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Magnesium in PDB 4dug: Crystal Structure of Circadian Clock Protein Kaic E318A Mutant

Enzymatic activity of Crystal Structure of Circadian Clock Protein Kaic E318A Mutant

All present enzymatic activity of Crystal Structure of Circadian Clock Protein Kaic E318A Mutant:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of Circadian Clock Protein Kaic E318A Mutant, PDB code: 4dug was solved by M.Egli, T.Mori, R.Pattanayek, Y.Xu, X.Qin, C.H.Johnson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.05 / 3.29
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 131.714, 135.058, 204.249, 90.00, 90.00, 90.00
R / Rfree (%) 24.5 / 30.3

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Circadian Clock Protein Kaic E318A Mutant (pdb code 4dug). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Crystal Structure of Circadian Clock Protein Kaic E318A Mutant, PDB code: 4dug:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 4dug

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Magnesium binding site 1 out of 12 in the Crystal Structure of Circadian Clock Protein Kaic E318A Mutant


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Circadian Clock Protein Kaic E318A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:0.0
occ:1.00
 OE2 A:GLU319 2.2 0.9 1.0
OG1 A:THR295 2.2 0.4 1.0
O A:HOH901 2.2 98.8 1.0
O3G A:ATP802 2.5 0.7 1.0
O3B A:ATP802 2.5 0.5 1.0
PG A:ATP802 2.8 0.5 1.0
O2G A:ATP802 3.0 1.0 1.0
CD A:GLU319 3.3 0.9 1.0
CB A:THR295 3.6 98.0 1.0
NH2 B:ARG459 3.7 0.8 1.0
PB A:ATP802 3.8 0.1 1.0
NE B:ARG459 3.9 0.5 1.0
CG A:GLU319 3.9 0.0 1.0
O3A A:ATP802 3.9 0.6 1.0
CZ B:ARG459 4.1 0.1 1.0
O1B A:ATP802 4.1 0.5 1.0
OD2 A:ASP378 4.3 0.8 1.0
O1G A:ATP802 4.3 96.4 1.0
OE1 A:GLU319 4.3 0.9 1.0
CG2 A:THR295 4.3 95.5 1.0
OD1 A:ASP378 4.4 0.4 1.0
O1A A:ATP802 4.5 0.8 1.0
N A:THR295 4.6 0.3 1.0
CA A:THR295 4.6 0.4 1.0
CG A:ASP378 4.6 0.3 1.0
CD B:ARG459 4.8 0.6 1.0
PA A:ATP802 4.9 0.1 1.0
O2B A:ATP802 5.0 0.8 1.0

Magnesium binding site 2 out of 12 in 4dug

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Magnesium binding site 2 out of 12 in the Crystal Structure of Circadian Clock Protein Kaic E318A Mutant


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Circadian Clock Protein Kaic E318A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg804

b:80.8
occ:1.00
 O2G A:ATP803 2.1 99.5 1.0
OG1 A:THR53 2.1 84.3 1.0
O3B A:ATP803 3.1 92.6 1.0
PG A:ATP803 3.1 0.4 1.0
OD2 A:ASP145 3.3 94.8 1.0
OD1 A:ASP145 3.4 96.0 1.0
CB A:THR53 3.5 81.0 1.0
O3G A:ATP803 3.8 0.0 1.0
CG A:ASP145 3.8 94.2 1.0
CG2 A:THR53 4.2 82.4 1.0
O3A A:ATP803 4.3 90.9 1.0
CA A:THR53 4.3 85.6 1.0
N A:THR53 4.4 87.8 1.0
PB A:ATP803 4.4 90.3 1.0
O1G A:ATP803 4.4 0.8 1.0
CG2 A:THR181 4.5 85.8 1.0
CE A:LYS52 4.6 83.6 1.0
NZ A:LYS52 4.8 78.8 1.0
NH2 B:ARG226 4.8 0.4 1.0
O2B A:ATP803 4.9 84.9 1.0
CB A:SER146 5.0 99.2 1.0

Magnesium binding site 3 out of 12 in 4dug

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Magnesium binding site 3 out of 12 in the Crystal Structure of Circadian Clock Protein Kaic E318A Mutant


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Circadian Clock Protein Kaic E318A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:0.9
occ:1.00
 O B:HOH710 2.1 30.0 1.0
O B:HOH711 2.1 30.0 1.0
O3B B:ATP602 2.1 0.8 1.0
PG B:ATP602 2.4 0.1 1.0
O2G B:ATP602 2.4 0.8 1.0
O3G B:ATP602 2.4 0.2 1.0
O2B B:ATP602 3.2 94.8 1.0
PB B:ATP602 3.3 0.6 1.0
OG1 B:THR295 3.4 89.9 1.0
NH2 C:ARG459 3.7 0.9 1.0
O1G B:ATP602 3.9 99.0 1.0
O3A B:ATP602 4.0 0.4 1.0
OE2 B:GLU319 4.3 0.7 1.0
OG1 B:THR415 4.3 98.4 1.0
CG2 C:TPO432 4.4 0.2 1.0
O1B B:ATP602 4.4 0.8 1.0
CZ C:ARG459 4.7 0.6 1.0
CE B:LYS294 4.8 88.4 1.0
CB B:THR295 4.8 96.7 1.0
OD1 B:ASP378 4.9 0.4 1.0
N B:THR295 5.0 87.8 1.0
NZ B:LYS294 5.0 95.6 1.0

Magnesium binding site 4 out of 12 in 4dug

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Magnesium binding site 4 out of 12 in the Crystal Structure of Circadian Clock Protein Kaic E318A Mutant


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 Circadian Clock Protein Kaic E318A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:0.3
occ:1.00
 O B:HOH701 2.1 0.7 1.0
OG1 B:THR53 2.1 0.6 1.0
O3B B:ATP603 2.2 0.1 1.0
O3G B:ATP603 2.3 0.8 1.0
PG B:ATP603 2.4 0.9 1.0
O2G B:ATP603 2.6 0.0 1.0
NZ B:LYS52 3.3 90.7 1.0
CB B:THR53 3.3 0.4 1.0
N B:THR53 3.4 0.9 1.0
PB B:ATP603 3.5 0.1 1.0
O3A B:ATP603 3.6 0.1 1.0
OD1 B:ASP145 3.7 0.9 1.0
CA B:THR53 3.8 99.1 1.0
O1G B:ATP603 3.9 98.4 1.0
CB B:LYS52 4.0 98.3 1.0
C B:LYS52 4.3 0.9 1.0
O1B B:ATP603 4.3 0.3 1.0
OD2 B:ASP145 4.3 0.7 1.0
CG2 B:THR181 4.4 0.3 1.0
CG B:ASP145 4.4 0.3 1.0
O2B B:ATP603 4.5 0.8 1.0
CG2 B:THR53 4.5 94.6 1.0
CA B:LYS52 4.6 0.5 1.0
NH2 C:ARG226 4.6 0.2 1.0
CE B:LYS52 4.7 87.4 1.0
O2A B:ATP603 4.7 1.0 1.0
PA B:ATP603 4.7 0.2 1.0
N B:LYS52 4.9 0.8 1.0

Magnesium binding site 5 out of 12 in 4dug

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Magnesium binding site 5 out of 12 in the Crystal Structure of Circadian Clock Protein Kaic E318A Mutant


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 Circadian Clock Protein Kaic E318A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:77.4
occ:1.00
 O C:HOH706 2.1 64.4 1.0
O2B C:ATP602 2.1 80.5 1.0
OG1 C:THR295 2.1 84.6 1.0
O2G C:ATP602 2.4 79.7 1.0
O3G C:ATP602 2.4 86.9 1.0
O3B C:ATP602 2.5 86.6 1.0
PG C:ATP602 2.5 94.8 1.0
PB C:ATP602 2.8 75.4 1.0
O2A C:ATP602 3.3 85.2 1.0
CB C:THR295 3.5 78.6 1.0
O1B C:ATP602 3.9 68.5 1.0
O3A C:ATP602 4.0 73.8 1.0
O1G C:ATP602 4.0 84.5 1.0
NH2 D:ARG459 4.1 85.7 1.0
PA C:ATP602 4.2 75.4 1.0
N C:THR295 4.2 77.4 1.0
OE2 C:GLU319 4.3 92.9 1.0
CG2 C:THR295 4.4 73.4 1.0
CA C:THR295 4.4 76.5 1.0
NE D:ARG459 4.5 81.4 1.0
OD2 C:ASP378 4.7 80.9 1.0
CZ D:ARG459 4.8 80.8 1.0
O1A C:ATP602 4.8 75.2 1.0

Magnesium binding site 6 out of 12 in 4dug

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Magnesium binding site 6 out of 12 in the Crystal Structure of Circadian Clock Protein Kaic E318A Mutant


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 Circadian Clock Protein Kaic E318A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg604

b:0.4
occ:1.00
 OG1 C:THR53 2.1 86.1 1.0
OE2 C:GLU78 2.1 0.0 1.0
O1G C:ATP603 2.4 96.2 1.0
NE D:ARG226 3.2 90.6 1.0
O2B C:ATP603 3.2 87.7 1.0
CB C:THR53 3.3 86.6 1.0
CD C:GLU78 3.3 1.0 1.0
NH2 D:ARG226 3.5 86.3 1.0
OD2 C:ASP145 3.5 92.4 1.0
PG C:ATP603 3.5 0.5 1.0
CZ D:ARG226 3.7 87.6 1.0
O2G C:ATP603 3.7 84.8 1.0
CG2 C:THR53 3.8 78.8 1.0
O2A C:ATP603 4.0 92.9 1.0
CD D:ARG226 4.1 85.1 1.0
OE1 C:GLU78 4.1 0.8 1.0
CG C:GLU78 4.2 0.4 1.0
PB C:ATP603 4.4 86.6 1.0
O3B C:ATP603 4.4 95.3 1.0
CG C:ASP145 4.4 94.2 1.0
OD1 C:ASP145 4.5 86.8 1.0
CA C:THR53 4.5 87.2 1.0
O3G C:ATP603 4.7 88.9 1.0
N C:THR53 4.8 81.5 1.0
NH1 D:ARG226 4.9 78.3 1.0

Magnesium binding site 7 out of 12 in 4dug

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Magnesium binding site 7 out of 12 in the Crystal Structure of Circadian Clock Protein Kaic E318A Mutant


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 Circadian Clock Protein Kaic E318A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:0.2
occ:1.00
 OG1 D:THR295 2.0 75.2 1.0
O D:HOH708 2.0 56.4 1.0
O3B D:ATP602 2.2 84.6 1.0
O2G D:ATP602 2.5 98.9 1.0
PG D:ATP602 3.0 93.5 1.0
OE2 D:GLU319 3.4 0.6 1.0
CB D:THR295 3.4 92.0 1.0
PB D:ATP602 3.5 91.3 1.0
O3A D:ATP602 3.7 85.3 1.0
OD1 D:ASP378 3.8 67.1 1.0
O3G D:ATP602 3.9 81.2 1.0
O1G D:ATP602 4.1 81.9 1.0
OD2 D:ASP378 4.1 77.3 1.0
O1B D:ATP602 4.1 76.2 1.0
CG2 D:THR295 4.2 89.8 1.0
N D:THR295 4.2 82.9 1.0
CG D:ASP378 4.3 76.7 1.0
NH2 E:ARG459 4.3 0.0 1.0
CA D:THR295 4.3 84.7 1.0
CD D:GLU319 4.5 0.9 1.0
OG D:SER379 4.6 92.8 1.0
O2B D:ATP602 4.6 97.6 1.0
CB D:LYS294 4.8 76.3 1.0

Magnesium binding site 8 out of 12 in 4dug

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Magnesium binding site 8 out of 12 in the Crystal Structure of Circadian Clock Protein Kaic E318A Mutant


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 Circadian Clock Protein Kaic E318A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg604

b:87.5
occ:1.00
 OG1 D:THR53 2.0 61.5 1.0
O D:HOH714 2.1 30.0 1.0
O D:HOH711 2.3 73.4 1.0
O2G D:ATP603 2.5 86.1 1.0
O3B D:ATP603 2.5 75.2 1.0
PG D:ATP603 3.1 91.3 1.0
OD1 D:ASP145 3.2 71.4 1.0
CB D:THR53 3.4 60.0 1.0
N D:THR53 3.6 59.2 1.0
CE D:LYS52 3.7 56.7 1.0
CA D:THR53 3.9 62.8 1.0
CG2 D:THR181 3.9 63.7 1.0
PB D:ATP603 3.9 56.9 1.0
CB D:LYS52 4.0 54.7 1.0
NZ D:LYS52 4.0 73.1 1.0
CG D:ASP145 4.0 72.9 1.0
O1G D:ATP603 4.1 67.3 1.0
OD2 D:ASP145 4.1 80.6 1.0
O3G D:ATP603 4.2 73.8 1.0
O3A D:ATP603 4.2 67.7 1.0
O1B D:ATP603 4.2 53.3 1.0
CG2 D:THR53 4.4 56.1 1.0
C D:LYS52 4.5 54.6 1.0
CD D:LYS52 4.6 51.1 1.0
CA D:LYS52 4.8 57.0 1.0
OE2 D:GLU78 4.9 73.9 1.0
CB D:SER146 4.9 77.5 1.0
CG D:LYS52 4.9 56.9 1.0

Magnesium binding site 9 out of 12 in 4dug

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Magnesium binding site 9 out of 12 in the Crystal Structure of Circadian Clock Protein Kaic E318A Mutant


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 Circadian Clock Protein Kaic E318A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg601

b:85.0
occ:1.00
 OG1 E:THR295 2.1 99.5 1.0
O E:HOH715 2.1 30.0 1.0
O2G E:ATP602 2.3 96.2 1.0
O3B E:ATP602 2.9 1.0 1.0
O2B E:ATP602 3.0 85.5 1.0
PG E:ATP602 3.2 91.7 1.0
CB E:THR295 3.5 97.7 1.0
PB E:ATP602 3.5 0.1 1.0
O3A E:ATP602 3.8 0.9 1.0
OD1 E:ASP378 4.0 81.5 1.0
O3G E:ATP602 4.1 78.7 1.0
OD2 E:ASP378 4.2 98.7 1.0
OE2 E:GLU319 4.3 0.2 1.0
N E:THR295 4.3 96.4 1.0
CG2 E:THR295 4.3 98.1 1.0
CA E:THR295 4.3 99.0 1.0
O1G E:ATP602 4.4 89.5 1.0
CG E:ASP378 4.4 91.4 1.0
O1P F:TPO432 4.7 0.1 1.0
O1B E:ATP602 4.9 95.8 1.0
CD E:GLU319 4.9 0.5 1.0

Magnesium binding site 10 out of 12 in 4dug

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Magnesium binding site 10 out of 12 in the Crystal Structure of Circadian Clock Protein Kaic E318A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Circadian Clock Protein Kaic E318A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg604

b:71.4
occ:1.00
 OG1 E:THR53 2.1 58.9 1.0
OD2 E:ASP145 2.2 78.1 1.0
O3G E:ATP603 2.4 88.5 1.0
O2G E:ATP603 2.7 67.7 1.0
PG E:ATP603 2.9 89.8 1.0
CG E:ASP145 3.1 70.8 1.0
OD1 E:ASP145 3.3 67.1 1.0
O E:HOH710 3.3 81.8 1.0
CB E:THR53 3.4 54.6 1.0
O3B E:ATP603 3.5 67.8 1.0
OE2 E:GLU78 3.7 78.8 1.0
CG2 E:THR53 3.9 52.2 1.0
CA E:THR53 4.3 58.4 1.0
O1G E:ATP603 4.4 59.3 1.0
CB E:ASP145 4.4 68.4 1.0
N E:THR53 4.5 54.7 1.0
CD E:GLU78 4.6 82.6 1.0
NH2 F:ARG226 4.6 84.4 1.0
PB E:ATP603 4.8 62.5 1.0
O3A E:ATP603 4.8 58.9 1.0
CB E:SER146 5.0 78.8 1.0

Reference:

M.Egli, T.Mori, R.Pattanayek, Y.Xu, X.Qin, C.H.Johnson. Dephosphorylation of the Core Clock Protein Kaic in the Cyanobacterial Kaiabc Circadian Oscillator Proceeds Via An Atp Synthase Mechanism. Biochemistry V. 51 1547 2012.
ISSN: ISSN 0006-2960
PubMed: 22304631
DOI: 10.1021/BI201525N
Page generated: Mon Aug 11 08:57:33 2025

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