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Magnesium in PDB 4ijm: Crystal Structure of Circadian Clock Protein Kaic A422V Mutant

Enzymatic activity of Crystal Structure of Circadian Clock Protein Kaic A422V Mutant

All present enzymatic activity of Crystal Structure of Circadian Clock Protein Kaic A422V Mutant:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of Circadian Clock Protein Kaic A422V Mutant, PDB code: 4ijm was solved by M.Egli, R.Pattanayek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.96 / 3.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 131.362, 134.468, 203.936, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 26.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Circadian Clock Protein Kaic A422V Mutant (pdb code 4ijm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of Circadian Clock Protein Kaic A422V Mutant, PDB code: 4ijm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4ijm

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Magnesium binding site 1 out of 7 in the Crystal Structure of Circadian Clock Protein Kaic A422V Mutant


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 Circadian Clock Protein Kaic A422V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:82.3
occ:1.00
 OE2 A:GLU319 2.1 84.5 1.0
O A:HOH950 2.1 0.8 1.0
O A:HOH902 2.1 58.6 1.0
OG1 A:THR295 2.2 62.7 1.0
O3G A:ATP802 2.4 86.0 1.0
CD A:GLU319 3.1 94.6 1.0
O3A A:ATP802 3.1 82.5 1.0
CB A:THR295 3.2 57.8 1.0
O3B A:ATP802 3.2 60.1 1.0
MG B:MG606 3.4 69.9 1.0
PG A:ATP802 3.4 68.7 1.0
CG2 A:THR295 3.5 67.4 1.0
CG A:GLU319 3.8 93.7 1.0
PB A:ATP802 3.9 59.5 1.0
O2G A:ATP802 3.9 90.1 1.0
NE B:ARG459 4.1 73.4 1.0
OE1 A:GLU319 4.1 92.8 1.0
OD2 A:ASP378 4.1 99.5 1.0
OE1 A:GLU318 4.2 0.2 1.0
O1A A:ATP802 4.2 82.0 1.0
PA A:ATP802 4.3 73.3 1.0
CA A:THR295 4.5 67.2 1.0
NH2 B:ARG459 4.5 72.0 1.0
CZ B:ARG459 4.6 79.1 1.0
O1G A:ATP802 4.7 79.0 1.0
O2B A:ATP802 4.7 58.2 1.0
CD B:ARG459 4.7 78.4 1.0
OD1 A:ASP378 4.8 72.2 1.0
CG B:ARG459 4.8 97.7 1.0
N A:THR295 4.9 74.4 1.0
CG A:ASP378 4.9 89.8 1.0

Magnesium binding site 2 out of 7 in 4ijm

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Magnesium binding site 2 out of 7 in the Crystal Structure of Circadian Clock Protein Kaic A422V Mutant


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 Circadian Clock Protein Kaic A422V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:63.1
occ:1.00
 O B:HOH720 2.1 73.6 1.0
OE1 B:GLU318 2.1 95.4 1.0
OG1 B:THR295 2.2 65.7 1.0
O3B B:ATP602 2.4 87.5 1.0
O2G B:ATP602 2.9 86.4 1.0
PG B:ATP602 3.1 93.0 1.0
CD B:GLU318 3.2 78.8 1.0
PB B:ATP602 3.4 65.4 1.0
O2B B:ATP602 3.5 52.8 1.0
O3G B:ATP602 3.5 58.6 1.0
OE2 B:GLU318 3.6 57.4 1.0
CB B:THR295 3.6 60.5 1.0
O3A B:ATP602 3.7 76.8 1.0
OD1 B:ASP378 3.7 66.6 1.0
OE2 B:GLU319 4.2 95.3 1.0
OD2 B:ASP378 4.3 66.9 1.0
N B:THR295 4.3 56.8 1.0
CG B:ASP378 4.4 70.2 1.0
CG2 B:THR295 4.4 62.4 1.0
CA B:THR295 4.4 56.6 1.0
O1G B:ATP602 4.5 74.6 1.0
CG B:GLU318 4.5 59.7 1.0
O1B B:ATP602 4.8 70.2 1.0
CB B:GLU318 4.8 60.9 1.0
CE B:LYS294 4.9 64.5 1.0

Magnesium binding site 3 out of 7 in 4ijm

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Magnesium binding site 3 out of 7 in the Crystal Structure of Circadian Clock Protein Kaic A422V Mutant


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 Circadian Clock Protein Kaic A422V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg606

b:69.9
occ:1.00
 CG B:ARG459 2.2 97.7 1.0
O3G A:ATP802 2.5 86.0 1.0
O1A A:ATP802 2.5 82.0 1.0
O3A A:ATP802 3.0 82.5 1.0
CD B:ARG459 3.1 78.4 1.0
NE B:ARG459 3.2 73.4 1.0
CB B:ARG459 3.2 0.9 1.0
PA A:ATP802 3.3 73.3 1.0
MG A:MG801 3.4 82.3 1.0
C5' A:ATP802 3.5 91.4 1.0
PG A:ATP802 3.6 68.7 1.0
CA B:ARG459 3.7 91.4 1.0
O5' A:ATP802 3.8 79.0 1.0
O1G A:ATP802 3.9 79.0 1.0
PB A:ATP802 4.0 59.5 1.0
OE2 A:GLU319 4.0 84.5 1.0
O3B A:ATP802 4.0 60.1 1.0
O1B A:ATP802 4.0 94.1 1.0
CZ B:ARG459 4.4 79.1 1.0
CD A:GLU319 4.5 94.6 1.0
OE1 A:GLU319 4.6 92.8 1.0
N B:ARG459 4.6 80.5 1.0
OG1 A:THR295 4.7 62.7 1.0
O B:ARG459 4.7 0.9 1.0
O2A A:ATP802 4.7 75.5 1.0
C B:ARG459 4.7 93.4 1.0
C4' A:ATP802 4.9 83.7 1.0
NZ B:LYS457 4.9 69.6 1.0
O2G A:ATP802 4.9 90.1 1.0
NH2 B:ARG459 5.0 72.0 1.0
CB A:THR295 5.0 57.8 1.0

Magnesium binding site 4 out of 7 in 4ijm

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Magnesium binding site 4 out of 7 in the Crystal Structure of Circadian Clock Protein Kaic A422V 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 A422V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:44.0
occ:1.00
 OG1 C:THR295 2.1 56.3 1.0
OE1 C:GLU318 2.1 0.9 1.0
O2G C:ATP602 2.2 82.5 1.0
O3B C:ATP602 2.5 63.7 1.0
PG C:ATP602 2.7 74.2 1.0
CD C:GLU318 3.1 66.4 1.0
O1G C:ATP602 3.2 74.9 1.0
CB C:THR295 3.5 47.6 1.0
OE2 C:GLU318 3.5 53.9 1.0
OE2 C:GLU319 3.6 84.1 1.0
OD1 C:ASP378 3.6 35.1 1.0
OD2 C:ASP378 3.9 49.6 1.0
PB C:ATP602 4.0 51.8 1.0
NH1 D:ARG459 4.0 82.2 1.0
CG2 C:THR295 4.1 35.1 1.0
CG C:ASP378 4.1 53.2 1.0
O3G C:ATP602 4.2 35.9 1.0
O3A C:ATP602 4.3 43.2 1.0
CA C:THR295 4.4 35.4 1.0
N C:THR295 4.4 41.0 1.0
CG C:GLU318 4.4 25.0 1.0
CB C:GLU318 4.7 49.2 1.0
CD C:GLU319 4.7 75.4 1.0
O2B C:ATP602 4.7 26.8 1.0
O2A C:ATP602 4.8 46.4 1.0
NH2 D:ARG459 4.8 41.4 1.0
O1B C:ATP602 4.9 67.1 1.0
CZ D:ARG459 4.9 61.2 1.0

Magnesium binding site 5 out of 7 in 4ijm

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Magnesium binding site 5 out of 7 in the Crystal Structure of Circadian Clock Protein Kaic A422V 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 A422V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:55.5
occ:1.00
 O D:HOH739 2.1 38.3 1.0
O3B D:ATP602 2.1 53.6 1.0
OG1 D:THR295 2.1 53.1 1.0
OE2 D:GLU319 2.3 84.0 1.0
O3G D:ATP602 2.5 45.4 1.0
PG D:ATP602 2.7 60.4 1.0
O2G D:ATP602 3.1 66.5 1.0
CB D:THR295 3.3 64.2 1.0
PB D:ATP602 3.5 43.0 1.0
CD D:GLU319 3.5 64.8 1.0
O3A D:ATP602 3.6 50.3 1.0
O2A D:ATP602 3.8 52.2 1.0
CG2 D:THR295 4.1 61.0 1.0
O1G D:ATP602 4.1 34.8 1.0
OE1 D:GLU318 4.1 70.8 1.0
O2B D:ATP602 4.1 66.9 1.0
CG D:GLU319 4.2 52.9 1.0
NE E:ARG459 4.3 58.2 1.0
NH2 E:ARG459 4.3 52.6 1.0
PA D:ATP602 4.4 48.5 1.0
OE1 D:GLU319 4.4 66.7 1.0
CA D:THR295 4.5 49.3 1.0
O1B D:ATP602 4.5 32.6 1.0
CZ E:ARG459 4.5 47.9 1.0
N D:THR295 4.5 48.4 1.0
OD2 D:ASP378 4.9 56.0 1.0
OD1 D:ASP378 4.9 37.6 1.0

Magnesium binding site 6 out of 7 in 4ijm

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Magnesium binding site 6 out of 7 in the Crystal Structure of Circadian Clock Protein Kaic A422V 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 A422V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg601

b:59.5
occ:1.00
 O E:HOH725 2.1 62.6 1.0
OE1 E:GLU318 2.1 0.8 1.0
OG1 E:THR295 2.2 56.0 1.0
O3B E:ATP602 2.2 86.2 1.0
O2G E:ATP602 2.6 82.0 1.0
PG E:ATP602 3.0 75.1 1.0
O F:HOH708 3.1 73.4 1.0
CD E:GLU318 3.3 82.9 1.0
PB E:ATP602 3.5 75.8 1.0
CB E:THR295 3.6 58.0 1.0
OE2 E:GLU319 3.7 77.3 1.0
O3A E:ATP602 3.8 94.5 1.0
O2B E:ATP602 3.8 39.0 1.0
OE2 E:GLU318 3.9 75.3 1.0
OD1 E:ASP378 3.9 49.0 1.0
OD2 E:ASP378 4.0 73.8 1.0
O1G E:ATP602 4.0 64.2 1.0
O3G E:ATP602 4.0 70.7 1.0
NH2 F:ARG459 4.2 67.7 1.0
CG E:ASP378 4.3 79.7 1.0
CG2 E:THR295 4.3 64.7 1.0
CG E:GLU318 4.5 52.1 1.0
CA E:THR295 4.5 68.3 1.0
N E:THR295 4.6 74.9 1.0
CB E:GLU318 4.6 62.4 1.0
O1B E:ATP602 4.7 55.9 1.0
CD E:GLU319 4.8 73.8 1.0

Magnesium binding site 7 out of 7 in 4ijm

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Magnesium binding site 7 out of 7 in the Crystal Structure of Circadian Clock Protein Kaic A422V 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 A422V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg601

b:85.6
occ:1.00
 OE1 F:GLU318 2.1 95.1 1.0
OG1 F:THR295 2.1 84.5 1.0
O2G F:ATP602 2.9 0.5 1.0
O3B F:ATP602 3.1 91.2 1.0
OE2 F:GLU319 3.2 0.3 1.0
CD F:GLU318 3.4 96.9 1.0
OD2 F:ASP378 3.5 77.5 1.0
CB F:THR295 3.5 67.8 1.0
O F:HOH740 3.7 60.4 1.0
PG F:ATP602 3.7 94.1 1.0
OD1 F:ASP378 3.9 75.3 1.0
CG2 F:THR295 3.9 75.3 1.0
CG F:ASP378 4.0 82.5 1.0
CB F:GLU318 4.1 91.3 1.0
CD F:GLU319 4.2 89.8 1.0
OE2 F:GLU318 4.2 94.2 1.0
O3G F:ATP602 4.3 0.4 1.0
CG F:GLU318 4.3 90.0 1.0
CG F:GLU319 4.3 83.8 1.0
NH2 A:ARG459 4.4 79.5 1.0
PB F:ATP602 4.5 82.7 1.0
CA F:THR295 4.6 74.2 1.0
O3A F:ATP602 4.7 90.3 1.0
NE A:ARG459 4.7 87.8 1.0
CZ A:ARG459 4.8 87.2 1.0
N F:THR295 4.8 81.7 1.0
O2B F:ATP602 4.9 66.2 1.0
O1G F:ATP602 4.9 70.3 1.0

Reference:

M.Egli, R.Pattanayek, J.H.Sheehan, Y.Xu, T.Mori, J.A.Smith, C.H.Johnson. Loop-Loop Interactions Regulate Kaia-Stimulated Kaic Phosphorylation in the Cyanobacterial Kaiabc Circadian Clock. Biochemistry V. 52 1208 2013.
ISSN: ISSN 0006-2960
PubMed: 23351065
DOI: 10.1021/BI301691A
Page generated: Mon Dec 14 18:53:25 2020

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