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Magnesium 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:

Arsenic (As) 11 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 7 binding sites of Magnesium where determined in the T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium., PDB code: 2ia5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 2ia5

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Magnesium binding site 1 out of 7 in the T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg901

b:66.2
occ:1.00
 O A:ASP167 1.8 70.9 1.0
C A:ASP167 2.9 73.0 1.0
OG1 A:THR169 3.3 31.2 1.0
CB A:ASP278 3.4 35.9 1.0
OD1 A:ASP277 3.5 45.9 1.0
OD1 A:ASP165 3.6 55.9 1.0
CG A:ASP165 3.6 49.8 1.0
N A:GLY168 3.8 69.2 1.0
N A:THR169 3.8 48.8 1.0
CA A:GLY168 3.8 58.2 1.0
N A:ASP278 3.9 20.5 1.0
CB A:ASP165 3.9 39.5 1.0
CA A:ASP167 4.0 75.2 1.0
OD2 A:ASP278 4.1 62.3 1.0
C A:GLY168 4.1 50.8 1.0
CA A:ASP278 4.1 24.4 1.0
OD2 A:ASP165 4.2 53.1 1.0
N A:ARG279 4.2 16.8 1.0
CB A:THR169 4.2 37.1 1.0
N A:ASP167 4.2 70.5 1.0
CG A:ASP278 4.3 50.8 1.0
CB A:ASP167 4.6 90.6 1.0
CG A:ASP277 4.6 36.1 1.0
C A:VAL166 4.6 61.3 1.0
CA A:THR169 4.6 42.9 1.0
O A:HOH2540 4.7 37.4 1.0
C A:ASP278 4.7 23.9 1.0
O A:VAL166 4.8 59.8 1.0
C A:ASP277 4.9 20.0 1.0
N A:VAL166 4.9 46.3 1.0

Magnesium binding site 2 out of 7 in 2ia5

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Magnesium binding site 2 out of 7 in the T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg902

b:43.5
occ:1.00
 O B:ASP167 1.9 64.0 1.0
OD2 B:ASP165 2.5 82.0 1.0
C B:ASP167 3.0 65.4 1.0
CB B:ASP167 3.1 77.6 1.0
OD1 B:ASP277 3.4 43.6 1.0
CA B:ASP167 3.5 68.4 1.0
N B:ARG279 3.6 35.6 1.0
CB B:ASP278 3.7 37.4 1.0
CG B:ASP165 3.7 74.9 1.0
OG1 B:THR169 3.9 44.4 1.0
CB B:ARG279 4.1 32.1 1.0
OD2 B:ASP278 4.1 57.2 1.0
N B:ASP278 4.1 36.6 1.0
N B:GLY168 4.1 62.0 1.0
CG B:ASP167 4.2 83.6 1.0
N B:ASP167 4.2 67.2 1.0
CA B:ASP278 4.3 38.7 1.0
OD2 B:ASP167 4.3 84.5 1.0
CG B:ASP278 4.4 50.1 1.0
C B:ASP278 4.5 39.6 1.0
CA B:ARG279 4.5 31.6 1.0
NZ B:LYS258 4.5 52.6 1.0
CB B:ASP165 4.5 63.5 1.0
OD1 B:ASP165 4.6 80.0 1.0
CA B:GLY168 4.6 61.5 1.0
CG B:ASP277 4.6 44.6 1.0
N B:THR169 4.8 52.7 1.0
C B:GLY168 4.9 58.0 1.0

Magnesium binding site 3 out of 7 in 2ia5

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Magnesium binding site 3 out of 7 in the T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg903

b:57.9
occ:1.00
 O C:ASP167 1.7 66.5 1.0
OD2 C:ASP165 2.3 79.6 1.0
C C:ASP167 2.9 68.3 1.0
O C:HOH2538 3.2 38.6 1.0
CG C:ASP165 3.5 74.6 1.0
O C:HOH2519 3.5 50.6 1.0
CA C:ASP167 3.9 71.1 1.0
N C:GLY168 3.9 64.5 1.0
OD1 C:ASP165 4.1 78.7 1.0
CA C:GLY168 4.1 64.2 1.0
CB C:ASP167 4.1 77.8 1.0
CB C:ASP278 4.1 57.5 1.0
OD1 C:ASP277 4.2 52.4 1.0
OD2 C:ASP278 4.2 78.4 1.0
OG1 C:THR169 4.2 51.5 1.0
N C:ASP167 4.3 70.5 1.0
N C:ARG279 4.5 37.5 1.0
N C:THR169 4.5 61.1 1.0
CB C:ASP165 4.6 64.2 1.0
CE C:MET173 4.7 86.6 1.0
C C:GLY168 4.7 62.8 1.0
CG C:ASP278 4.7 70.0 1.0
NZ C:LYS258 4.7 63.4 1.0
CB C:ARG279 4.8 28.4 1.0
N C:ASP278 4.8 43.3 1.0
CA C:ASP278 4.9 47.8 1.0
C C:VAL166 5.0 65.5 1.0

Magnesium binding site 4 out of 7 in 2ia5

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Magnesium binding site 4 out of 7 in the T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg904

b:52.6
occ:1.00
 O D:ASP167 1.7 61.1 1.0
C D:ASP167 2.8 60.2 1.0
OD1 D:ASP165 2.8 49.0 1.0
CG D:ASP165 3.4 43.0 1.0
CB D:ASP278 3.5 38.5 1.0
N D:GLY168 3.6 58.1 1.0
CA D:GLY168 3.6 54.2 1.0
O D:HOH2544 3.6 38.4 1.0
O D:HOH2565 3.6 40.9 1.0
OG1 D:THR169 3.7 47.6 1.0
N D:THR169 3.8 51.1 1.0
OD2 D:ASP165 3.8 47.0 1.0
OD2 D:ASP278 3.9 65.9 1.0
CA D:ASP167 3.9 59.6 1.0
OD1 D:ASP277 4.0 37.8 1.0
C D:GLY168 4.0 51.3 1.0
CB D:ASP165 4.2 31.1 1.0
CG D:ASP278 4.2 53.6 1.0
N D:ASP167 4.2 55.2 1.0
N D:ASP278 4.2 26.4 1.0
N D:ARG279 4.3 28.4 1.0
CA D:ASP278 4.4 29.1 1.0
CB D:ASP167 4.5 67.3 1.0
CB D:THR169 4.6 45.1 1.0
C D:VAL166 4.7 46.6 1.0
O D:VAL166 4.8 52.9 1.0
CA D:THR169 4.8 47.2 1.0
C D:ASP278 4.8 31.8 1.0
O D:HOH2476 4.8 23.6 1.0
CB D:ARG279 5.0 39.3 1.0

Magnesium binding site 5 out of 7 in 2ia5

Go back to Magnesium Binding Sites List in 2ia5
Magnesium binding site 5 out of 7 in the T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg905

b:51.0
occ:1.00
 O E:ASP167 2.1 64.2 1.0
OD1 E:ASP165 2.3 85.3 1.0
C E:ASP167 3.1 67.4 1.0
O E:HOH2494 3.3 47.4 1.0
CG E:ASP165 3.4 79.9 1.0
CA E:ASP167 3.5 65.3 1.0
CB E:ASP167 3.5 69.2 1.0
N E:ASP167 3.6 65.4 1.0
NZ E:LYS258 4.1 52.6 1.0
OD2 E:ASP165 4.1 83.8 1.0
CB E:ASP165 4.2 71.0 1.0
N E:GLY168 4.3 67.4 1.0
OD1 E:ASP277 4.4 42.3 1.0
OD2 E:ASP167 4.4 72.4 1.0
C E:VAL166 4.4 62.4 1.0
CG E:ASP167 4.5 71.0 1.0
N E:VAL166 4.6 57.0 1.0
OG1 E:THR169 4.7 72.0 1.0
CA E:GLY168 4.8 68.4 1.0
CB E:ASP278 5.0 52.5 1.0

Magnesium binding site 6 out of 7 in 2ia5

Go back to Magnesium Binding Sites List in 2ia5
Magnesium binding site 6 out of 7 in the T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
H:Mg906

b:82.0
occ:1.00
 OD2 H:ASP165 1.8 73.5 1.0
O H:ASP167 1.9 86.1 1.0
C H:ASP167 2.7 86.8 1.0
CB H:ASP167 2.9 0.3 1.0
CG H:ASP165 3.1 73.4 1.0
CA H:ASP167 3.2 89.7 1.0
OD1 H:ASP277 3.4 43.0 1.0
N H:ASP167 3.6 82.8 1.0
N H:GLY168 3.8 79.5 1.0
OD1 H:ASP165 3.8 72.1 1.0
OG1 H:THR169 3.8 60.6 1.0
CB H:ASP278 4.0 58.5 1.0
CB H:ASP165 4.0 68.5 1.0
NZ H:LYS258 4.3 96.7 1.0
N H:ARG279 4.3 49.3 1.0
N H:ASP278 4.3 49.7 1.0
CG H:ASP167 4.3 1.0 1.0
CA H:GLY168 4.4 71.2 1.0
N H:THR169 4.5 63.0 1.0
CG H:ASP277 4.5 53.8 1.0
C H:VAL166 4.6 77.5 1.0
OD2 H:ASP278 4.6 75.0 1.0
C H:GLY168 4.6 65.2 1.0
CA H:ASP278 4.6 50.0 1.0
CB H:ARG279 4.7 47.9 1.0
CB H:THR169 4.9 59.1 1.0
CG H:ASP278 4.9 70.7 1.0
OD2 H:ASP167 4.9 0.4 1.0
N H:VAL166 5.0 68.0 1.0
C H:ASP278 5.0 51.2 1.0

Magnesium binding site 7 out of 7 in 2ia5

Go back to Magnesium Binding Sites List in 2ia5
Magnesium binding site 7 out of 7 in the T4 Polynucleotide Kinase/Phosphatase with Bound Sulfate and Magnesium.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
J:Mg907

b:64.4
occ:1.00
 O J:ASP167 2.2 82.8 1.0
CB J:ASP278 3.1 52.7 1.0
C J:ASP167 3.2 83.9 1.0
OG1 J:THR169 3.3 71.1 1.0
CA J:GLY168 3.3 82.0 1.0
N J:THR169 3.5 71.0 1.0
C J:GLY168 3.7 76.8 1.0
N J:GLY168 3.7 83.2 1.0
OD1 J:ASP277 3.7 46.1 1.0
OD2 J:ASP278 3.7 69.6 1.0
N J:ASP278 3.8 43.2 1.0
OD1 J:ASP165 3.9 85.8 1.0
CG J:ASP278 3.9 63.1 1.0
CA J:ASP278 3.9 48.9 1.0
N J:ARG279 4.0 46.3 1.0
CG J:ASP165 4.0 79.3 1.0
CB J:ASP165 4.2 65.2 1.0
CB J:THR169 4.3 68.4 1.0
C J:ASP278 4.5 49.7 1.0
CA J:THR169 4.5 67.3 1.0
CA J:ASP167 4.5 85.0 1.0
O J:GLY168 4.6 78.3 1.0
OD2 J:ASP165 4.6 83.4 1.0
O J:VAL166 4.7 61.2 1.0
CG J:ASP277 4.8 48.2 1.0
N J:ASP167 4.9 78.3 1.0
C J:ASP277 4.9 35.2 1.0
CB J:ARG279 4.9 35.5 1.0
C J:VAL166 5.0 68.0 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: Mon Dec 14 07:27:04 2020

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