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Magnesium in PDB 4tla: 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: 4tla 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) 38.88 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 79.785, 133.593, 153.977, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 21.7

Other elements in 4tla:

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

Magnesium binding site 1 out of 6 in 4tla

Go back to Magnesium Binding Sites List in 4tla
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:48.8
occ:1.00
 O3G A:ANP301 1.8 39.3 0.6
OG1 A:THR53 2.0 35.8 1.0
O A:HOH453 2.1 37.6 1.0
O1B A:ANP301 2.1 30.6 1.0
O A:HOH451 2.2 48.1 1.0
O A:HOH452 2.3 48.8 1.0
CB A:THR53 3.2 33.5 1.0
PG A:ANP301 3.2 45.2 0.6
PB A:ANP301 3.3 32.8 1.0
OD2 A:ASP145 3.7 45.8 0.5
N3B A:ANP301 3.7 36.3 1.0
N A:THR53 3.9 27.3 1.0
O A:HOH454 3.9 59.5 1.0
OD1 A:ASP145 3.9 50.8 0.5
OE2 A:GLU78 4.0 63.9 1.0
O1G A:ANP301 4.0 60.8 1.0
CA A:THR53 4.0 31.8 1.0
O2G A:ANP301 4.2 46.6 0.8
OD2 A:ASP145 4.2 44.8 0.5
CG2 A:THR53 4.2 33.2 1.0
OD1 A:ASP145 4.3 48.2 0.5
O1A A:ANP301 4.4 34.1 1.0
O2B A:ANP301 4.4 34.1 1.0
CG A:ASP145 4.4 48.1 0.5
O3A A:ANP301 4.4 41.9 1.0
CG A:ASP145 4.5 46.4 0.5
NH2 B:ARG226 4.6 43.7 1.0
NE B:ARG226 4.7 45.3 1.0
PA A:ANP301 4.8 37.2 1.0
O2A A:ANP301 4.9 38.9 1.0
CE A:LYS52 4.9 34.4 1.0
CB A:LYS52 5.0 31.9 1.0
C A:LYS52 5.0 27.9 1.0

Magnesium binding site 2 out of 6 in 4tla

Go back to Magnesium Binding Sites List in 4tla
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:35.5
occ:1.00
 OG1 B:THR53 2.0 31.1 1.0
O2B B:ADP301 2.1 26.5 1.0
O B:HOH506 2.1 30.0 1.0
O B:HOH504 2.2 36.7 1.0
O B:HOH505 2.2 34.5 1.0
O B:HOH503 2.3 34.1 1.0
CB B:THR53 3.1 28.4 1.0
PB B:ADP301 3.3 27.7 1.0
O1B B:ADP301 3.6 28.2 1.0
OD1 B:ASP145 3.7 38.8 0.3
OD2 B:ASP145 3.8 37.8 0.3
N B:THR53 3.8 24.5 1.0
CA B:THR53 4.0 24.6 1.0
OD2 B:ASP145 4.0 35.6 0.7
OD1 B:ASP145 4.1 40.3 0.7
OE2 B:GLU77 4.1 61.5 0.6
OE2 B:GLU78 4.1 55.0 1.0
CG B:ASP145 4.2 38.8 0.3
O1A B:ADP301 4.2 28.1 1.0
CG2 B:THR53 4.2 29.1 1.0
O B:HOH519 4.2 54.1 1.0
O3A B:ADP301 4.3 31.6 1.0
NH2 C:ARG226 4.3 42.5 1.0
O3B B:ADP301 4.4 31.2 1.0
NZ C:LYS224 4.4 31.6 0.7
CG B:ASP145 4.4 39.1 0.7
PA B:ADP301 4.6 29.3 1.0
O2A B:ADP301 4.7 32.1 1.0
NE C:ARG226 4.8 38.5 1.0
CD B:GLU77 4.8 66.5 0.6
CB B:LYS52 4.9 29.6 1.0
C B:LYS52 4.9 26.1 1.0
CE B:LYS52 5.0 28.5 1.0
CZ C:ARG226 5.0 47.7 1.0

Magnesium binding site 3 out of 6 in 4tla

Go back to Magnesium Binding Sites List in 4tla
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:31.7
occ:1.00
 O1B C:ADP301 2.0 28.9 1.0
OG1 C:THR53 2.0 29.8 1.0
O D:HOH539 2.1 30.3 1.0
O C:HOH495 2.2 30.5 1.0
O C:HOH493 2.2 28.6 1.0
O C:HOH494 2.3 36.2 1.0
CB C:THR53 3.1 31.9 1.0
PB C:ADP301 3.2 27.9 1.0
O2B C:ADP301 3.7 29.6 1.0
N C:THR53 3.9 24.8 1.0
NZ D:LYS224 3.9 28.9 1.0
OE1 C:GLU77 4.0 39.7 1.0
O1A C:ADP301 4.0 29.2 1.0
OD2 C:ASP145 4.0 37.9 1.0
CA C:THR53 4.0 29.1 1.0
OD1 C:ASP145 4.0 37.7 1.0
OE2 C:GLU78 4.1 38.9 1.0
O3A C:ADP301 4.2 27.2 1.0
CG2 C:THR53 4.2 31.9 1.0
O3B C:ADP301 4.3 26.9 1.0
O C:HOH438 4.4 37.8 1.0
PA C:ADP301 4.5 27.4 1.0
CG C:ASP145 4.5 36.5 1.0
NH2 D:ARG226 4.6 38.2 1.0
O2A C:ADP301 4.7 32.0 1.0
CE C:LYS52 4.7 28.3 1.0
O C:HOH414 4.8 22.5 1.0
CB C:LYS52 4.8 26.6 1.0
NZ C:LYS52 4.9 29.0 1.0
CD C:GLU77 5.0 45.0 1.0
C C:LYS52 5.0 28.7 1.0

Magnesium binding site 4 out of 6 in 4tla

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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:29.6
occ:1.00
 O1B D:ADP301 2.0 25.9 1.0
O D:HOH537 2.0 29.9 1.0
O D:HOH538 2.1 30.9 1.0
OG1 D:THR53 2.1 25.1 1.0
O D:HOH535 2.1 30.8 1.0
O D:HOH536 2.2 27.7 1.0
CB D:THR53 3.2 27.6 1.0
PB D:ADP301 3.2 24.5 1.0
O3B D:ADP301 3.5 27.3 1.0
N D:THR53 3.9 25.1 1.0
OD2 D:ASP145 4.0 34.0 1.0
OE2 D:GLU77 4.0 48.8 0.5
OE2 D:GLU78 4.1 38.2 1.0
CA D:THR53 4.1 27.2 1.0
O2A D:ADP301 4.1 28.1 1.0
OD1 D:ASP145 4.1 41.2 1.0
CG2 D:THR53 4.3 27.5 1.0
O3A D:ADP301 4.3 24.7 1.0
O D:HOH472 4.3 46.1 1.0
O D:HOH483 4.3 47.4 1.0
NH2 E:ARG226 4.3 36.3 1.0
O2B D:ADP301 4.4 26.4 1.0
O E:HOH444 4.4 36.3 1.0
CG D:ASP145 4.5 35.7 1.0
PA D:ADP301 4.5 25.2 1.0
OG D:SER146 4.7 60.5 1.0
NE E:ARG226 4.8 32.9 1.0
O1A D:ADP301 4.8 24.4 1.0
CB D:LYS52 4.9 25.1 1.0
CD D:GLU77 4.9 50.4 0.5
CE D:LYS52 5.0 29.8 1.0
CZ E:ARG226 5.0 39.1 1.0
C D:LYS52 5.0 25.3 1.0

Magnesium binding site 5 out of 6 in 4tla

Go back to Magnesium Binding Sites List in 4tla
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:27.0
occ:1.00
 O E:HOH519 2.1 26.7 1.0
OG1 E:THR53 2.1 28.3 1.0
O E:HOH522 2.1 25.1 1.0
O1B E:ADP301 2.1 20.1 1.0
O E:HOH520 2.2 24.0 1.0
O E:HOH521 2.3 25.3 1.0
CB E:THR53 3.2 25.2 1.0
PB E:ADP301 3.4 22.7 1.0
O2B E:ADP301 3.7 24.0 1.0
OE1 E:GLU77 3.9 30.7 1.0
NZ F:LYS224 3.9 29.1 1.0
OD2 E:ASP145 4.0 36.4 1.0
OD1 E:ASP145 4.1 31.4 1.0
N E:THR53 4.1 23.4 1.0
O2A E:ADP301 4.1 26.8 1.0
CA E:THR53 4.2 23.2 1.0
CG2 E:THR53 4.2 26.2 1.0
OE1 E:GLU78 4.2 43.3 1.0
O3A E:ADP301 4.3 22.9 1.0
O E:HOH450 4.5 30.2 1.0
NH2 F:ARG226 4.5 30.4 1.0
CG E:ASP145 4.5 29.2 1.0
O3B E:ADP301 4.5 24.3 1.0
PA E:ADP301 4.6 24.0 1.0
O1A E:ADP301 4.8 26.3 1.0
CD E:GLU77 4.8 36.7 1.0
CE E:LYS52 4.9 23.9 1.0
NZ E:LYS52 4.9 20.9 1.0

Magnesium binding site 6 out of 6 in 4tla

Go back to Magnesium Binding Sites List in 4tla
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:31.7
occ:1.00
 O2G F:ANP301 1.9 22.7 0.6
O2B F:ANP301 2.0 24.2 1.0
OG1 F:THR53 2.0 28.3 1.0
O F:HOH520 2.1 28.7 1.0
O F:HOH519 2.2 28.2 1.0
O F:HOH518 2.2 34.1 1.0
PG F:ANP301 3.1 30.9 0.4
PB F:ANP301 3.2 25.6 1.0
CB F:THR53 3.2 24.5 1.0
N3B F:ANP301 3.6 29.5 1.0
O3G F:ANP301 3.9 38.6 0.9
N F:THR53 3.9 22.0 1.0
OD2 F:ASP145 3.9 35.0 1.0
OE2 F:GLU78 4.0 44.3 1.0
CA F:THR53 4.1 23.9 1.0
OD1 F:ASP145 4.1 36.8 1.0
O1A F:ANP301 4.1 25.4 1.0
CG2 F:THR53 4.2 28.5 1.0
O3A F:ANP301 4.2 26.0 1.0
O1G F:ANP301 4.3 32.3 0.6
O1B F:ANP301 4.3 22.4 1.0
CG F:ASP145 4.5 37.5 1.0
O F:HOH463 4.5 41.2 1.0
PA F:ANP301 4.5 27.1 1.0
NH2 A:ARG226 4.6 43.6 1.0
O2A F:ANP301 4.7 30.0 1.0
NE A:ARG226 4.8 37.5 1.0
NZ F:LYS52 4.9 23.8 1.0
CB F:LYS52 5.0 26.2 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 03:46:07 2024

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