Atomistry » Magnesium » PDB 7duj-7e20 » 7dy2
Atomistry »
  Magnesium »
    PDB 7duj-7e20 »
      7dy2 »

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

Go back to Magnesium Binding Sites List in 7dy2
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

Go back to Magnesium Binding Sites List in 7dy2
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

Go back to Magnesium Binding Sites List in 7dy2
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

Go back to Magnesium Binding Sites List in 7dy2
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

Go back to Magnesium Binding Sites List in 7dy2
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

Go back to Magnesium Binding Sites List in 7dy2
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

Go back to Magnesium Binding Sites List in 7dy2
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

Go back to Magnesium Binding Sites List in 7dy2
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

Go back to Magnesium Binding Sites List in 7dy2
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

Go back to Magnesium Binding Sites List in 7dy2
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

Last articles

Mg in 5LAJ
Mg in 5LAI
Mg in 5LBA
Mg in 5LB5
Mg in 5LB3
Mg in 5LAQ
Mg in 5LA6
Mg in 5LA3
Mg in 5L9H
Mg in 5L8F
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy