As959

b:0.7
occ:1.00
 O I:HOH2897 2.8 36.0 1.0
CD2 I:TRP231 3.7 67.4 1.0
CG I:TRP231 3.8 70.0 1.0
CE2 I:TRP231 3.8 66.7 1.0
CD1 I:TRP231 4.0 70.1 1.0
NE1 I:TRP231 4.0 68.8 1.0
CE3 I:TRP231 4.2 63.5 1.0
CB I:ALA171 4.4 75.5 1.0
CZ2 I:TRP231 4.5 66.4 1.0
CB I:TRP231 4.5 76.2 1.0
SG I:CYS184 4.7 0.6 1.0
CG1 I:VAL188 4.7 84.0 1.0
CZ3 I:TRP231 4.7 61.2 1.0
CH2 I:TRP231 4.9 65.0 1.0
CG2 I:VAL188 4.9 81.9 1.0

Arsenic binding site 10 out of 11 in 2ia5

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Arsenic binding site 10 out of 11 in the T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium.


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 10 of T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium. within 5.0Å range:
probe atom residue distance (Å) B Occ
J:As960

b:1.0
occ:1.00
 CD2 J:TRP231 3.8 54.7 1.0
CG J:TRP231 3.8 54.4 1.0
SG J:CYS184 4.1 0.7 0.5
CE3 J:TRP231 4.1 52.9 1.0
CE2 J:TRP231 4.2 54.1 1.0
CD1 J:TRP231 4.2 58.6 1.0
CB J:TRP231 4.3 62.1 1.0
NH2 J:ARG213 4.3 0.8 1.0
NE1 J:TRP231 4.4 58.1 1.0
CG1 J:VAL166 4.6 50.6 1.0
CB J:ALA171 4.6 63.3 1.0
CZ3 J:TRP231 4.8 55.0 1.0
CZ2 J:TRP231 4.9 54.5 1.0
CB J:CYS184 4.9 0.9 1.0
CA J:CYS184 5.0 0.0 1.0

Reference:

H.Zhu, P.Smith, L.K.Wang, S.Shuman. Structure-Function Analysis of the 3' Phosphatase Component of T4 Polynucleotide Kinase/Phosphatase. Virology V. 366 126 2007.
ISSN: ISSN 0042-6822
PubMed: 17493655
DOI: 10.1016/J.VIROL.2007.03.059
Page generated: Wed Jul 10 11:24:09 2024

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