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Magnesium in PDB 4tle: 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: 4tle 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) 42.60 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 79.927, 133.322, 151.057, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22.9

Other elements in 4tle:

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

Magnesium binding site 1 out of 6 in 4tle

Go back to Magnesium Binding Sites List in 4tle
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:35.6
occ:1.00
 O2G A:AGS303 1.9 35.5 1.0
O A:HOH458 2.0 32.2 1.0
O A:HOH457 2.1 37.3 1.0
OG1 A:THR53 2.1 32.7 1.0
O A:HOH456 2.1 38.3 1.0
O2B A:AGS303 2.1 32.2 1.0
PG A:AGS303 3.2 37.4 1.0
CB A:THR53 3.2 33.5 1.0
PB A:AGS303 3.3 32.6 1.0
O3B A:AGS303 3.6 36.1 1.0
OD2 A:ASP145 3.6 38.4 0.5
OE1 A:GLU78 3.9 48.2 1.0
N A:THR53 3.9 28.0 1.0
OD2 A:ASP145 4.0 33.9 0.5
CA A:THR53 4.1 33.9 1.0
O3G A:AGS303 4.1 37.7 1.0
OD1 A:ASP145 4.1 39.3 0.5
OD1 A:ASP145 4.1 38.1 0.5
O2A A:AGS303 4.3 33.3 1.0
CG2 A:THR53 4.3 36.1 1.0
CG A:ASP145 4.3 39.4 0.5
O1B A:AGS303 4.3 30.8 1.0
O3A A:AGS303 4.4 33.4 1.0
CG A:ASP145 4.5 37.0 0.5
NH2 B:ARG226 4.5 48.2 1.0
S1G A:AGS303 4.6 40.7 1.0
NE B:ARG226 4.7 40.9 1.0
PA A:AGS303 4.7 34.1 1.0
O1A A:AGS303 4.9 39.1 1.0
CB A:LYS52 4.9 26.6 1.0
CZ B:ARG226 4.9 49.9 1.0
CD A:GLU78 4.9 54.6 1.0
C A:LYS52 5.0 30.6 1.0

Magnesium binding site 2 out of 6 in 4tle

Go back to Magnesium Binding Sites List in 4tle
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:30.2
occ:1.00
 OG1 B:THR53 1.9 25.8 1.0
O2G B:AGS303 2.0 28.3 1.0
O B:HOH497 2.0 35.2 1.0
O B:HOH498 2.1 29.9 1.0
O2B B:AGS303 2.1 23.4 1.0
O B:HOH499 2.1 29.4 1.0
CB B:THR53 3.1 24.9 1.0
PG B:AGS303 3.2 42.0 1.0
PB B:AGS303 3.3 26.4 1.0
O3B B:AGS303 3.5 33.6 1.0
OD2 B:ASP145 3.9 31.6 0.5
N B:THR53 4.0 20.5 1.0
O B:HOH452 4.0 44.0 1.0
OE1 B:GLU78 4.0 37.7 1.0
O3G B:AGS303 4.0 33.9 1.0
OD2 B:ASP145 4.1 29.9 0.5
CA B:THR53 4.1 21.3 1.0
O2A B:AGS303 4.1 26.0 1.0
OD1 B:ASP145 4.1 31.8 0.5
CG2 B:THR53 4.2 22.7 1.0
OD1 B:ASP145 4.2 33.2 0.5
O3A B:AGS303 4.3 35.0 1.0
O1B B:AGS303 4.4 24.8 1.0
NH2 C:ARG226 4.4 43.3 1.0
CG B:ASP145 4.4 34.5 0.5
CG B:ASP145 4.5 33.4 0.5
PA B:AGS303 4.6 27.1 1.0
NE C:ARG226 4.6 33.3 1.0
S1G B:AGS303 4.6 41.9 1.0
O1A B:AGS303 4.8 28.0 1.0
CZ C:ARG226 4.9 39.5 1.0
O B:HOH477 4.9 51.6 1.0

Magnesium binding site 3 out of 6 in 4tle

Go back to Magnesium Binding Sites List in 4tle
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:30.0
occ:1.00
 O2G C:AGS303 1.9 40.0 1.0
O C:HOH492 2.0 31.1 1.0
O2B C:AGS303 2.0 21.5 1.0
OG1 C:THR53 2.1 28.5 1.0
O C:HOH493 2.1 27.5 1.0
O C:HOH494 2.3 26.4 1.0
PG C:AGS303 3.1 41.7 1.0
CB C:THR53 3.1 29.3 1.0
PB C:AGS303 3.2 26.4 1.0
O3B C:AGS303 3.4 42.5 1.0
OE1 C:GLU78 3.8 43.3 1.0
O3G C:AGS303 3.8 36.5 1.0
OD2 C:ASP145 3.8 33.6 0.5
OD2 C:ASP145 3.9 34.5 0.5
N C:THR53 4.0 23.4 1.0
O2A C:AGS303 4.1 27.8 1.0
O C:HOH480 4.1 43.8 1.0
CA C:THR53 4.1 27.0 1.0
CG2 C:THR53 4.2 26.0 1.0
OD1 C:ASP145 4.2 24.8 0.5
O3A C:AGS303 4.3 25.5 1.0
NH2 D:ARG226 4.3 41.9 1.0
O1B C:AGS303 4.3 28.3 1.0
OD1 C:ASP145 4.3 28.4 0.5
CG C:ASP145 4.5 30.9 0.5
CG C:ASP145 4.5 30.3 0.5
PA C:AGS303 4.5 25.5 1.0
S1G C:AGS303 4.6 41.9 1.0
NE D:ARG226 4.7 36.2 1.0
O1A C:AGS303 4.8 27.0 1.0
CZ D:ARG226 4.9 40.1 1.0
CD C:GLU78 4.9 51.8 1.0

Magnesium binding site 4 out of 6 in 4tle

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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:29.7
occ:1.00
 O2G D:AGS303 1.9 37.5 1.0
OG1 D:THR53 2.0 21.7 1.0
O D:HOH495 2.1 28.7 1.0
O2B D:AGS303 2.1 23.8 1.0
O D:HOH497 2.1 28.1 1.0
O D:HOH496 2.2 30.2 1.0
CB D:THR53 3.1 29.1 1.0
PG D:AGS303 3.2 36.1 1.0
PB D:AGS303 3.3 24.1 1.0
O3B D:AGS303 3.5 37.7 1.0
OD2 D:ASP145 3.8 36.5 0.6
N D:THR53 4.0 24.8 1.0
O3G D:AGS303 4.0 34.5 1.0
OE1 D:GLU78 4.0 34.7 1.0
CA D:THR53 4.1 26.8 1.0
OD2 D:ASP145 4.1 34.5 0.5
CG2 D:THR53 4.2 26.9 1.0
O1A D:AGS303 4.2 29.5 1.0
OD1 D:ASP145 4.2 38.1 0.5
OD1 D:ASP145 4.3 38.2 0.6
O3A D:AGS303 4.3 27.3 1.0
O1B D:AGS303 4.4 24.2 1.0
NH2 E:ARG226 4.4 35.6 1.0
CG D:ASP145 4.5 36.9 0.6
NE E:ARG226 4.5 29.4 1.0
CG D:ASP145 4.5 35.6 0.5
S1G D:AGS303 4.6 43.5 1.0
PA D:AGS303 4.6 26.3 1.0
O2A D:AGS303 4.8 27.9 1.0
CZ E:ARG226 4.8 37.0 1.0

Magnesium binding site 5 out of 6 in 4tle

Go back to Magnesium Binding Sites List in 4tle
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:30.9
occ:1.00
 O2G E:AGS303 1.9 35.8 1.0
O2B E:AGS303 2.0 20.4 1.0
O E:HOH474 2.0 29.2 1.0
OG1 E:THR53 2.1 32.5 1.0
O E:HOH473 2.1 27.7 1.0
O E:HOH475 2.2 26.2 1.0
PG E:AGS303 3.1 35.3 1.0
CB E:THR53 3.2 28.1 1.0
PB E:AGS303 3.3 24.6 1.0
O3B E:AGS303 3.5 29.3 1.0
O3G E:AGS303 3.8 34.3 1.0
OD2 E:ASP145 3.9 26.0 0.4
OD2 E:ASP145 3.9 32.2 0.6
N E:THR53 3.9 23.0 1.0
O E:HOH440 4.0 30.6 1.0
O1A E:AGS303 4.0 23.5 1.0
CA E:THR53 4.1 29.0 1.0
OD1 E:ASP145 4.2 28.0 0.4
OD1 E:ASP145 4.2 28.0 0.6
CG2 E:THR53 4.3 22.6 1.0
O3A E:AGS303 4.3 24.8 1.0
O1B E:AGS303 4.4 22.5 1.0
CG E:ASP145 4.4 29.6 0.4
OE2 E:GLU78 4.5 50.9 1.0
CG E:ASP145 4.5 29.9 0.6
NH2 F:ARG226 4.5 34.2 1.0
S1G E:AGS303 4.6 41.6 1.0
PA E:AGS303 4.6 24.3 1.0
NE F:ARG226 4.7 32.4 1.0
O E:HOH472 4.8 44.3 1.0
O2A E:AGS303 4.8 26.9 1.0
CZ F:ARG226 5.0 34.8 1.0

Magnesium binding site 6 out of 6 in 4tle

Go back to Magnesium Binding Sites List in 4tle
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:28.8
occ:1.00
 O2G F:AGS303 1.9 35.0 1.0
O F:HOH478 2.0 37.3 1.0
OG1 F:THR53 2.0 24.0 1.0
O1B F:AGS303 2.0 23.0 1.0
O F:HOH477 2.1 28.8 1.0
O F:HOH479 2.2 29.9 1.0
PG F:AGS303 3.1 38.1 1.0
CB F:THR53 3.1 24.9 1.0
PB F:AGS303 3.3 26.7 1.0
O3B F:AGS303 3.4 59.1 1.0
OD2 F:ASP145 3.7 27.1 0.4
O F:HOH448 3.9 45.1 1.0
N F:THR53 3.9 25.1 1.0
O3G F:AGS303 4.0 32.4 1.0
CA F:THR53 4.1 22.0 1.0
CG2 F:THR53 4.1 23.6 1.0
OD2 F:ASP145 4.1 29.3 0.6
OD1 F:ASP145 4.1 29.6 0.6
O2A F:AGS303 4.1 28.5 1.0
OD1 F:ASP145 4.2 29.9 0.4
OE1 F:GLU78 4.3 48.5 1.0
O3A F:AGS303 4.3 31.6 1.0
O2B F:AGS303 4.3 22.9 1.0
CG F:ASP145 4.4 30.4 0.4
CG F:ASP145 4.5 30.4 0.6
NH2 A:ARG226 4.5 45.1 1.0
S1G F:AGS303 4.5 38.7 1.0
PA F:AGS303 4.6 27.3 1.0
NE A:ARG226 4.7 32.4 1.0
O1A F:AGS303 4.8 26.6 1.0
CZ A:ARG226 4.9 43.3 1.0
CB F:LYS52 4.9 23.4 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. 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 03:47:36 2024

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