Atomistry » Magnesium » PDB 7dug-7e1h » 7dy1
Atomistry »
  Magnesium »
    PDB 7dug-7e1h »
      7dy1 »

Magnesium in PDB 7dy1: 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: 7dy1 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) 47.28 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 131.103, 136.492, 190.772, 90, 90, 90
R / Rfree (%) 23.3 / 28.4

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 7dy1). 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: 7dy1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 7dy1

Go back to Magnesium Binding Sites List in 7dy1
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:35.3
occ:1.00
 OG1 A:THR54 2.0 17.1 1.0
O A:HOH716 2.1 15.7 1.0
O2G A:ATP601 2.1 17.3 1.0
O A:HOH746 2.1 21.3 1.0
O2B A:ATP601 2.2 18.5 1.0
CB A:THR54 3.1 16.3 1.0
PG A:ATP601 3.3 21.8 1.0
PB A:ATP601 3.4 17.9 1.0
O3B A:ATP601 3.6 18.1 1.0
O A:HOH715 3.8 30.4 1.0
OD2 A:ASP146 3.8 29.6 1.0
O1G A:ATP601 3.9 19.4 1.0
N A:THR54 4.0 15.7 1.0
CG2 A:THR54 4.0 15.7 1.0
CA A:THR54 4.1 16.8 1.0
OD1 A:ASP146 4.1 30.2 1.0
O1A A:ATP601 4.1 22.4 1.0
O3A A:ATP601 4.2 21.8 1.0
OE2 A:GLU79 4.2 45.9 1.0
NH2 B:ARG227 4.4 23.1 1.0
CG A:ASP146 4.4 30.4 1.0
NE B:ARG227 4.4 24.4 1.0
PA A:ATP601 4.5 22.3 1.0
O1B A:ATP601 4.6 17.5 1.0
O3G A:ATP601 4.6 16.4 1.0
O2A A:ATP601 4.6 19.8 1.0
CZ B:ARG227 4.8 24.8 1.0
O A:HOH712 4.9 44.2 1.0

Magnesium binding site 2 out of 12 in 7dy1

Go back to Magnesium Binding Sites List in 7dy1
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
A:Mg604

b:19.1
occ:1.00
 O A:HOH719 1.8 15.4 1.0
O A:HOH779 2.1 17.4 1.0
O2B A:ATP602 2.1 16.2 1.0
O1G A:ATP602 2.1 23.6 1.0
OG1 A:THR295 2.1 19.6 1.0
O A:HOH722 2.2 19.2 1.0
CB A:THR295 3.2 21.0 1.0
PB A:ATP602 3.3 17.7 1.0
PG A:ATP602 3.3 25.2 1.0
O3B A:ATP602 3.4 21.9 1.0
O A:HOH714 3.7 27.4 1.0
N A:THR295 3.9 20.5 1.0
OE2 A:GLU319 3.9 32.1 1.0
O1A A:ATP602 4.0 19.3 1.0
O3G A:ATP602 4.0 26.1 1.0
OD1 A:ASP378 4.1 32.3 1.0
CA A:THR295 4.1 22.6 1.0
OD2 A:ASP378 4.1 29.9 1.0
OE1 A:GLU318 4.2 39.2 1.0
O3A A:ATP602 4.3 18.5 1.0
O A:HOH764 4.3 19.6 1.0
CG2 A:THR295 4.3 20.5 1.0
O1B A:ATP602 4.4 17.9 1.0
PA A:ATP602 4.4 21.4 1.0
O2G A:ATP602 4.5 27.5 1.0
O2A A:ATP602 4.5 19.0 1.0
CG A:ASP378 4.5 28.9 1.0
CB A:LYS294 4.7 26.0 1.0
NH2 B:ARG459 4.7 21.7 1.0
C A:LYS294 5.0 22.2 1.0

Magnesium binding site 3 out of 12 in 7dy1

Go back to Magnesium Binding Sites List in 7dy1
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
B:Mg603

b:30.9
occ:1.00
 O2G B:ATP601 2.1 29.1 1.0
O B:HOH764 2.1 21.8 1.0
OG1 B:THR54 2.1 19.5 1.0
O2B B:ATP601 2.2 23.1 1.0
O B:HOH728 2.3 24.7 1.0
O B:HOH720 2.3 30.1 1.0
PG B:ATP601 3.2 28.1 1.0
CB B:THR54 3.3 20.4 1.0
PB B:ATP601 3.4 21.9 1.0
O1G B:ATP601 3.6 26.1 1.0
O3B B:ATP601 3.6 24.3 1.0
NH2 C:ARG227 3.9 23.8 1.0
OD1 B:ASP146 4.0 33.5 1.0
O B:HOH739 4.0 27.6 1.0
O3A B:ATP601 4.1 23.6 1.0
O1A B:ATP601 4.2 21.0 1.0
N B:THR54 4.2 20.7 1.0
CG2 B:THR54 4.2 21.8 1.0
NE C:ARG227 4.2 23.4 1.0
OE2 B:GLU79 4.3 40.6 1.0
CA B:THR54 4.3 20.9 1.0
OD2 B:ASP146 4.4 35.5 1.0
CZ C:ARG227 4.5 25.2 1.0
PA B:ATP601 4.5 21.3 1.0
O3G B:ATP601 4.5 28.8 1.0
O1B B:ATP601 4.5 22.2 1.0
CG B:ASP146 4.6 32.5 1.0
O2A B:ATP601 4.7 18.0 1.0

Magnesium binding site 4 out of 12 in 7dy1

Go back to Magnesium Binding Sites List in 7dy1
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
B:Mg604

b:23.8
occ:1.00
 O2B B:ATP602 1.9 21.0 1.0
OG1 B:THR295 2.0 21.8 1.0
O B:HOH740 2.0 20.2 1.0
O B:HOH745 2.0 27.2 1.0
O2G B:ATP602 2.1 25.4 1.0
O B:HOH753 2.2 22.8 1.0
PB B:ATP602 3.1 23.9 1.0
PG B:ATP602 3.3 26.8 1.0
CB B:THR295 3.3 24.9 1.0
O3B B:ATP602 3.4 24.0 1.0
N B:THR295 3.9 22.3 1.0
O B:HOH729 3.9 29.7 1.0
OE1 B:GLU318 4.0 40.9 1.0
OD1 B:ASP378 4.0 22.7 1.0
O B:HOH771 4.1 26.6 1.0
O3G B:ATP602 4.1 25.4 1.0
CA B:THR295 4.1 23.8 1.0
O3A B:ATP602 4.1 22.2 1.0
O1A B:ATP602 4.2 22.4 1.0
O1B B:ATP602 4.2 22.3 1.0
OD2 B:ASP378 4.2 23.1 1.0
OE2 B:GLU319 4.2 28.3 1.0
CG2 B:THR295 4.3 24.2 1.0
O1G B:ATP602 4.4 29.0 1.0
PA B:ATP602 4.5 22.6 1.0
CG B:ASP378 4.5 23.5 1.0
O2A B:ATP602 4.6 20.1 1.0
NH2 C:ARG459 4.7 26.8 1.0
CB B:LYS294 4.7 26.7 1.0
C B:LYS294 4.9 22.1 1.0

Magnesium binding site 5 out of 12 in 7dy1

Go back to Magnesium Binding Sites List in 7dy1
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
C:Mg603

b:30.4
occ:1.00
 O2G C:ATP601 2.0 24.9 1.0
O2B C:ATP601 2.1 22.5 1.0
O C:HOH734 2.1 22.5 1.0
O C:HOH719 2.2 31.0 1.0
O C:HOH809 2.2 30.3 1.0
OG1 C:THR54 2.2 18.0 1.0
PG C:ATP601 3.2 25.9 1.0
PB C:ATP601 3.2 22.8 1.0
CB C:THR54 3.3 17.6 1.0
O3B C:ATP601 3.5 22.2 1.0
O1G C:ATP601 3.9 26.9 1.0
O3A C:ATP601 4.0 20.1 1.0
O1A C:ATP601 4.1 20.4 1.0
OE2 C:GLU79 4.1 31.8 1.0
OD2 C:ASP146 4.1 30.4 1.0
NH2 D:ARG227 4.1 24.5 1.0
NE D:ARG227 4.1 26.0 1.0
N C:THR54 4.1 18.8 1.0
CG2 C:THR54 4.2 17.4 1.0
OD1 C:ASP146 4.2 28.9 1.0
CA C:THR54 4.3 17.5 1.0
O C:HOH829 4.3 31.4 1.0
O C:HOH781 4.4 30.8 1.0
O3G C:ATP601 4.4 28.5 1.0
CZ D:ARG227 4.5 25.2 1.0
O1B C:ATP601 4.5 21.0 1.0
PA C:ATP601 4.5 20.8 1.0
CG C:ASP146 4.6 29.2 1.0
O2A C:ATP601 4.7 18.9 1.0
O C:HOH738 4.8 22.3 1.0

Magnesium binding site 6 out of 12 in 7dy1

Go back to Magnesium Binding Sites List in 7dy1
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:Mg604

b:25.6
occ:1.00
 O1B C:ATP602 2.0 17.8 1.0
O C:HOH732 2.0 20.6 1.0
OG1 C:THR295 2.1 21.2 1.0
O C:HOH722 2.3 29.5 1.0
O2G C:ATP602 2.3 32.6 1.0
O C:HOH701 2.3 15.4 1.0
CB C:THR295 3.2 22.7 1.0
PG C:ATP602 3.2 29.3 1.0
PB C:ATP602 3.2 21.2 1.0
O3B C:ATP602 3.5 23.8 1.0
O3G C:ATP602 3.5 37.7 1.0
OE1 C:GLU319 3.8 27.8 1.0
OE2 C:GLU318 3.9 41.9 1.0
N C:THR295 4.0 21.9 1.0
O1A C:ATP602 4.0 21.8 1.0
OD1 C:ASP378 4.1 27.8 1.0
OD2 C:ASP378 4.1 25.3 1.0
O C:HOH727 4.1 23.9 1.0
CA C:THR295 4.1 22.0 1.0
O3A C:ATP602 4.2 21.8 1.0
CG2 C:THR295 4.2 22.6 1.0
O2B C:ATP602 4.3 20.1 1.0
NH2 D:ARG459 4.4 20.4 1.0
CG C:ASP378 4.5 26.1 1.0
PA C:ATP602 4.5 22.6 1.0
O1G C:ATP602 4.6 33.2 1.0
O2A C:ATP602 4.7 20.8 1.0
CD C:GLU319 5.0 31.0 1.0
CB C:LYS294 5.0 24.3 1.0

Magnesium binding site 7 out of 12 in 7dy1

Go back to Magnesium Binding Sites List in 7dy1
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:17.6
occ:1.00
 O D:HOH717 1.9 20.4 1.0
O2B D:ATP601 2.0 16.0 1.0
OG1 D:THR54 2.0 15.9 1.0
O D:HOH778 2.1 20.6 1.0
O2G D:ATP601 2.1 20.4 1.0
O D:HOH806 2.2 16.3 1.0
CB D:THR54 3.0 16.2 1.0
PB D:ATP601 3.1 18.8 1.0
PG D:ATP601 3.3 21.1 1.0
O3B D:ATP601 3.4 19.4 1.0
O1A D:ATP601 3.9 22.2 1.0
O1G D:ATP601 3.9 20.9 1.0
O3A D:ATP601 4.0 20.5 1.0
OD2 D:ASP146 4.0 27.6 1.0
NH2 E:ARG227 4.0 20.0 1.0
CG2 D:THR54 4.0 17.1 1.0
N D:THR54 4.0 14.9 1.0
CA D:THR54 4.1 17.1 1.0
NE E:ARG227 4.2 19.2 1.0
O E:HOH820 4.3 18.9 1.0
PA D:ATP601 4.3 21.7 1.0
O1B D:ATP601 4.4 16.5 1.0
O D:HOH741 4.4 22.7 1.0
OD1 D:ASP146 4.4 28.7 1.0
CZ E:ARG227 4.5 18.7 1.0
OE2 D:GLU79 4.5 44.2 1.0
O3G D:ATP601 4.5 23.0 1.0
O2A D:ATP601 4.5 17.8 1.0
CG D:ASP146 4.6 27.9 1.0

Magnesium binding site 8 out of 12 in 7dy1

Go back to Magnesium Binding Sites List in 7dy1
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
D:Mg604

b:17.3
occ:1.00
 OG1 D:THR295 2.0 18.7 1.0
O D:HOH754 2.0 19.4 1.0
O D:HOH819 2.0 18.8 1.0
O D:HOH750 2.1 20.5 1.0
O1B D:ATP602 2.2 18.1 1.0
O3G D:ATP602 2.2 25.5 1.0
CB D:THR295 3.3 21.3 1.0
PB D:ATP602 3.4 19.6 1.0
PG D:ATP602 3.4 27.0 1.0
O3B D:ATP602 3.4 22.1 1.0
O D:HOH723 4.0 22.5 1.0
OD2 D:ASP378 4.1 23.4 1.0
N D:THR295 4.1 19.0 1.0
O1A D:ATP602 4.1 20.2 1.0
OD1 D:ASP378 4.2 26.1 1.0
OE1 D:GLU318 4.2 40.3 1.0
CA D:THR295 4.2 21.5 1.0
O D:HOH795 4.2 25.2 1.0
CG2 D:THR295 4.2 19.6 1.0
O3A D:ATP602 4.3 20.3 1.0
OE2 D:GLU319 4.3 30.9 1.0
O2G D:ATP602 4.3 25.1 1.0
O1G D:ATP602 4.4 23.9 1.0
O2B D:ATP602 4.5 16.5 1.0
CG D:ASP378 4.5 23.2 1.0
NH2 E:ARG459 4.6 20.7 1.0
PA D:ATP602 4.6 19.6 1.0
O2A D:ATP602 4.8 20.9 1.0

Magnesium binding site 9 out of 12 in 7dy1

Go back to Magnesium Binding Sites List in 7dy1
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
E:Mg603

b:25.3
occ:1.00
 OG1 E:THR54 1.9 20.7 1.0
O E:HOH731 2.0 24.6 1.0
O E:HOH721 2.0 35.6 1.0
O E:HOH795 2.1 34.1 1.0
O2B E:ATP601 2.2 17.3 1.0
O2G E:ATP601 2.2 28.6 1.0
CB E:THR54 3.2 22.9 1.0
PG E:ATP601 3.5 26.3 1.0
PB E:ATP601 3.5 21.2 1.0
OD1 E:ASP146 3.8 36.0 1.0
O3B E:ATP601 3.9 22.9 1.0
OD2 E:ASP146 3.9 32.5 1.0
N E:THR54 4.0 22.0 1.0
O1G E:ATP601 4.0 25.5 1.0
CA E:THR54 4.1 22.2 1.0
CG2 E:THR54 4.1 24.4 1.0
O F:HOH824 4.1 40.7 1.0
CG E:ASP146 4.3 32.8 1.0
O3A E:ATP601 4.3 21.2 1.0
NH2 F:ARG227 4.4 21.7 1.0
O1A E:ATP601 4.4 21.3 1.0
NE F:ARG227 4.5 22.3 1.0
O1B E:ATP601 4.6 24.1 1.0
PA E:ATP601 4.7 20.0 1.0
O3G E:ATP601 4.7 28.1 1.0
O2A E:ATP601 4.8 19.4 1.0
O E:HOH759 4.8 42.2 1.0
CZ F:ARG227 4.9 22.6 1.0
CB E:LYS53 5.0 18.2 1.0

Magnesium binding site 10 out of 12 in 7dy1

Go back to Magnesium Binding Sites List in 7dy1
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
E:Mg604

b:27.0
occ:1.00
 O1B E:ATP602 2.0 17.0 1.0
O E:HOH767 2.0 23.8 1.0
O E:HOH740 2.0 24.6 1.0
O1G E:ATP602 2.1 24.6 1.0
OG1 E:THR295 2.1 19.6 1.0
O E:HOH739 2.3 17.3 1.0
PB E:ATP602 3.2 20.5 1.0
CB E:THR295 3.2 20.7 1.0
PG E:ATP602 3.3 26.8 1.0
O3B E:ATP602 3.4 23.3 1.0
OE2 E:GLU319 4.0 34.7 1.0
N E:THR295 4.0 20.3 1.0
OD2 E:ASP378 4.0 27.8 1.0
OE1 E:GLU318 4.0 50.5 1.0
OD1 E:ASP378 4.1 27.9 1.0
CA E:THR295 4.1 21.4 1.0
O3A E:ATP602 4.2 22.1 1.0
O1A E:ATP602 4.2 22.1 1.0
O3G E:ATP602 4.2 25.6 1.0
O E:HOH702 4.2 39.9 1.0
CG2 E:THR295 4.2 21.7 1.0
CG E:LYS294 4.3 26.2 1.0
O2B E:ATP602 4.3 19.8 1.0
O E:HOH763 4.4 20.2 1.0
O2G E:ATP602 4.4 26.1 1.0
CG E:ASP378 4.5 26.7 1.0
PA E:ATP602 4.6 21.5 1.0
O2A E:ATP602 4.7 23.7 1.0
NH2 F:ARG459 4.7 29.0 1.0
CD E:GLU318 5.0 45.1 1.0

Reference:

Y.Furuike, A.Mukaiyama, S.I.Koda, D.Simon, D.Ouyang, K.Ito-Miwa, S.Saito, E.Yamashita, T.Nishiwaki-Ohkawa, K.Terauchi, T.Kondo, S.Akiyama. Regulation Mechanisms of the Dual Atpase in Kaic. Proc.Natl.Acad.Sci.Usa V. 119 27119 2022.
ISSN: ESSN 1091-6490
PubMed: 35507871
DOI: 10.1073/PNAS.2119627119
Page generated: Wed Oct 2 17:32:39 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy