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Magnesium in PDB 4tl7: Crystal Structure of N-Terminal C1 Domain of Kaic

Enzymatic activity of Crystal Structure of N-Terminal C1 Domain of Kaic

All present enzymatic activity of Crystal Structure of N-Terminal C1 Domain of Kaic:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of N-Terminal C1 Domain of Kaic, PDB code: 4tl7 was solved by J.Abe, T.B.Hiyama, A.Mukaiyama, S.Son, S.Akiyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.85 / 1.94
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 108.165, 108.165, 224.880, 90.00, 90.00, 120.00
R / Rfree (%) 15 / 19.1

Other elements in 4tl7:

The structure of Crystal Structure of N-Terminal C1 Domain of Kaic also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of N-Terminal C1 Domain of Kaic (pdb code 4tl7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of N-Terminal C1 Domain of Kaic, PDB code: 4tl7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4tl7

Go back to Magnesium Binding Sites List in 4tl7
Magnesium binding site 1 out of 6 in the Crystal Structure of N-Terminal C1 Domain of 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 N-Terminal C1 Domain of Kaic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:19.9
occ:1.00
 O1G A:ATP301 2.0 19.6 1.0
O1B A:ATP301 2.1 17.3 1.0
O A:HOH498 2.1 19.6 1.0
OG1 A:THR53 2.1 20.7 1.0
O A:HOH499 2.1 20.5 1.0
O A:HOH497 2.1 21.1 1.0
PB A:ATP301 3.2 19.3 1.0
CB A:THR53 3.2 23.4 1.0
PG A:ATP301 3.3 23.5 1.0
O3B A:ATP301 3.3 30.1 1.0
O3G A:ATP301 3.9 29.4 1.0
OD2 A:ASP145 3.9 23.0 0.6
N A:THR53 4.0 18.0 1.0
O A:HOH432 4.0 23.9 1.0
O1A A:ATP301 4.1 23.0 1.0
OD2 A:ASP145 4.1 22.5 0.4
CA A:THR53 4.1 18.6 1.0
O B:HOH479 4.2 44.7 1.0
O A:HOH520 4.2 30.5 1.0
OD1 A:ASP145 4.2 23.3 0.6
OD1 A:ASP145 4.2 23.1 0.4
O3A A:ATP301 4.2 20.0 1.0
CG2 A:THR53 4.3 19.9 1.0
O2B A:ATP301 4.3 17.7 1.0
NH2 B:ARG226 4.4 20.0 1.0
NE B:ARG226 4.5 22.4 1.0
O2G A:ATP301 4.5 37.1 1.0
CG A:ASP145 4.5 24.6 0.6
PA A:ATP301 4.6 22.1 1.0
O A:HOH459 4.6 35.9 1.0
CG A:ASP145 4.6 24.8 0.4
O2A A:ATP301 4.8 26.6 1.0
CZ B:ARG226 4.8 24.0 1.0
CB A:LYS52 5.0 16.9 1.0

Magnesium binding site 2 out of 6 in 4tl7

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Magnesium binding site 2 out of 6 in the Crystal Structure of N-Terminal C1 Domain of 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 N-Terminal C1 Domain of Kaic within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:21.4
occ:1.00
 O1B B:ATP301 2.0 19.1 1.0
O1G B:ATP301 2.0 21.6 1.0
O B:HOH493 2.1 21.8 1.0
OG1 B:THR53 2.1 21.4 1.0
O B:HOH494 2.1 24.6 1.0
O B:HOH495 2.1 20.2 1.0
CB B:THR53 3.1 26.4 1.0
PB B:ATP301 3.2 19.7 1.0
PG B:ATP301 3.3 24.7 1.0
O3B B:ATP301 3.4 27.7 1.0
N B:THR53 3.9 21.6 1.0
OD2 B:ASP145 4.0 24.9 0.7
O B:HOH441 4.0 28.9 1.0
O3G B:ATP301 4.0 27.7 1.0
OD2 B:ASP145 4.0 25.8 0.3
CA B:THR53 4.1 20.9 1.0
OD1 B:ASP145 4.1 26.9 0.7
O2A B:ATP301 4.1 26.3 1.0
OD1 B:ASP145 4.1 26.7 0.3
O B:HOH433 4.2 27.5 1.0
O3A B:ATP301 4.2 20.0 1.0
O2B B:ATP301 4.3 20.8 1.0
CG2 B:THR53 4.3 21.1 1.0
O B:HOH506 4.3 34.5 1.0
CG B:ASP145 4.5 25.7 0.7
CG B:ASP145 4.5 26.2 0.3
O2G B:ATP301 4.5 40.6 1.0
NE C:ARG226 4.6 23.8 1.0
NH2 C:ARG226 4.6 23.6 1.0
PA B:ATP301 4.6 22.6 1.0
O1A B:ATP301 4.8 28.1 1.0
C B:LYS52 5.0 20.1 1.0

Magnesium binding site 3 out of 6 in 4tl7

Go back to Magnesium Binding Sites List in 4tl7
Magnesium binding site 3 out of 6 in the Crystal Structure of N-Terminal C1 Domain of 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 N-Terminal C1 Domain of Kaic within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:22.7
occ:1.00
 O2B C:ATP301 2.0 16.5 1.0
O C:HOH500 2.0 19.7 1.0
OG1 C:THR53 2.1 22.8 1.0
O2G C:ATP301 2.1 23.9 1.0
O C:HOH502 2.1 20.3 1.0
O C:HOH501 2.2 22.7 1.0
CB C:THR53 3.2 24.2 1.0
PB C:ATP301 3.2 20.4 1.0
PG C:ATP301 3.3 26.8 1.0
O3B C:ATP301 3.4 31.8 1.0
O1G C:ATP301 3.8 30.6 1.0
O C:HOH521 3.9 27.3 1.0
OD2 C:ASP145 3.9 27.8 0.6
N C:THR53 3.9 16.9 1.0
OD2 C:ASP145 4.0 24.7 0.5
CA C:THR53 4.1 20.8 1.0
OD1 C:ASP145 4.1 24.9 0.6
O2A C:ATP301 4.1 24.9 1.0
O C:HOH520 4.2 35.5 1.0
O3A C:ATP301 4.2 20.6 1.0
OD1 C:ASP145 4.2 25.7 0.5
CG2 C:THR53 4.3 22.3 1.0
O1B C:ATP301 4.3 22.2 1.0
O C:HOH441 4.4 33.6 1.0
CG C:ASP145 4.4 28.0 0.6
NH2 D:ARG226 4.5 24.8 1.0
NE D:ARG226 4.5 23.0 1.0
CG C:ASP145 4.5 27.0 0.5
O3G C:ATP301 4.6 35.1 1.0
PA C:ATP301 4.6 22.7 1.0
CZ D:ARG226 4.9 26.6 1.0
O1A C:ATP301 4.9 25.0 1.0
CB C:LYS52 4.9 24.1 1.0

Magnesium binding site 4 out of 6 in 4tl7

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Magnesium binding site 4 out of 6 in the Crystal Structure of N-Terminal C1 Domain of 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 N-Terminal C1 Domain of Kaic within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:22.6
occ:1.00
 O3G D:ATP301 1.9 20.2 1.0
OG1 D:THR53 2.1 20.6 1.0
O2B D:ATP301 2.1 18.3 1.0
O D:HOH516 2.1 21.3 1.0
O D:HOH515 2.1 20.7 1.0
O D:HOH514 2.1 20.1 1.0
CB D:THR53 3.1 19.0 1.0
PG D:ATP301 3.2 25.7 1.0
PB D:ATP301 3.2 17.0 1.0
O3B D:ATP301 3.4 37.5 1.0
OD2 D:ASP145 3.9 22.8 0.6
N D:THR53 3.9 19.0 1.0
O1G D:ATP301 4.0 31.4 1.0
O D:HOH536 4.0 53.6 1.0
O D:HOH443 4.1 29.2 1.0
CA D:THR53 4.1 20.4 1.0
OD2 D:ASP145 4.1 23.6 0.4
O2A D:ATP301 4.1 21.1 1.0
O2G D:ATP301 4.2 45.2 1.0
OD1 D:ASP145 4.2 24.7 0.4
O D:HOH440 4.2 26.9 1.0
CG2 D:THR53 4.2 24.4 1.0
O3A D:ATP301 4.2 19.4 1.0
OD1 D:ASP145 4.2 26.1 0.6
O1B D:ATP301 4.3 17.4 1.0
NH2 E:ARG226 4.4 28.7 1.0
NE E:ARG226 4.5 25.2 1.0
CG D:ASP145 4.5 24.9 0.6
O D:HOH450 4.5 32.3 1.0
PA D:ATP301 4.6 23.1 1.0
CG D:ASP145 4.6 24.5 0.4
O1A D:ATP301 4.8 27.3 1.0
CZ E:ARG226 4.9 28.4 1.0
CB D:LYS52 5.0 19.1 1.0

Magnesium binding site 5 out of 6 in 4tl7

Go back to Magnesium Binding Sites List in 4tl7
Magnesium binding site 5 out of 6 in the Crystal Structure of N-Terminal C1 Domain of 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 N-Terminal C1 Domain of Kaic within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg302

b:19.7
occ:1.00
 O3G E:ATP301 2.0 21.6 1.0
O E:HOH502 2.0 21.7 1.0
O2B E:ATP301 2.1 18.9 1.0
OG1 E:THR53 2.1 19.2 1.0
O E:HOH503 2.1 20.1 1.0
O E:HOH501 2.1 18.4 1.0
CB E:THR53 3.2 18.3 1.0
PG E:ATP301 3.2 24.1 1.0
PB E:ATP301 3.2 20.0 1.0
O3B E:ATP301 3.4 29.3 1.0
O2G E:ATP301 3.8 26.0 1.0
O E:HOH425 3.9 25.5 1.0
OD2 E:ASP145 3.9 23.7 0.6
N E:THR53 4.0 22.9 1.0
OD2 E:ASP145 4.0 23.3 0.4
O1A E:ATP301 4.0 22.6 1.0
CA E:THR53 4.1 24.7 1.0
OD1 E:ASP145 4.2 22.7 0.6
O E:HOH521 4.2 28.4 1.0
OD1 E:ASP145 4.2 23.6 0.4
O3A E:ATP301 4.2 20.9 1.0
CG2 E:THR53 4.3 18.9 1.0
O1B E:ATP301 4.3 20.4 1.0
NH2 F:ARG226 4.4 23.8 1.0
NE F:ARG226 4.4 22.7 1.0
O1G E:ATP301 4.4 36.0 1.0
O E:HOH519 4.5 31.9 1.0
CG E:ASP145 4.5 23.5 0.6
CG E:ASP145 4.5 24.6 0.4
PA E:ATP301 4.6 23.1 1.0
O2A E:ATP301 4.8 28.6 1.0
CZ F:ARG226 4.8 26.5 1.0
CB E:LYS52 5.0 21.1 1.0

Magnesium binding site 6 out of 6 in 4tl7

Go back to Magnesium Binding Sites List in 4tl7
Magnesium binding site 6 out of 6 in the Crystal Structure of N-Terminal C1 Domain of 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 N-Terminal C1 Domain of Kaic within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg302

b:24.1
occ:1.00
 O F:HOH486 2.0 21.0 1.0
O2B F:ATP301 2.0 19.1 1.0
O2G F:ATP301 2.0 23.0 1.0
OG1 F:THR53 2.1 26.3 1.0
O F:HOH488 2.1 22.2 1.0
O F:HOH487 2.2 27.2 1.0
PB F:ATP301 3.1 21.1 1.0
CB F:THR53 3.2 24.8 1.0
PG F:ATP301 3.2 27.6 1.0
O3B F:ATP301 3.3 29.0 1.0
N F:THR53 3.8 20.4 1.0
O3G F:ATP301 3.9 32.7 1.0
OD2 F:ASP145 4.0 27.0 0.6
O1A F:ATP301 4.1 28.0 1.0
CA F:THR53 4.1 22.7 1.0
O F:HOH423 4.1 29.9 1.0
OD2 F:ASP145 4.1 23.0 0.5
O3A F:ATP301 4.1 21.3 1.0
O1B F:ATP301 4.2 20.8 1.0
O F:HOH506 4.2 29.8 1.0
OD1 F:ASP145 4.3 29.1 0.6
OD1 F:ASP145 4.3 26.1 0.5
CG2 F:THR53 4.3 24.4 1.0
O F:HOH435 4.3 37.0 1.0
NE A:ARG226 4.5 24.5 1.0
PA F:ATP301 4.5 26.8 1.0
NH2 A:ARG226 4.5 21.9 1.0
O1G F:ATP301 4.5 38.1 1.0
CG F:ASP145 4.6 27.8 0.6
CG F:ASP145 4.6 26.7 0.5
O2A F:ATP301 4.7 30.6 1.0
CZ A:ARG226 4.9 25.2 1.0
CB F:LYS52 4.9 20.1 1.0
C F:LYS52 5.0 24.6 1.0

Reference:

J.Abe, T.B.Hiyama, A.Mukaiyama, S.Son, T.Mori, S.Saito, M.Osako, J.Wolanin, E.Yamashita, T.Kondo, S.Akiyama. Circadian Rhythms. Atomic-Scale Origins of Slowness in the Cyanobacterial Circadian Clock. Science V. 349 312 2015.
ISSN: ESSN 1095-9203
PubMed: 26113637
DOI: 10.1126/SCIENCE.1261040
Page generated: Tue Aug 20 03:45:27 2024

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