Magnesium in PDB 7wdc: 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: 7wdc 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)	46.13 / 2.84
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	95.261, 95.261, 182.682, 90, 90, 120
R / Rfree (%)	28.3 / 32.5

The binding sites of Magnesium atom in the Crystal Structure of Cyanobacterial Circadian Clock Protein Kaic (pdb code 7wdc). 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: 7wdc:
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:62.4 occ:1.00 O2G A:ATP601 1.8 76.4 1.0 OG1 A:THR53 2.0 71.8 1.0 O2B A:ATP601 2.2 78.6 1.0 O A:HOH706 2.5 71.3 1.0 O A:HOH702 2.5 63.6 1.0 OD1 A:ASP145 3.1 90.7 1.0 PG A:ATP601 3.2 77.7 1.0 OD2 A:ASP145 3.3 90.2 1.0 CB A:THR53 3.3 73.5 1.0 PB A:ATP601 3.4 78.3 1.0 O3B A:ATP601 3.5 78.5 1.0 CG A:ASP145 3.5 89.8 1.0 N A:THR53 3.8 73.8 1.0 O1G A:ATP601 3.9 77.5 1.0 CA A:THR53 4.0 73.7 1.0 O3G A:ATP601 4.3 76.0 1.0 CG2 A:THR53 4.3 74.0 1.0 O1B A:ATP601 4.4 77.0 1.0 O3A A:ATP601 4.5 79.5 1.0 CB A:LYS52 4.5 72.1 1.0 C A:LYS52 4.6 72.5 1.0 CE A:LYS52 4.7 70.0 1.0 CG2 A:THR181 4.8 86.3 1.0 O1A A:ATP601 4.9 81.7 1.0 NZ A:LYS52 5.0 70.1 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:48.5 occ:1.00 O A:HOH701 2.0 45.4 1.0 OG1 A:THR295 2.0 58.6 1.0 O A:HOH704 2.1 56.5 1.0 O2B A:ATP602 2.2 66.0 1.0 O2G A:ATP602 2.2 72.4 1.0 O A:HOH705 2.7 81.9 1.0 O3B A:ATP602 2.8 68.2 1.0 PG A:ATP602 2.9 71.0 1.0 PB A:ATP602 3.0 66.6 1.0 OE1 A:GLU319 3.1 87.1 1.0 CB A:THR295 3.3 57.9 1.0 O3G A:ATP602 3.4 71.2 1.0 OE1 A:GLU318 3.7 80.5 1.0 O1A A:ATP602 3.9 61.1 1.0 N A:THR295 3.9 57.5 1.0 O3A A:ATP602 4.0 63.0 1.0 O1B A:ATP602 4.1 65.1 1.0 CA A:THR295 4.2 57.0 1.0 OD2 A:ASP378 4.2 60.9 1.0 O1G A:ATP602 4.3 71.0 1.0 CG2 A:THR295 4.3 57.9 1.0 CD A:GLU319 4.3 84.9 1.0 OD1 A:ASP378 4.3 63.9 1.0 PA A:ATP602 4.3 61.4 1.0 O2A A:ATP602 4.5 60.4 1.0 CG A:ASP378 4.6 62.6 1.0 NH2 B:ARG459 4.7 66.8 1.0 CB A:LYS294 4.8 57.0 1.0 CD A:GLU318 4.9 79.1 1.0 OE2 A:GLU319 4.9 84.8 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:64.5 occ:1.00 O2G B:ATP601 1.8 77.7 1.0 OG1 B:THR53 2.0 77.2 1.0 O B:HOH701 2.1 71.3 1.0 O B:HOH706 2.2 66.0 1.0 O2B B:ATP601 2.6 80.1 1.0 PG B:ATP601 2.9 79.7 1.0 OD2 B:ASP145 3.3 101.1 1.0 O3G B:ATP601 3.3 79.2 1.0 CB B:THR53 3.3 76.9 1.0 OD1 B:ASP145 3.3 99.8 1.0 O3B B:ATP601 3.5 79.3 1.0 PB B:ATP601 3.6 79.6 1.0 CG B:ASP145 3.7 98.7 1.0 CG2 B:THR53 4.1 76.8 1.0 O1G B:ATP601 4.2 77.9 1.0 N B:THR53 4.2 75.5 1.0 CA B:THR53 4.3 77.0 1.0 O1A B:ATP601 4.5 80.9 1.0 O3A B:ATP601 4.6 80.5 1.0 O1B B:ATP601 4.7 80.0 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:49.0 occ:1.00 O1B B:ATP602 1.8 66.1 1.0 O B:HOH702 1.9 42.5 1.0 O1G B:ATP602 2.0 73.2 1.0 O B:HOH704 2.0 55.6 1.0 OG1 B:THR295 2.1 56.1 1.0 O B:HOH705 2.4 56.5 1.0 PB B:ATP602 3.0 66.6 1.0 PG B:ATP602 3.1 73.0 1.0 O3B B:ATP602 3.2 69.1 1.0 CB B:THR295 3.3 55.4 1.0 OE1 B:GLU319 3.3 88.6 1.0 O3G B:ATP602 3.8 72.4 1.0 OE1 B:GLU318 3.8 76.8 1.0 O1A B:ATP602 4.0 63.4 1.0 N B:THR295 4.0 55.3 1.0 O3A B:ATP602 4.0 65.1 1.0 O2B B:ATP602 4.1 66.0 1.0 OD2 B:ASP378 4.2 65.8 1.0 CA B:THR295 4.2 54.3 1.0 O2G B:ATP602 4.3 73.2 1.0 CG2 B:THR295 4.3 56.2 1.0 OD1 B:ASP378 4.4 68.2 1.0 PA B:ATP602 4.4 63.1 1.0 CD B:GLU319 4.6 87.8 1.0 CG B:ASP378 4.6 66.8 1.0 O2A B:ATP602 4.7 63.6 1.0 CB B:LYS294 4.8 54.8 1.0 CD B:GLU318 4.9 75.7 1.0

A.Mukaiyama, Y.Furuike, E.Yamashita, S.Akiyama. Highly Sensitive Tryptophan Fluorescence Probe For Detecting Rhythmic Conformational Changes of Kaic in the Cyanobacterial Circadian Clock System. Biochem.J. V. 479 1505 2022.
ISSN: ESSN 1470-8728
PubMed: 35771042
DOI: 10.1042/BCJ20210544