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Magnesium in PDB 3k0f: Crystal Structure of the Phosphorylation-Site Double Mutant T426A/T432A of the Kaic Circadian Clock Protein

Enzymatic activity of Crystal Structure of the Phosphorylation-Site Double Mutant T426A/T432A of the Kaic Circadian Clock Protein

All present enzymatic activity of Crystal Structure of the Phosphorylation-Site Double Mutant T426A/T432A of the Kaic Circadian Clock Protein:
2.7.11.17;

Protein crystallography data

The structure of Crystal Structure of the Phosphorylation-Site Double Mutant T426A/T432A of the Kaic Circadian Clock Protein, PDB code: 3k0f was solved by R.Pattanayek, M.Egli, S.Pattanayek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 132.927, 135.415, 205.618, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 28.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Phosphorylation-Site Double Mutant T426A/T432A of the Kaic Circadian Clock Protein (pdb code 3k0f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of the Phosphorylation-Site Double Mutant T426A/T432A of the Kaic Circadian Clock Protein, PDB code: 3k0f:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 3k0f

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Magnesium binding site 1 out of 9 in the Crystal Structure of the Phosphorylation-Site Double Mutant T426A/T432A of the Kaic Circadian Clock Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Phosphorylation-Site Double Mutant T426A/T432A of the Kaic Circadian Clock Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:54.7
occ:1.00
 O3B A:ATP901 2.3 77.6 1.0
PG A:ATP901 2.3 77.5 1.0
O3G A:ATP901 2.3 77.6 1.0
O2G A:ATP901 2.3 75.9 1.0
OG1 A:THR295 2.7 65.1 1.0
O A:HOH523 3.1 40.1 1.0
O3A A:ATP901 3.1 80.9 1.0
OE1 A:GLU318 3.2 91.7 1.0
PB A:ATP901 3.3 77.5 1.0
NH2 B:ARG459 3.4 76.6 1.0
OE2 A:GLU319 3.7 95.4 1.0
O1G A:ATP901 3.8 78.5 1.0
CB A:THR295 3.9 65.5 1.0
O1B A:ATP901 4.0 77.7 1.0
NE B:ARG459 4.0 75.8 1.0
CZ B:ARG459 4.2 76.1 1.0
O2A A:ATP901 4.2 82.2 1.0
CD A:GLU318 4.3 91.1 1.0
PA A:ATP901 4.3 83.1 1.0
O A:HOH541 4.3 55.5 1.0
CD A:GLU319 4.5 95.1 1.0
CG2 A:THR295 4.5 64.7 1.0
O2B A:ATP901 4.6 79.0 1.0
OD2 A:ASP378 4.8 76.6 1.0
OE2 A:GLU318 4.8 91.8 1.0
CG A:GLU319 4.9 94.2 1.0
OD1 A:ASP378 4.9 74.8 1.0
CB B:ALA432 5.0 90.2 1.0

Magnesium binding site 2 out of 9 in 3k0f

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Magnesium binding site 2 out of 9 in the Crystal Structure of the Phosphorylation-Site Double Mutant T426A/T432A of the Kaic Circadian Clock Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Phosphorylation-Site Double Mutant T426A/T432A of the Kaic Circadian Clock Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg521

b:23.7
occ:1.00
 O2G A:ATP903 2.2 51.1 1.0
OG1 A:THR53 2.3 34.3 1.0
O3B A:ATP903 2.8 49.0 1.0
PG A:ATP903 3.0 54.7 1.0
OD2 A:ASP145 3.3 56.5 1.0
CB A:THR53 3.6 32.1 1.0
N A:THR53 3.7 31.6 1.0
O1G A:ATP903 3.8 49.1 1.0
OD1 A:ASP145 3.9 57.6 1.0
CG A:ASP145 4.0 56.4 1.0
PB A:ATP903 4.0 46.8 1.0
O3A A:ATP903 4.0 43.8 1.0
CA A:THR53 4.1 31.6 1.0
CB A:LYS52 4.2 30.5 1.0
NZ A:LYS52 4.2 42.8 1.0
CG2 A:THR181 4.2 39.6 1.0
O3G A:ATP903 4.3 53.3 1.0
O1B A:ATP903 4.4 45.2 1.0
CE A:LYS52 4.4 35.5 1.0
CG2 A:THR53 4.6 30.9 1.0
NH2 B:ARG226 4.7 51.3 1.0
C A:LYS52 4.8 31.9 1.0
CD A:LYS52 4.9 31.8 1.0

Magnesium binding site 3 out of 9 in 3k0f

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Magnesium binding site 3 out of 9 in the Crystal Structure of the Phosphorylation-Site Double Mutant T426A/T432A of the Kaic Circadian Clock Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Phosphorylation-Site Double Mutant T426A/T432A of the Kaic Circadian Clock Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:92.7
occ:1.00
 O2G B:ATP901 2.3 75.3 1.0
OG1 B:THR295 2.4 46.7 1.0
O3B B:ATP901 2.5 72.4 1.0
PG B:ATP901 2.8 74.8 1.0
OE1 B:GLU318 2.9 79.8 1.0
O3G B:ATP901 3.7 77.0 1.0
PB B:ATP901 3.7 71.2 1.0
CB B:THR295 3.9 49.5 1.0
O3A B:ATP901 3.9 69.0 1.0
O1B B:ATP901 4.0 71.1 1.0
OD1 B:ASP378 4.1 67.0 1.0
O1G B:ATP901 4.1 73.9 1.0
CD B:GLU318 4.1 79.6 1.0
CE B:LYS294 4.2 54.9 1.0
NZ B:LYS294 4.2 57.3 1.0
N B:THR295 4.3 49.4 1.0
NH2 C:ARG459 4.5 51.0 1.0
CG2 B:THR413 4.5 67.0 1.0
CA B:THR295 4.5 49.7 1.0
CG B:ASP378 4.7 66.9 1.0
CG2 B:THR295 4.7 46.1 1.0
OG1 B:THR415 4.7 64.8 1.0
OE2 B:GLU319 4.7 74.8 1.0
OD2 B:ASP378 4.8 68.0 1.0
CB B:LYS294 4.8 52.7 1.0
OE2 B:GLU318 4.8 81.4 1.0

Magnesium binding site 4 out of 9 in 3k0f

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Magnesium binding site 4 out of 9 in the Crystal Structure of the Phosphorylation-Site Double Mutant T426A/T432A of the Kaic Circadian Clock Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Phosphorylation-Site Double Mutant T426A/T432A of the Kaic Circadian Clock Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg803

b:16.6
occ:1.00
 O2G C:ATP901 2.3 35.5 1.0
O3B C:ATP901 2.4 36.7 1.0
OG1 C:THR295 2.6 42.6 1.0
PG C:ATP901 2.8 37.0 1.0
O3A C:ATP901 3.2 37.9 1.0
PB C:ATP901 3.3 36.7 1.0
OE1 C:GLU318 3.5 45.0 1.0
O C:HOH541 3.6 67.1 1.0
CB C:THR295 3.6 41.3 1.0
O1B C:ATP901 3.6 36.1 1.0
O3G C:ATP901 3.6 36.7 1.0
O1G C:ATP901 4.1 31.4 1.0
OE2 C:GLU319 4.1 52.5 1.0
NH2 D:ARG459 4.2 41.2 1.0
CG2 C:THR295 4.5 42.3 1.0
OD1 C:ASP378 4.5 50.9 1.0
N C:THR295 4.6 42.6 1.0
PA C:ATP901 4.6 40.7 1.0
O2A C:ATP901 4.6 39.3 1.0
CA C:THR295 4.7 39.7 1.0
O2B C:ATP901 4.7 33.4 1.0
CD C:GLU318 4.7 42.1 1.0
NE D:ARG459 4.8 40.0 1.0
CZ D:ARG459 4.9 42.4 1.0
CD C:GLU319 4.9 50.7 1.0

Magnesium binding site 5 out of 9 in 3k0f

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Magnesium binding site 5 out of 9 in the Crystal Structure of the Phosphorylation-Site Double Mutant T426A/T432A of the Kaic Circadian Clock Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Phosphorylation-Site Double Mutant T426A/T432A of the Kaic Circadian Clock Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg521

b:33.9
occ:1.00
 O2G B:ATP903 2.4 70.1 1.0
OG1 B:THR53 2.7 43.2 1.0
O3B B:ATP903 2.9 66.3 1.0
PG B:ATP903 3.1 69.5 1.0
OD2 B:ASP145 3.4 77.9 1.0
OD1 B:ASP145 3.8 78.7 1.0
O1G B:ATP903 4.0 65.6 1.0
CG B:ASP145 4.0 77.4 1.0
CB B:THR53 4.1 45.9 1.0
PB B:ATP903 4.1 63.3 1.0
NZ B:LYS52 4.3 49.4 1.0
CG2 B:THR181 4.3 50.9 1.0
O3A B:ATP903 4.3 61.6 1.0
N B:THR53 4.4 46.7 1.0
O1B B:ATP903 4.4 63.6 1.0
O3G B:ATP903 4.4 67.5 1.0
OE2 B:GLU78 4.6 89.0 1.0
CA B:THR53 4.6 45.6 1.0
CB B:LYS52 4.6 47.4 1.0
NH2 C:ARG226 4.8 53.8 1.0
CE B:LYS52 4.8 47.0 1.0
CD B:LYS52 4.9 45.9 1.0
CG2 B:THR53 4.9 43.3 1.0
CB B:SER146 5.0 77.2 1.0

Magnesium binding site 6 out of 9 in 3k0f

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Magnesium binding site 6 out of 9 in the Crystal Structure of the Phosphorylation-Site Double Mutant T426A/T432A of the Kaic Circadian Clock Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Phosphorylation-Site Double Mutant T426A/T432A of the Kaic Circadian Clock Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg804

b:17.3
occ:1.00
 O2G D:ATP901 2.3 51.8 1.0
O3B D:ATP901 2.3 50.3 1.0
PG D:ATP901 2.4 50.7 1.0
O3G D:ATP901 2.6 49.7 1.0
OG1 D:THR295 2.8 40.6 1.0
O3A D:ATP901 2.9 51.2 1.0
O D:HOH524 3.1 29.4 1.0
PB D:ATP901 3.2 50.1 1.0
CB D:THR295 3.6 42.9 1.0
OE2 D:GLU319 3.6 55.5 1.0
O1B D:ATP901 3.8 52.5 1.0
O1G D:ATP901 3.9 48.8 1.0
NH2 E:ARG459 3.9 63.1 1.0
NE E:ARG459 4.1 63.4 1.0
PA D:ATP901 4.2 54.5 1.0
O2A D:ATP901 4.2 55.2 1.0
OE1 D:GLU318 4.3 52.3 1.0
CG2 D:THR295 4.4 41.5 1.0
O2B D:ATP901 4.5 52.4 1.0
CZ E:ARG459 4.5 63.6 1.0
CD D:GLU319 4.6 54.6 1.0
N D:THR295 4.9 43.3 1.0
CA D:THR295 4.9 43.1 1.0

Magnesium binding site 7 out of 9 in 3k0f

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Magnesium binding site 7 out of 9 in the Crystal Structure of the Phosphorylation-Site Double Mutant T426A/T432A of the Kaic Circadian Clock Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the Phosphorylation-Site Double Mutant T426A/T432A of the Kaic Circadian Clock Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg522

b:38.2
occ:1.00
 O2G C:ATP903 2.3 72.7 1.0
OG1 C:THR53 2.4 43.6 1.0
O3B C:ATP903 3.0 66.0 1.0
PG C:ATP903 3.1 71.3 1.0
OD2 C:ASP145 3.5 76.2 1.0
OD1 C:ASP145 3.7 78.0 1.0
CB C:THR53 3.9 43.0 1.0
CG C:ASP145 3.9 77.9 1.0
O1G C:ATP903 3.9 66.9 1.0
OE2 C:GLU78 4.1 79.4 1.0
O3A C:ATP903 4.1 59.2 1.0
PB C:ATP903 4.1 63.0 1.0
N C:THR53 4.3 42.2 1.0
O3G C:ATP903 4.4 72.2 1.0
O1B C:ATP903 4.4 64.6 1.0
CA C:THR53 4.5 42.1 1.0
CG2 C:THR181 4.6 59.6 1.0
CG2 C:THR53 4.6 41.8 1.0
CE C:LYS52 4.7 38.3 1.0
NZ C:LYS52 4.7 39.0 1.0
CB C:LYS52 4.9 39.2 1.0
NH2 D:ARG226 4.9 25.5 1.0

Magnesium binding site 8 out of 9 in 3k0f

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Magnesium binding site 8 out of 9 in the Crystal Structure of the Phosphorylation-Site Double Mutant T426A/T432A of the Kaic Circadian Clock Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the Phosphorylation-Site Double Mutant T426A/T432A of the Kaic Circadian Clock Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg805

b:25.2
occ:1.00
 O2G E:ATP901 2.3 60.0 1.0
O3G E:ATP901 2.4 63.3 1.0
PG E:ATP901 2.4 62.3 1.0
O3B E:ATP901 2.5 61.0 1.0
O F:HOH526 2.7 49.8 1.0
OG1 E:THR295 2.8 52.8 1.0
O3A E:ATP901 2.9 64.1 1.0
PB E:ATP901 3.3 61.3 1.0
CB E:THR295 3.7 53.0 1.0
OE2 E:GLU319 3.7 76.5 1.0
O1G E:ATP901 3.9 63.1 1.0
O2A E:ATP901 3.9 67.5 1.0
OE1 E:GLU318 3.9 74.3 1.0
NH2 F:ARG459 4.0 70.5 1.0
O1B E:ATP901 4.0 64.0 1.0
PA E:ATP901 4.0 67.1 1.0
NE F:ARG459 4.1 70.6 1.0
CG2 E:THR295 4.4 52.0 1.0
CZ F:ARG459 4.4 70.5 1.0
CD E:GLU319 4.5 76.7 1.0
O2B E:ATP901 4.5 63.2 1.0
O E:HOH553 4.7 41.3 1.0
O5' E:ATP901 4.8 67.6 1.0
NZ F:LYS457 4.8 60.7 1.0
CA E:THR295 4.9 54.5 1.0
CG E:GLU319 4.9 75.8 1.0
CD E:GLU318 4.9 72.9 1.0
N E:THR295 4.9 53.3 1.0

Magnesium binding site 9 out of 9 in 3k0f

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Magnesium binding site 9 out of 9 in the Crystal Structure of the Phosphorylation-Site Double Mutant T426A/T432A of the Kaic Circadian Clock Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the Phosphorylation-Site Double Mutant T426A/T432A of the Kaic Circadian Clock Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg806

b:54.7
occ:1.00
 O3G F:ATP901 2.2 80.6 1.0
O2G F:ATP901 2.3 78.5 1.0
PG F:ATP901 2.4 78.7 1.0
O3B F:ATP901 2.6 80.0 1.0
OG1 F:THR295 2.6 64.8 1.0
O3A F:ATP901 3.2 83.5 1.0
PB F:ATP901 3.5 81.6 1.0
CB F:THR295 3.6 64.8 1.0
OE1 F:GLU318 3.8 93.6 1.0
O1G F:ATP901 3.9 78.5 1.0
NH2 A:ARG459 3.9 70.2 1.0
O2A F:ATP901 4.0 85.3 1.0
NE A:ARG459 4.1 71.9 1.0
CG2 F:THR295 4.2 63.2 1.0
PA F:ATP901 4.2 85.0 1.0
OE2 F:GLU319 4.3 94.4 1.0
O1B F:ATP901 4.3 81.7 1.0
CZ A:ARG459 4.4 71.1 1.0
O F:HOH523 4.5 35.5 1.0
O2B F:ATP901 4.7 82.4 1.0
CD F:GLU318 4.7 94.0 1.0
CA F:THR295 4.8 65.5 1.0
CD F:GLU319 4.8 92.7 1.0
N F:THR295 4.9 65.5 1.0
OD1 F:ASP378 5.0 69.3 1.0

Reference:

R.Pattanayek, T.Mori, Y.Xu, S.Pattanayek, C.H.Johnson, M.Egli. Structures of Kaic Circadian Clock Mutant Proteins: A New Phosphorylation Site at T426 and Mechanisms of Kinase, Atpase and Phosphatase. Plos One V. 4 E7529 2009.
ISSN: ESSN 1932-6203
PubMed: 19956664
DOI: 10.1371/JOURNAL.PONE.0007529
Page generated: Wed Aug 14 17:47:40 2024

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