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Magnesium in PDB 4tl9: 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: 4tl9 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) 38.98 / 1.82
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.134, 133.820, 151.167, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.7

Other elements in 4tl9:

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 4tl9). 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: 4tl9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4tl9

Go back to Magnesium Binding Sites List in 4tl9
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:Mg301

b:22.5
occ:1.00
 O2G A:AGS303 2.0 24.9 1.0
OG1 A:THR53 2.0 22.8 1.0
O1B A:AGS303 2.0 18.5 1.0
O A:HOH525 2.1 24.6 1.0
O A:HOH527 2.2 23.8 1.0
O A:HOH526 2.2 27.5 1.0
CB A:THR53 3.0 22.0 1.0
PG A:AGS303 3.2 24.7 1.0
PB A:AGS303 3.3 20.4 1.0
O3B A:AGS303 3.5 22.3 1.0
N A:THR53 3.8 19.9 1.0
OD2 A:ASP145 3.9 26.3 0.6
CA A:THR53 4.0 21.3 1.0
OD2 A:ASP145 4.1 25.8 0.4
OE2 A:GLU78 4.1 39.1 1.0
O1A A:AGS303 4.1 22.2 1.0
OD1 A:ASP145 4.1 28.1 0.4
CG2 A:THR53 4.1 22.9 1.0
O3G A:AGS303 4.2 22.1 1.0
O A:HOH528 4.2 36.6 1.0
OD1 A:ASP145 4.2 26.8 0.6
O3A A:AGS303 4.3 25.5 1.0
O2B A:AGS303 4.4 19.9 1.0
CG A:ASP145 4.5 27.6 0.4
PA A:AGS303 4.5 23.0 1.0
CG A:ASP145 4.5 28.7 0.6
NH2 B:ARG226 4.5 31.5 1.0
NE B:ARG226 4.6 26.1 1.0
O2A A:AGS303 4.6 28.2 1.0
S1G A:AGS303 4.7 26.8 1.0
CZ B:ARG226 4.9 34.6 1.0
CB A:LYS52 5.0 19.4 1.0
C A:LYS52 5.0 20.6 1.0

Magnesium binding site 2 out of 6 in 4tl9

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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:Mg301

b:19.6
occ:1.00
 OG1 B:THR53 2.0 16.2 1.0
O2G B:AGS303 2.0 20.8 1.0
O B:HOH552 2.1 21.5 1.0
O B:HOH554 2.1 18.8 1.0
O1B B:AGS303 2.1 16.4 1.0
O B:HOH553 2.1 19.8 1.0
CB B:THR53 3.1 15.1 1.0
PG B:AGS303 3.2 19.4 1.0
PB B:AGS303 3.3 17.5 1.0
O3B B:AGS303 3.6 19.4 1.0
OE1 B:GLU78 3.8 27.0 1.0
OD2 B:ASP145 3.9 18.6 0.5
N B:THR53 3.9 14.5 1.0
OD2 B:ASP145 3.9 19.6 0.5
CA B:THR53 4.0 14.9 1.0
O1A B:AGS303 4.1 17.8 1.0
O3G B:AGS303 4.1 17.2 1.0
CG2 B:THR53 4.1 18.7 1.0
OD1 B:ASP145 4.2 22.5 0.5
O B:HOH462 4.2 32.1 1.0
OD1 B:ASP145 4.3 21.7 0.5
O B:HOH557 4.3 39.7 1.0
O3A B:AGS303 4.3 17.9 1.0
O2B B:AGS303 4.4 14.6 1.0
NH2 C:ARG226 4.4 26.4 1.0
CG B:ASP145 4.4 22.2 0.5
CG B:ASP145 4.5 22.0 0.5
PA B:AGS303 4.5 18.2 1.0
S1G B:AGS303 4.6 23.7 1.0
NE C:ARG226 4.7 19.3 1.0
O2A B:AGS303 4.7 20.0 1.0
O B:HOH485 4.8 31.0 1.0
CZ C:ARG226 4.9 23.4 1.0
CD B:GLU78 4.9 31.6 1.0
CB B:LYS52 5.0 17.9 1.0

Magnesium binding site 3 out of 6 in 4tl9

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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:Mg301

b:19.6
occ:1.00
 O2G C:AGS303 1.9 22.5 1.0
OG1 C:THR53 2.0 19.4 1.0
O1B C:AGS303 2.1 17.6 1.0
O C:HOH553 2.1 23.8 1.0
O C:HOH554 2.1 22.2 1.0
O C:HOH555 2.1 20.0 1.0
CB C:THR53 3.1 15.0 1.0
PG C:AGS303 3.2 23.6 1.0
PB C:AGS303 3.2 16.6 1.0
O3B C:AGS303 3.5 19.5 1.0
OE2 C:GLU78 3.8 34.4 1.0
OD2 C:ASP145 3.8 16.7 0.5
N C:THR53 3.9 18.3 1.0
O C:HOH546 3.9 31.4 1.0
O3G C:AGS303 4.0 20.1 1.0
CA C:THR53 4.0 17.7 1.0
O1A C:AGS303 4.1 19.7 1.0
CG2 C:THR53 4.1 16.7 1.0
OD1 C:ASP145 4.1 16.4 0.5
OD2 C:ASP145 4.2 18.9 0.5
OD1 C:ASP145 4.2 16.5 0.5
O3A C:AGS303 4.3 14.2 1.0
O2B C:AGS303 4.4 14.6 1.0
NH2 D:ARG226 4.4 28.4 1.0
CG C:ASP145 4.4 17.1 0.5
CG C:ASP145 4.5 17.2 0.5
S1G C:AGS303 4.5 28.0 1.0
PA C:AGS303 4.6 17.4 1.0
NE D:ARG226 4.8 21.1 1.0
O2A C:AGS303 4.8 18.8 1.0
CD C:GLU78 4.9 37.9 1.0
CZ D:ARG226 5.0 25.0 1.0
CB C:LYS52 5.0 15.9 1.0

Magnesium binding site 4 out of 6 in 4tl9

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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:Mg301

b:17.8
occ:1.00
 O2G D:AGS303 1.9 22.0 1.0
OG1 D:THR53 2.0 15.4 1.0
O D:HOH545 2.0 16.9 1.0
O1B D:AGS303 2.1 15.1 1.0
O D:HOH544 2.1 19.4 1.0
O D:HOH543 2.2 21.2 1.0
CB D:THR53 3.1 20.3 1.0
PG D:AGS303 3.2 21.8 1.0
PB D:AGS303 3.3 15.2 1.0
O3B D:AGS303 3.5 17.4 1.0
OD2 D:ASP145 3.8 20.6 0.6
OE1 D:GLU78 3.9 32.0 1.0
N D:THR53 3.9 13.8 1.0
O D:HOH546 4.0 33.6 1.0
OD2 D:ASP145 4.0 18.0 0.5
CA D:THR53 4.1 14.4 1.0
O3G D:AGS303 4.1 23.4 1.0
CG2 D:THR53 4.1 19.1 1.0
OD1 D:ASP145 4.2 22.1 0.5
OD1 D:ASP145 4.2 21.8 0.6
O2A D:AGS303 4.2 18.5 1.0
O D:HOH547 4.2 31.7 1.0
O3A D:AGS303 4.3 14.7 1.0
O2B D:AGS303 4.4 15.0 1.0
CG D:ASP145 4.4 21.2 0.6
CG D:ASP145 4.5 20.1 0.5
NH2 E:ARG226 4.6 25.5 1.0
PA D:AGS303 4.6 15.2 1.0
S1G D:AGS303 4.6 25.2 1.0
NE E:ARG226 4.7 17.0 1.0
O1A D:AGS303 4.8 18.2 1.0
O D:HOH581 4.9 36.1 1.0
CZ E:ARG226 4.9 24.9 1.0
CB D:LYS52 5.0 17.2 1.0

Magnesium binding site 5 out of 6 in 4tl9

Go back to Magnesium Binding Sites List in 4tl9
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:Mg301

b:20.5
occ:1.00
 O2G E:AGS303 1.9 24.5 1.0
OG1 E:THR53 2.0 19.1 1.0
O1B E:AGS303 2.0 14.8 1.0
O E:HOH515 2.1 23.3 1.0
O E:HOH514 2.1 21.6 1.0
O E:HOH516 2.2 19.8 1.0
CB E:THR53 3.0 19.2 1.0
PG E:AGS303 3.1 27.5 1.0
PB E:AGS303 3.3 18.3 1.0
O3B E:AGS303 3.5 21.0 1.0
OD2 E:ASP145 3.8 24.6 0.6
N E:THR53 3.9 15.9 1.0
CA E:THR53 4.0 16.4 1.0
O E:HOH479 4.0 51.4 1.0
O E:HOH463 4.0 32.0 1.0
O3G E:AGS303 4.0 22.7 1.0
OE1 E:GLU78 4.0 34.4 1.0
O2A E:AGS303 4.0 18.5 1.0
OD2 E:ASP145 4.0 24.2 0.4
OD1 E:ASP145 4.1 22.0 0.6
CG2 E:THR53 4.2 17.0 1.0
OD1 E:ASP145 4.2 20.6 0.4
O3A E:AGS303 4.3 18.0 1.0
O2B E:AGS303 4.4 17.4 1.0
CG E:ASP145 4.4 23.5 0.6
PA E:AGS303 4.5 16.8 1.0
CG E:ASP145 4.5 23.2 0.4
S1G E:AGS303 4.5 33.0 1.0
NH2 F:ARG226 4.6 26.8 1.0
O1A E:AGS303 4.7 20.2 1.0
NE F:ARG226 4.8 25.0 1.0
C E:LYS52 5.0 14.6 1.0

Magnesium binding site 6 out of 6 in 4tl9

Go back to Magnesium Binding Sites List in 4tl9
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:Mg301

b:22.2
occ:1.00
 O2G F:AGS303 1.9 25.5 1.0
OG1 F:THR53 2.0 19.1 1.0
O F:HOH510 2.1 26.9 1.0
O F:HOH511 2.1 22.7 1.0
O2B F:AGS303 2.1 18.3 1.0
O F:HOH509 2.2 20.9 1.0
PG F:AGS303 3.1 23.8 1.0
CB F:THR53 3.2 14.5 1.0
PB F:AGS303 3.4 17.8 1.0
O3B F:AGS303 3.6 20.7 1.0
OD2 F:ASP145 3.7 21.5 0.5
N F:THR53 4.0 17.4 1.0
OE2 F:GLU78 4.0 38.8 1.0
O3G F:AGS303 4.0 19.4 1.0
O F:HOH461 4.1 33.4 1.0
OD2 F:ASP145 4.1 20.5 0.6
CA F:THR53 4.1 14.2 1.0
OD1 F:ASP145 4.1 20.1 0.5
O1A F:AGS303 4.1 18.2 1.0
OD1 F:ASP145 4.2 17.2 0.6
CG2 F:THR53 4.2 19.0 1.0
CG F:ASP145 4.3 22.2 0.5
O3A F:AGS303 4.4 16.9 1.0
CG F:ASP145 4.5 22.3 0.6
O1B F:AGS303 4.5 16.0 1.0
NH2 A:ARG226 4.5 30.7 1.0
S1G F:AGS303 4.5 26.5 1.0
PA F:AGS303 4.6 17.2 1.0
NE A:ARG226 4.7 22.8 1.0
O F:HOH500 4.7 41.1 1.0
O2A F:AGS303 4.8 17.4 1.0
CZ A:ARG226 4.9 30.8 1.0
CB F:LYS52 5.0 14.3 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 03:46:06 2024

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