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Magnesium in PDB 4tlb: 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: 4tlb 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) 29.43 / 1.98
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.060, 133.562, 150.835, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 19.9

Other elements in 4tlb:

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

Magnesium binding site 1 out of 6 in 4tlb

Go back to Magnesium Binding Sites List in 4tlb
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:20.3
occ:1.00
 O2G A:AGS303 1.9 15.9 1.0
O A:HOH506 2.0 24.3 1.0
OG1 A:THR53 2.0 22.0 1.0
O2B A:AGS303 2.0 16.8 1.0
O A:HOH504 2.1 25.6 1.0
O A:HOH505 2.2 20.5 1.0
CB A:THR53 3.1 22.9 1.0
PG A:AGS303 3.2 19.5 1.0
PB A:AGS303 3.3 20.7 1.0
O3B A:AGS303 3.5 19.6 1.0
O A:HOH445 3.9 27.4 1.0
OD2 A:ASP145 3.9 22.5 1.0
N A:THR53 3.9 16.9 1.0
OE2 A:GLU78 4.0 30.4 1.0
O3G A:AGS303 4.1 18.9 1.0
CA A:THR53 4.1 19.5 1.0
O2A A:AGS303 4.1 18.9 1.0
CG2 A:THR53 4.2 24.8 1.0
OD1 A:ASP145 4.3 30.2 1.0
O1B A:AGS303 4.3 19.6 1.0
O3A A:AGS303 4.3 22.0 1.0
NE B:ARG226 4.5 24.2 1.0
CG A:ASP145 4.5 30.0 1.0
PA A:AGS303 4.5 19.7 1.0
NH2 B:ARG226 4.6 25.6 1.0
S1G A:AGS303 4.7 23.5 1.0
O1A A:AGS303 4.7 22.9 1.0
CZ B:ARG226 4.9 29.9 1.0
CB A:LYS52 4.9 21.5 1.0

Magnesium binding site 2 out of 6 in 4tlb

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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:14.7
occ:1.00
 O2G B:AGS303 2.0 15.6 1.0
OG1 B:THR53 2.0 13.3 1.0
O2B B:AGS303 2.0 15.0 1.0
O B:HOH556 2.1 15.8 1.0
O B:HOH558 2.1 15.8 1.0
O B:HOH557 2.2 16.5 1.0
CB B:THR53 3.1 13.4 1.0
PG B:AGS303 3.2 17.1 1.0
PB B:AGS303 3.2 14.5 1.0
O3B B:AGS303 3.5 16.9 1.0
OE1 B:GLU78 3.9 21.4 1.0
N B:THR53 3.9 13.1 1.0
OD2 B:ASP145 3.9 15.6 1.0
O B:HOH474 4.0 27.2 1.0
CA B:THR53 4.1 13.6 1.0
O2A B:AGS303 4.1 13.8 1.0
O3G B:AGS303 4.1 16.6 1.0
CG2 B:THR53 4.2 13.8 1.0
OD1 B:ASP145 4.2 16.1 1.0
O3A B:AGS303 4.3 17.7 1.0
O1B B:AGS303 4.3 14.7 1.0
O B:HOH535 4.5 45.1 1.0
CG B:ASP145 4.5 23.4 1.0
PA B:AGS303 4.5 14.9 1.0
NE C:ARG226 4.6 19.1 1.0
NH2 C:ARG226 4.6 20.8 1.0
S1G B:AGS303 4.6 20.4 1.0
O1A B:AGS303 4.7 16.6 1.0
O B:HOH531 4.8 35.6 1.0
CZ C:ARG226 4.9 18.9 1.0
CD B:GLU78 5.0 31.0 1.0
CB B:LYS52 5.0 12.5 1.0

Magnesium binding site 3 out of 6 in 4tlb

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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:16.6
occ:1.00
 O2G C:AGS303 2.0 13.4 1.0
O2B C:AGS303 2.0 11.9 1.0
O C:HOH539 2.1 18.1 1.0
OG1 C:THR53 2.1 16.2 1.0
O C:HOH540 2.1 19.5 1.0
O C:HOH541 2.1 15.4 1.0
CB C:THR53 3.1 12.0 1.0
PG C:AGS303 3.2 18.1 1.0
PB C:AGS303 3.3 13.3 1.0
O3B C:AGS303 3.5 15.7 1.0
OE2 C:GLU78 3.8 28.5 1.0
O C:HOH485 3.9 28.5 1.0
OD2 C:ASP145 3.9 17.9 1.0
N C:THR53 3.9 12.1 1.0
O3G C:AGS303 4.1 17.2 1.0
CA C:THR53 4.1 11.9 1.0
O2A C:AGS303 4.1 16.7 1.0
CG2 C:THR53 4.2 12.9 1.0
OD1 C:ASP145 4.2 17.3 1.0
O1B C:AGS303 4.3 15.9 1.0
O3A C:AGS303 4.4 13.2 1.0
CG C:ASP145 4.5 20.6 1.0
NH2 D:ARG226 4.6 25.7 1.0
PA C:AGS303 4.6 13.6 1.0
S1G C:AGS303 4.7 19.8 1.0
NE D:ARG226 4.7 19.2 1.0
O1A C:AGS303 4.8 17.9 1.0
CZ D:ARG226 5.0 25.9 1.0
CD C:GLU78 5.0 36.2 1.0

Magnesium binding site 4 out of 6 in 4tlb

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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:19.7
occ:1.00
 O2G D:AGS303 1.9 20.9 1.0
OG1 D:THR53 2.0 13.9 1.0
O D:HOH547 2.0 14.8 1.0
O2B D:AGS303 2.1 13.3 1.0
O D:HOH545 2.2 17.7 1.0
O D:HOH546 2.2 17.0 1.0
CB D:THR53 3.1 15.1 1.0
PG D:AGS303 3.2 24.0 1.0
PB D:AGS303 3.2 12.6 1.0
O3B D:AGS303 3.6 15.3 1.0
OE1 D:GLU78 3.9 24.5 1.0
OD2 D:ASP145 3.9 18.8 1.0
N D:THR53 3.9 11.8 1.0
O D:HOH511 4.0 27.4 1.0
CA D:THR53 4.0 14.7 1.0
O3G D:AGS303 4.1 23.1 1.0
CG2 D:THR53 4.2 14.8 1.0
O1A D:AGS303 4.2 17.0 1.0
OD1 D:ASP145 4.2 18.8 1.0
O3A D:AGS303 4.3 14.3 1.0
O1B D:AGS303 4.3 15.8 1.0
NH2 E:ARG226 4.4 24.4 1.0
CG D:ASP145 4.5 25.4 1.0
O D:HOH565 4.5 44.4 1.0
NE E:ARG226 4.6 20.1 1.0
PA D:AGS303 4.6 14.9 1.0
S1G D:AGS303 4.6 24.7 1.0
O2A D:AGS303 4.8 14.9 1.0
CZ E:ARG226 4.9 25.8 1.0

Magnesium binding site 5 out of 6 in 4tlb

Go back to Magnesium Binding Sites List in 4tlb
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:16.3
occ:1.00
 O2G E:AGS303 1.9 18.9 1.0
O2B E:AGS303 2.0 9.9 1.0
OG1 E:THR53 2.0 16.4 1.0
O E:HOH532 2.0 16.4 1.0
O E:HOH531 2.1 13.9 1.0
O E:HOH533 2.2 14.4 1.0
CB E:THR53 3.1 19.9 1.0
PG E:AGS303 3.1 19.9 1.0
PB E:AGS303 3.2 12.7 1.0
O3B E:AGS303 3.5 16.9 1.0
N E:THR53 3.9 10.1 1.0
O3G E:AGS303 3.9 17.4 1.0
OD2 E:ASP145 4.0 19.5 1.0
CA E:THR53 4.0 14.8 1.0
O1A E:AGS303 4.0 12.0 1.0
O E:HOH470 4.1 23.7 1.0
OD1 E:ASP145 4.1 19.7 1.0
O E:HOH553 4.1 40.6 1.0
OE1 E:GLU78 4.1 20.9 1.0
CG2 E:THR53 4.1 11.6 1.0
O E:HOH474 4.2 34.9 1.0
O3A E:AGS303 4.2 16.4 1.0
O1B E:AGS303 4.3 12.8 1.0
CG E:ASP145 4.5 18.9 1.0
PA E:AGS303 4.5 12.3 1.0
NE F:ARG226 4.7 16.8 1.0
NH2 F:ARG226 4.7 19.4 1.0
S1G E:AGS303 4.7 24.8 1.0
O2A E:AGS303 4.7 15.2 1.0
CZ F:ARG226 5.0 21.5 1.0
C E:LYS52 5.0 10.0 1.0

Magnesium binding site 6 out of 6 in 4tlb

Go back to Magnesium Binding Sites List in 4tlb
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:17.0
occ:1.00
 O2G F:AGS301 2.0 17.5 1.0
OG1 F:THR53 2.0 16.6 1.0
O1B F:AGS301 2.1 12.9 1.0
O F:HOH540 2.1 16.6 1.0
O F:HOH532 2.2 17.9 1.0
O F:HOH447 2.2 15.6 1.0
CB F:THR53 3.1 16.6 1.0
PG F:AGS301 3.2 19.1 1.0
PB F:AGS301 3.3 15.6 1.0
O3B F:AGS301 3.5 18.1 1.0
N F:THR53 4.0 12.4 1.0
OD2 F:ASP145 4.0 17.1 1.0
O F:HOH541 4.0 26.1 1.0
OE2 F:GLU78 4.0 29.1 1.0
O3G F:AGS301 4.0 18.5 1.0
CA F:THR53 4.1 12.9 1.0
OD1 F:ASP145 4.1 17.9 1.0
CG2 F:THR53 4.1 16.8 1.0
O2A F:AGS301 4.2 18.4 1.0
O F:HOH526 4.4 49.4 1.0
O3A F:AGS301 4.4 14.4 1.0
O2B F:AGS301 4.4 14.0 1.0
CG F:ASP145 4.5 21.0 1.0
NH2 A:ARG226 4.6 23.9 1.0
S1G F:AGS301 4.6 22.3 1.0
PA F:AGS301 4.7 15.4 1.0
NE A:ARG226 4.7 20.5 1.0
O1A F:AGS301 4.8 14.6 1.0
CZ A:ARG226 4.9 27.2 1.0
CE F:LYS52 5.0 24.5 1.0
CB F:LYS52 5.0 16.8 1.0
O F:HOH509 5.0 38.5 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 03:46:51 2024

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