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Magnesium in PDB 7dy2: Crystal Structure of Cyanobacterial Circadian Clock Protein Kaic

Enzymatic activity of Crystal Structure of Cyanobacterial Circadian Clock Protein Kaic

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

Protein crystallography data

The structure of Crystal Structure of Cyanobacterial Circadian Clock Protein Kaic, PDB code: 7dy2 was solved by Y.Furuike, S.Akiyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.24 / 3.04
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 92.803, 206.6, 168.383, 90, 94.69, 90
R / Rfree (%) 26.3 / 32.6

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 Cyanobacterial Circadian Clock Protein Kaic (pdb code 7dy2). 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 Cyanobacterial Circadian Clock Protein Kaic, PDB code: 7dy2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 7dy2

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


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 Cyanobacterial Circadian Clock Protein Kaic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:68.2
occ:1.00
 OG1 A:THR295 1.8 58.7 1.0
O A:HOH704 2.0 49.5 1.0
O2G A:ATP602 2.1 63.2 1.0
O A:HOH701 2.2 50.5 1.0
O A:HOH703 2.2 58.9 1.0
O2B A:ATP602 2.5 60.0 1.0
CB A:THR295 3.2 59.0 1.0
PG A:ATP602 3.2 63.6 1.0
O3G A:ATP602 3.5 64.3 1.0
PB A:ATP602 3.6 60.5 1.0
CG2 A:THR295 3.6 59.0 1.0
O3B A:ATP602 3.7 62.1 1.0
O1A A:ATP602 3.8 60.8 1.0
OD2 A:ASP378 3.8 52.4 1.0
OE1 A:GLU318 3.9 71.8 1.0
OE2 A:GLU319 4.0 74.2 1.0
N A:THR295 4.1 57.3 1.0
CA A:THR295 4.1 58.4 1.0
O3A A:ATP602 4.1 60.6 1.0
NH2 B:ARG459 4.2 62.9 1.0
PA A:ATP602 4.4 60.1 1.0
OD1 A:ASP378 4.5 51.4 1.0
O1G A:ATP602 4.5 64.3 1.0
CG A:ASP378 4.6 51.4 1.0
O2A A:ATP602 4.6 59.5 1.0
CG A:GLU319 4.7 72.6 1.0
CD A:GLU319 4.8 73.7 1.0
O1B A:ATP602 5.0 60.1 1.0

Magnesium binding site 2 out of 12 in 7dy2

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


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 Cyanobacterial Circadian Clock Protein Kaic within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg703

b:60.4
occ:1.00
 OG1 B:THR295 2.0 51.4 1.0
O2G B:ATP701 2.2 62.8 1.0
O1B B:ATP701 2.7 62.6 1.0
CB B:THR295 3.2 51.5 1.0
PG B:ATP701 3.5 62.2 1.0
OD1 B:ASP378 3.5 63.4 1.0
OE1 B:GLU318 3.6 69.7 1.0
OE2 B:GLU319 3.6 68.6 1.0
PB B:ATP701 3.8 62.8 1.0
OD2 B:ASP378 4.0 62.1 1.0
O3B B:ATP701 4.0 62.6 1.0
CG2 B:THR295 4.0 51.7 1.0
NH2 C:ARG459 4.0 61.9 1.0
O1G B:ATP701 4.1 61.7 1.0
CG B:ASP378 4.2 62.2 1.0
O3A B:ATP701 4.2 63.5 1.0
O1A B:ATP701 4.3 64.1 1.0
CD B:GLU319 4.3 69.2 1.0
CA B:THR295 4.3 51.5 1.0
N B:THR295 4.4 51.2 1.0
PA B:ATP701 4.6 64.0 1.0
O3G B:ATP701 4.7 63.0 1.0
OE1 B:GLU319 4.7 69.8 1.0
O2A B:ATP701 4.7 64.4 1.0
CZ C:ARG459 4.8 62.2 1.0
CD B:GLU318 4.8 69.3 1.0
NE C:ARG459 4.9 62.7 1.0

Magnesium binding site 3 out of 12 in 7dy2

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


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 Cyanobacterial Circadian Clock Protein Kaic within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg603

b:59.4
occ:1.00
 O1B E:ATP601 2.2 86.9 1.0
OG1 E:THR53 2.3 59.0 1.0
O2G E:ATP601 2.4 93.8 1.0
PG E:ATP601 3.4 93.4 1.0
PB E:ATP601 3.5 86.2 1.0
CB E:THR53 3.6 58.9 1.0
NZ E:LYS52 3.6 57.0 1.0
OD2 E:ASP145 3.6 69.3 1.0
O3G E:ATP601 3.7 93.0 1.0
O3B E:ATP601 3.8 89.4 1.0
OD1 E:ASP145 4.1 70.8 1.0
O1A E:ATP601 4.2 83.4 1.0
N E:THR53 4.2 57.6 1.0
CG E:ASP145 4.2 70.2 1.0
O2B E:ATP601 4.4 84.3 1.0
CA E:THR53 4.4 58.6 1.0
CG2 E:THR181 4.4 70.0 1.0
OE2 E:GLU78 4.4 81.5 1.0
CG2 E:THR53 4.6 59.4 1.0
O3A E:ATP601 4.7 83.9 1.0
NH2 F:ARG226 4.7 78.3 1.0
O1G E:ATP601 4.8 94.3 1.0
CB E:LYS52 4.9 55.7 1.0
CE E:LYS52 4.9 56.3 1.0
NE F:ARG226 4.9 78.8 1.0

Magnesium binding site 4 out of 12 in 7dy2

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


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

b:84.8
occ:1.00
 O2G E:ATP602 2.3 73.2 1.0
O2B E:ATP602 2.6 66.7 1.0
OG1 E:THR295 2.7 51.0 1.0
OE1 E:GLU318 2.7 76.8 1.0
OD1 E:ASP378 2.9 61.5 1.0
OD2 E:ASP378 3.5 61.3 1.0
CG E:ASP378 3.6 61.7 1.0
PG E:ATP602 3.6 72.6 1.0
CD E:GLU318 3.8 76.0 1.0
PB E:ATP602 3.8 66.6 1.0
CG2 E:THR413 3.8 57.6 1.0
O1G E:ATP602 4.0 72.4 1.0
CB E:THR295 4.0 50.8 1.0
O3B E:ATP602 4.1 69.5 1.0
N E:THR295 4.2 49.4 1.0
OE2 E:GLU318 4.3 77.5 1.0
CE E:LYS294 4.4 47.5 1.0
CB E:LYS294 4.4 47.8 1.0
CA E:THR295 4.5 50.4 1.0
O1B E:ATP602 4.6 66.5 1.0
CB E:SER379 4.8 60.1 1.0
OG1 E:THR415 4.8 61.5 1.0
CG2 E:THR295 4.8 51.2 1.0
O3G E:ATP602 4.8 72.1 1.0
CB E:THR413 4.9 57.6 1.0
C E:LYS294 5.0 48.4 1.0

Magnesium binding site 5 out of 12 in 7dy2

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


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 Cyanobacterial Circadian Clock Protein Kaic within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg603

b:76.2
occ:1.00
 OG1 F:THR295 2.2 54.5 1.0
O3G F:ATP602 2.3 62.5 1.0
CB F:THR295 3.3 54.8 1.0
PG F:ATP602 3.3 62.1 1.0
O1B F:ATP602 3.4 60.6 1.0
CG2 F:THR295 3.5 55.0 1.0
OE1 F:GLU318 3.6 62.3 1.0
O1G F:ATP602 3.7 63.3 1.0
O3B F:ATP602 3.7 61.5 1.0
O1A F:ATP602 3.8 62.7 1.0
NH2 A:ARG459 4.0 58.2 1.0
CG F:GLU319 4.2 62.8 1.0
PB F:ATP602 4.2 60.8 1.0
CD F:GLU319 4.3 63.1 1.0
CZ A:ARG459 4.3 58.4 1.0
NE A:ARG459 4.3 58.8 1.0
OD2 F:ASP378 4.4 59.3 1.0
OE2 F:GLU319 4.5 63.1 1.0
OD1 F:ASP378 4.5 59.9 1.0
CA F:THR295 4.5 54.5 1.0
O2G F:ATP602 4.7 60.9 1.0
CG F:ASP378 4.8 59.0 1.0
OE1 F:GLU319 4.8 63.6 1.0
CD F:GLU318 4.8 61.6 1.0
N F:THR295 4.9 53.9 1.0
O3A F:ATP602 4.9 60.9 1.0
CB F:GLU318 4.9 61.5 1.0
PA F:ATP602 4.9 61.8 1.0

Magnesium binding site 6 out of 12 in 7dy2

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


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 Cyanobacterial Circadian Clock Protein Kaic within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg603

b:73.6
occ:1.00
 O3G C:ATP602 2.5 71.3 1.0
OG1 C:THR295 2.6 49.9 1.0
O1B C:ATP602 2.8 64.7 1.0
OD1 C:ASP378 3.1 55.9 1.0
OD2 C:ASP378 3.1 56.6 1.0
OE1 C:GLU318 3.2 57.1 1.0
CG C:ASP378 3.4 55.8 1.0
CB C:LYS294 3.6 47.1 1.0
N C:THR295 3.7 49.9 1.0
CB C:THR295 3.9 50.1 1.0
PG C:ATP602 3.9 70.8 1.0
NZ C:LYS294 4.0 45.8 1.0
PB C:ATP602 4.0 65.1 1.0
CA C:THR295 4.1 50.2 1.0
O3B C:ATP602 4.3 67.6 1.0
CD C:GLU318 4.3 57.0 1.0
C C:LYS294 4.4 48.9 1.0
O1G C:ATP602 4.5 70.7 1.0
CA C:LYS294 4.5 48.1 1.0
OG1 C:THR415 4.6 64.1 1.0
CG2 C:THR295 4.6 50.2 1.0
CG C:LYS294 4.7 46.3 1.0
O2B C:ATP602 4.7 65.5 1.0
CE C:LYS294 4.8 45.8 1.0
CB C:SER379 4.8 53.4 1.0
CB C:ASP378 4.9 55.1 1.0

Magnesium binding site 7 out of 12 in 7dy2

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


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 Cyanobacterial Circadian Clock Protein Kaic within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg603

b:49.5
occ:1.00
 OG1 D:THR295 2.2 49.0 1.0
OE2 D:GLU319 2.5 69.7 1.0
O2B D:ADP602 3.0 53.4 1.0
OE1 D:GLU318 3.2 70.5 1.0
CD D:GLU319 3.3 70.1 1.0
CB D:THR295 3.4 49.0 1.0
O1B D:ADP602 3.6 54.4 1.0
NH2 E:ARG459 3.7 62.3 1.0
CG2 D:THR295 3.9 49.3 1.0
PB D:ADP602 3.9 54.1 1.0
O1A D:ADP602 4.0 56.3 1.0
OE1 D:GLU319 4.0 70.8 1.0
CG D:GLU319 4.1 70.2 1.0
CD D:GLU318 4.5 69.7 1.0
CZ E:ARG459 4.5 62.3 1.0
NE E:ARG459 4.5 62.5 1.0
CA D:THR295 4.6 48.4 1.0
O3A D:ADP602 4.8 55.5 1.0
CB D:GLU318 4.8 68.0 1.0
N D:THR295 4.9 48.6 1.0
PA D:ADP602 4.9 56.3 1.0

Magnesium binding site 8 out of 12 in 7dy2

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


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 Cyanobacterial Circadian Clock Protein Kaic within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg603

b:41.5
occ:1.00
 OG1 G:THR295 2.0 66.6 1.0
O G:HOH701 2.2 68.3 1.0
O1G G:ATP602 2.2 76.8 1.0
OE2 G:GLU318 2.3 72.7 1.0
O1B G:ATP602 2.5 76.4 1.0
O G:HOH702 2.5 57.2 1.0
OE2 G:GLU319 3.2 77.4 1.0
CB G:THR295 3.4 66.7 1.0
PG G:ATP602 3.5 76.4 1.0
CD G:GLU318 3.5 74.1 1.0
PB G:ATP602 3.7 74.9 1.0
OD2 G:ASP378 3.7 67.9 1.0
OD1 G:ASP378 3.8 67.8 1.0
O1A G:ATP602 3.8 75.3 1.0
O3B G:ATP602 3.8 75.7 1.0
O3G G:ATP602 4.0 76.0 1.0
N G:THR295 4.1 66.3 1.0
CG2 G:THR295 4.1 67.1 1.0
CG G:ASP378 4.2 67.8 1.0
CA G:THR295 4.2 66.8 1.0
CG G:GLU318 4.2 74.9 1.0
OE1 G:GLU318 4.4 73.8 1.0
CD G:GLU319 4.4 77.8 1.0
O3A G:ATP602 4.6 74.6 1.0
O2G G:ATP602 4.7 75.4 1.0
CB G:LYS294 4.7 65.3 1.0
PA G:ATP602 4.8 74.4 1.0
O2B G:ATP602 4.9 74.2 1.0
NH2 H:ARG459 5.0 67.7 1.0

Magnesium binding site 9 out of 12 in 7dy2

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


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 Cyanobacterial Circadian Clock Protein Kaic within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg603

b:48.1
occ:1.00
 O1G H:ATP602 1.9 78.1 1.0
OG1 H:THR295 2.1 52.5 1.0
O2B H:ATP602 2.2 72.4 1.0
O H:HOH701 2.7 83.1 1.0
O H:HOH703 2.8 47.2 1.0
CB H:THR295 3.1 53.4 1.0
PG H:ATP602 3.2 78.8 1.0
PB H:ATP602 3.3 72.0 1.0
OD1 H:ASP378 3.4 55.5 1.0
OE1 H:GLU318 3.4 61.1 1.0
OD2 H:ASP378 3.4 54.2 1.0
O3B H:ATP602 3.5 75.0 1.0
OE2 H:GLU319 3.8 62.3 1.0
CG H:ASP378 3.8 54.5 1.0
N H:THR295 3.9 52.6 1.0
O3A H:ATP602 3.9 71.1 1.0
CA H:THR295 4.0 53.3 1.0
CG2 H:THR295 4.2 54.1 1.0
O2G H:ATP602 4.2 78.6 1.0
O3G H:ATP602 4.2 78.8 1.0
NH2 I:ARG459 4.2 60.0 1.0
CD H:GLU318 4.6 60.5 1.0
O1B H:ATP602 4.7 71.3 1.0
CB H:LYS294 4.8 51.2 1.0
CD H:GLU319 4.8 62.3 1.0
O1A H:ATP602 4.9 70.1 1.0
C H:LYS294 4.9 52.0 1.0

Magnesium binding site 10 out of 12 in 7dy2

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


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 Cyanobacterial Circadian Clock Protein Kaic within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg603

b:84.2
occ:1.00
 O1G K:ATP602 2.2 76.7 1.0
O1B K:ATP602 2.4 72.3 1.0
OG1 K:THR295 2.5 67.3 1.0
PG K:ATP602 3.1 76.3 1.0
O2G K:ATP602 3.2 75.9 1.0
CB K:THR295 3.4 67.1 1.0
PB K:ATP602 3.5 73.0 1.0
O3B K:ATP602 3.6 74.6 1.0
NH2 L:ARG459 3.8 68.0 1.0
O3A K:ATP602 4.1 72.9 1.0
OD2 K:ASP378 4.1 65.7 1.0
OE2 K:GLU319 4.2 80.2 1.0
O1A K:ATP602 4.3 73.2 1.0
CG2 K:THR295 4.3 67.8 1.0
N K:THR295 4.4 66.3 1.0
OD1 K:ASP378 4.4 65.9 1.0
CA K:THR295 4.5 66.1 1.0
O3G K:ATP602 4.5 75.9 1.0
CZ L:ARG459 4.6 68.7 1.0
PA K:ATP602 4.6 72.3 1.0
CG K:GLU318 4.6 73.1 1.0
CB K:GLU318 4.6 73.1 1.0
CG K:ASP378 4.7 65.8 1.0
CD K:GLU319 4.7 80.1 1.0
NE L:ARG459 4.8 69.2 1.0
O2A K:ATP602 4.8 71.5 1.0
O2B K:ATP602 4.9 72.2 1.0

Reference:

Y.Furuike, A.Mukaiyama, D.Ouyang, K.Ito-Miwa, D.Simon, E.Yamashita, T.Kondo, S.Akiyama. Elucidation of Master Allostery Essential For Circadian Clock Oscillation in Cyanobacteria. Sci Adv V. 8 M8990 2022.
ISSN: ESSN 2375-2548
PubMed: 35427168
DOI: 10.1126/SCIADV.ABM8990
Page generated: Wed Oct 2 17:32:57 2024

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