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Magnesium in PDB 3dvl: Crystal Structure of Full Length Circadian Clock Protein Kaic with Correct Geometry at Phosphorylation Sites

Enzymatic activity of Crystal Structure of Full Length Circadian Clock Protein Kaic with Correct Geometry at Phosphorylation Sites

All present enzymatic activity of Crystal Structure of Full Length Circadian Clock Protein Kaic with Correct Geometry at Phosphorylation Sites:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of Full Length Circadian Clock Protein Kaic with Correct Geometry at Phosphorylation Sites, PDB code: 3dvl was solved by R.Pattanayek, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 132.873, 135.576, 204.951, 90.00, 90.00, 90.00
R / Rfree (%) 23.9 / 28.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Full Length Circadian Clock Protein Kaic with Correct Geometry at Phosphorylation Sites (pdb code 3dvl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Full Length Circadian Clock Protein Kaic with Correct Geometry at Phosphorylation Sites, PDB code: 3dvl:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3dvl

Go back to Magnesium Binding Sites List in 3dvl
Magnesium binding site 1 out of 6 in the Crystal Structure of Full Length Circadian Clock Protein Kaic with Correct Geometry at Phosphorylation Sites


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 Full Length Circadian Clock Protein Kaic with Correct Geometry at Phosphorylation Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:18.8
occ:1.00
 OG1 A:THR295 2.5 71.2 1.0
O2G A:ATP901 2.8 0.1 1.0
OE1 A:GLU318 3.2 0.6 1.0
PG A:ATP901 3.2 0.4 1.0
O3B A:ATP901 3.2 95.9 1.0
O3G A:ATP901 3.3 96.7 1.0
OE2 A:GLU319 3.4 98.9 1.0
NH2 B:ARG459 3.5 86.3 1.0
CB A:THR295 3.6 71.2 1.0
O3A A:ATP901 3.8 88.0 1.0
CG2 A:THR295 3.9 71.1 1.0
OD2 A:ASP378 3.9 90.9 1.0
CD A:GLU319 4.1 95.6 1.0
PB A:ATP901 4.2 84.9 1.0
CG A:GLU319 4.2 91.9 1.0
CZ B:ARG459 4.3 82.5 1.0
NE B:ARG459 4.3 80.6 1.0
OD1 A:ASP378 4.4 81.7 1.0
O2A A:ATP901 4.4 85.7 1.0
CD A:GLU318 4.4 0.0 1.0
CG A:ASP378 4.5 87.3 1.0
O1G A:ATP901 4.6 0.7 1.0
O1B A:ATP901 4.6 82.9 1.0
CB A:GLU318 4.7 90.2 1.0
PA A:ATP901 4.8 85.5 1.0
CA A:THR295 4.8 70.0 1.0

Magnesium binding site 2 out of 6 in 3dvl

Go back to Magnesium Binding Sites List in 3dvl
Magnesium binding site 2 out of 6 in the Crystal Structure of Full Length Circadian Clock Protein Kaic with Correct Geometry at Phosphorylation Sites


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 Full Length Circadian Clock Protein Kaic with Correct Geometry at Phosphorylation Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:73.1
occ:1.00
 OE1 B:GLU318 2.4 90.1 1.0
O2G B:ATP901 3.0 0.6 1.0
OG1 B:THR415 3.1 65.5 1.0
CD B:GLU318 3.2 85.7 1.0
O3B B:ATP901 3.3 99.6 1.0
OE2 B:GLU318 3.4 87.2 1.0
PG B:ATP901 3.8 0.8 1.0
CE B:LYS294 3.8 62.9 1.0
NZ B:LYS294 3.9 61.9 1.0
OD1 B:ASP378 4.0 73.6 1.0
OG1 B:THR295 4.0 38.8 1.0
CG2 B:THR413 4.1 87.6 1.0
CB B:SER379 4.2 76.5 1.0
OG B:SER379 4.3 84.4 1.0
O1B B:ATP901 4.4 86.4 1.0
CB B:THR415 4.5 56.9 1.0
O1G B:ATP901 4.6 0.9 1.0
CG B:GLU318 4.6 83.1 1.0
PB B:ATP901 4.6 83.4 1.0
CA B:SER379 5.0 72.8 1.0
CG B:ASP378 5.0 71.9 1.0
O3G B:ATP901 5.0 0.1 1.0

Magnesium binding site 3 out of 6 in 3dvl

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Magnesium binding site 3 out of 6 in the Crystal Structure of Full Length Circadian Clock Protein Kaic with Correct Geometry at Phosphorylation Sites


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 Full Length Circadian Clock Protein Kaic with Correct Geometry at Phosphorylation Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg803

b:18.8
occ:1.00
 OG1 C:THR295 2.3 53.6 1.0
O3B C:ATP901 2.9 87.7 1.0
O2G C:ATP901 2.9 0.7 1.0
O3G C:ATP901 3.0 96.7 1.0
PG C:ATP901 3.1 0.8 1.0
CB C:THR295 3.1 58.4 1.0
O3A C:ATP901 3.2 60.6 1.0
OE2 C:GLU319 3.2 86.5 1.0
CG2 C:THR295 3.6 46.7 1.0
PB C:ATP901 3.6 60.7 1.0
O2A C:ATP901 3.7 63.8 1.0
NH2 D:ARG459 4.0 44.9 1.0
O1B C:ATP901 4.1 67.2 1.0
CD C:GLU319 4.1 79.1 1.0
OE1 C:GLU318 4.1 76.2 1.0
PA C:ATP901 4.1 60.6 1.0
OD2 C:ASP378 4.3 62.0 1.0
NE D:ARG459 4.3 35.8 1.0
CA C:THR295 4.4 52.2 1.0
O1G C:ATP901 4.5 90.2 1.0
CG C:GLU319 4.6 75.1 1.0
N C:THR295 4.6 54.4 1.0
CZ D:ARG459 4.6 44.4 1.0
OE1 C:GLU319 4.9 78.2 1.0
CG C:ASP378 5.0 63.5 1.0

Magnesium binding site 4 out of 6 in 3dvl

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Magnesium binding site 4 out of 6 in the Crystal Structure of Full Length Circadian Clock Protein Kaic with Correct Geometry at Phosphorylation Sites


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 Full Length Circadian Clock Protein Kaic with Correct Geometry at Phosphorylation Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg804

b:18.8
occ:1.00
 OG1 D:THR295 1.9 39.0 1.0
CB D:THR295 2.8 53.9 1.0
O3B D:ATP901 2.8 76.0 1.0
O3A D:ATP901 3.0 62.1 1.0
O3G D:ATP901 3.1 94.8 1.0
O2G D:ATP901 3.1 0.2 1.0
PG D:ATP901 3.2 89.0 1.0
CG2 D:THR295 3.4 44.2 1.0
PB D:ATP901 3.5 59.2 1.0
OE2 D:GLU319 3.5 88.6 1.0
O1B D:ATP901 3.8 66.3 1.0
O2A D:ATP901 3.8 66.4 1.0
OE1 D:GLU318 3.9 79.1 1.0
PA D:ATP901 4.1 63.1 1.0
CA D:THR295 4.1 52.6 1.0
NH2 E:ARG459 4.3 76.2 1.0
OD2 D:ASP378 4.3 52.9 1.0
N D:THR295 4.3 56.1 1.0
CD D:GLU319 4.4 78.5 1.0
OD1 D:ASP378 4.5 53.5 1.0
NE E:ARG459 4.6 66.6 1.0
O1G D:ATP901 4.6 78.8 1.0
CG D:ASP378 4.8 58.7 1.0
CG D:GLU319 4.8 74.5 1.0
O2B D:ATP901 4.9 65.5 1.0
CZ E:ARG459 4.9 70.4 1.0
O1A D:ATP901 4.9 60.4 1.0

Magnesium binding site 5 out of 6 in 3dvl

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Magnesium binding site 5 out of 6 in the Crystal Structure of Full Length Circadian Clock Protein Kaic with Correct Geometry at Phosphorylation Sites


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 Full Length Circadian Clock Protein Kaic with Correct Geometry at Phosphorylation Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg805

b:18.8
occ:1.00
 OG1 E:THR295 2.1 60.1 1.0
O3B E:ATP901 2.8 88.0 1.0
O2G E:ATP901 3.0 0.1 1.0
PG E:ATP901 3.2 0.5 1.0
CB E:THR295 3.3 57.8 1.0
O3A E:ATP901 3.3 72.8 1.0
O3G E:ATP901 3.3 99.7 1.0
OE1 E:GLU318 3.5 86.4 1.0
PB E:ATP901 3.6 66.5 1.0
OE2 E:GLU319 3.7 97.2 1.0
CG2 E:THR295 3.7 55.0 1.0
OD2 E:ASP378 3.8 70.0 1.0
O1B E:ATP901 3.9 66.5 1.0
NH2 F:ARG459 4.2 76.1 1.0
O2A E:ATP901 4.3 70.0 1.0
OD1 E:ASP378 4.3 51.9 1.0
CA E:THR295 4.4 58.4 1.0
CG E:ASP378 4.4 63.1 1.0
N E:THR295 4.5 56.2 1.0
PA E:ATP901 4.5 68.4 1.0
CD E:GLU319 4.5 89.7 1.0
O1G E:ATP901 4.6 0.4 1.0
CD E:GLU318 4.7 82.7 1.0
NE F:ARG459 4.7 73.4 1.0
CG E:GLU319 4.8 85.0 1.0
CZ F:ARG459 4.9 76.3 1.0
O2B E:ATP901 4.9 79.4 1.0

Magnesium binding site 6 out of 6 in 3dvl

Go back to Magnesium Binding Sites List in 3dvl
Magnesium binding site 6 out of 6 in the Crystal Structure of Full Length Circadian Clock Protein Kaic with Correct Geometry at Phosphorylation Sites


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 Full Length Circadian Clock Protein Kaic with Correct Geometry at Phosphorylation Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg806

b:18.8
occ:1.00
 OG1 F:THR295 2.5 75.9 1.0
O2G F:ATP901 2.8 0.7 1.0
OE2 F:GLU319 3.1 0.6 1.0
O F:HOH543 3.2 18.8 1.0
O3G F:ATP901 3.3 0.3 1.0
PG F:ATP901 3.3 0.5 1.0
O3B F:ATP901 3.4 0.0 1.0
CB F:THR295 3.5 71.4 1.0
OE1 F:GLU318 3.6 0.4 1.0
NH2 A:ARG459 3.6 72.5 1.0
CG2 F:THR295 3.7 69.9 1.0
CD F:GLU319 3.8 99.1 1.0
O3A F:ATP901 3.9 88.0 1.0
OD2 F:ASP378 3.9 74.8 1.0
CG F:GLU319 4.0 97.9 1.0
NE A:ARG459 4.3 63.9 1.0
CZ A:ARG459 4.3 63.6 1.0
O2A F:ATP901 4.4 87.8 1.0
PB F:ATP901 4.4 90.2 1.0
CB F:GLU318 4.6 88.7 1.0
CD F:GLU318 4.6 98.9 1.0
CG F:ASP378 4.7 73.3 1.0
O1G F:ATP901 4.8 0.8 1.0
OE1 F:GLU319 4.8 96.1 1.0
CA F:THR295 4.8 68.4 1.0
OD1 F:ASP378 4.8 69.5 1.0
PA F:ATP901 4.9 80.3 1.0
O1B F:ATP901 4.9 83.8 1.0
O F:HOH520 4.9 60.1 1.0

Reference:

R.Pattanayek, D.R.Williams, S.Pattanayek, Y.Xu, T.Mori, C.H.Johnson, P.L.Stewart, M.Egli. Crystal Structure of Full Length Circadian Clock Protein Kaic with Correct Geometry at Phosphorylation Sites To Be Published.
Page generated: Wed Aug 14 12:44:41 2024

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