Magnesium in PDB 7dyk: 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;

The structure of Crystal Structure of Cyanobacterial Circadian Clock Protein Kaic, PDB code: 7dyk 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)	48.55 / 2.99
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	94.847, 94.847, 180.56, 90, 90, 120
R / Rfree (%)	27.4 / 32.8

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

Magnesium binding site 1 out of 4 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:36.0 occ:1.00 OG1 A:THR53 1.9 61.4 1.0 O2B A:ATP601 2.1 63.3 1.0 O A:HOH702 2.2 41.9 1.0 O2G A:ATP601 2.2 60.0 1.0 O A:HOH704 2.3 65.2 1.0 PG A:ATP601 3.0 60.5 1.0 CB A:THR53 3.1 63.2 1.0 PB A:ATP601 3.2 63.6 1.0 O3B A:ATP601 3.2 62.1 1.0 O1G A:ATP601 3.2 58.9 1.0 OD1 A:ASP145 3.7 88.2 1.0 OD2 A:ASP145 3.7 88.7 1.0 O1A A:ATP601 3.8 69.7 1.0 NE B:ARG226 4.0 74.5 1.0 N A:THR53 4.0 64.5 1.0 CG2 A:THR53 4.1 63.2 1.0 O3A A:ATP601 4.1 64.9 1.0 CA A:THR53 4.1 64.4 1.0 CG A:ASP145 4.1 88.3 1.0 NH1 B:ARG226 4.3 75.7 1.0 O1B A:ATP601 4.4 63.8 1.0 OE2 A:GLU78 4.4 95.2 1.0 PA A:ATP601 4.4 67.1 1.0 O3G A:ATP601 4.4 60.0 1.0 CZ B:ARG226 4.6 75.5 1.0 O2A A:ATP601 4.8 66.4 1.0 NZ A:LYS52 4.9 66.9 1.0 CD B:ARG226 4.9 73.6 1.0 CB A:LYS52 4.9 64.6 1.0

Magnesium binding site 2 out of 4 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 A:Mg604 b:47.9 occ:1.00 O A:HOH705 2.0 55.0 1.0 OG1 A:THR295 2.0 55.6 1.0 O A:HOH701 2.0 43.9 1.0 O2G A:ATP602 2.3 67.3 1.0 O1B A:ATP602 2.5 60.5 1.0 OE1 A:GLU319 3.1 72.6 1.0 CB A:THR295 3.4 54.5 1.0 PG A:ATP602 3.4 67.0 1.0 O3B A:ATP602 3.4 63.0 1.0 OE1 A:GLU318 3.4 70.1 1.0 PB A:ATP602 3.5 60.5 1.0 OD1 A:ASP378 3.5 55.7 1.0 OD2 A:ASP378 3.8 55.2 1.0 CG A:ASP378 4.0 55.6 1.0 O1A A:ATP602 4.0 58.0 1.0 N A:THR295 4.1 52.7 1.0 O1G A:ATP602 4.1 65.8 1.0 CA A:THR295 4.2 52.9 1.0 CG2 A:THR295 4.2 55.0 1.0 CD A:GLU319 4.3 72.5 1.0 CD A:GLU318 4.4 68.3 1.0 O3A A:ATP602 4.5 59.6 1.0 O3G A:ATP602 4.6 66.1 1.0 O2B A:ATP602 4.7 60.8 1.0 OE2 A:GLU319 4.8 74.4 1.0 NH2 B:ARG459 4.8 62.5 1.0 PA A:ATP602 4.8 57.8 1.0 CB A:LYS294 4.9 51.1 1.0 CG A:GLU318 5.0 67.4 1.0

Magnesium binding site 3 out of 4 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 B:Mg603 b:45.4 occ:1.00 O3G B:ATP601 2.2 78.3 1.0 OG1 B:THR53 2.3 69.2 1.0 O2B B:ATP601 2.4 76.3 1.0 PG B:ATP601 3.0 78.3 1.0 O3B B:ATP601 3.2 75.3 1.0 O1A B:ATP601 3.3 71.4 1.0 PB B:ATP601 3.4 74.7 1.0 CB B:THR53 3.4 69.6 1.0 O1G B:ATP601 3.4 78.5 1.0 OD1 B:ASP145 3.7 88.9 1.0 OD2 B:ASP145 4.0 92.1 1.0 O3A B:ATP601 4.1 72.6 1.0 CG2 B:THR53 4.2 69.2 1.0 PA B:ATP601 4.3 70.4 1.0 CG B:ASP145 4.3 89.4 1.0 N B:THR53 4.4 70.5 1.0 O2G B:ATP601 4.5 77.9 1.0 CA B:THR53 4.5 70.1 1.0 O1B B:ATP601 4.6 75.9 1.0

Magnesium binding site 4 out of 4 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 B:Mg604 b:35.9 occ:1.00 O B:HOH702 1.9 54.6 1.0 O3G B:ATP602 1.9 64.8 1.0 O B:HOH701 2.0 37.2 1.0 OG1 B:THR295 2.1 48.7 1.0 O1B B:ATP602 2.1 58.3 1.0 PG B:ATP602 3.1 65.0 1.0 O3B B:ATP602 3.2 62.0 1.0 PB B:ATP602 3.2 59.2 1.0 OE1 B:GLU319 3.3 77.5 1.0 CB B:THR295 3.4 48.1 1.0 OE1 B:GLU318 3.6 72.7 1.0 O1G B:ATP602 4.0 65.1 1.0 O2A B:ATP602 4.1 57.3 1.0 N B:THR295 4.1 48.1 1.0 OD1 B:ASP378 4.2 57.0 1.0 O3A B:ATP602 4.2 58.2 1.0 O2G B:ATP602 4.2 64.7 1.0 CG2 B:THR295 4.3 48.5 1.0 CA B:THR295 4.3 47.8 1.0 OD2 B:ASP378 4.3 57.4 1.0 O2B B:ATP602 4.4 59.1 1.0 CD B:GLU319 4.4 77.0 1.0 PA B:ATP602 4.5 57.4 1.0 CG B:ASP378 4.5 57.3 1.0 CD B:GLU318 4.7 71.4 1.0 O1A B:ATP602 4.8 58.6 1.0 OE2 B:GLU319 5.0 78.4 1.0

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