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Magnesium in PDB 5yz8: 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: 5yz8 was solved by A.Mukaiyama, Y.Furuike, J.Abe, S.Akiyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.81
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 108.072, 108.072, 224.069, 90.00, 90.00, 120.00
R / Rfree (%) 24.1 / 30

Other elements in 5yz8:

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 5yz8). 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: 5yz8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5yz8

Go back to Magnesium Binding Sites List in 5yz8
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:32.8
occ:1.00
 O1G A:ANP301 1.8 39.3 1.0
O A:HOH403 1.9 27.0 1.0
OG1 A:THR53 1.9 31.1 1.0
O A:HOH404 2.1 23.8 1.0
O1B A:ANP301 2.3 34.2 1.0
PG A:ANP301 3.0 38.9 1.0
CB A:THR53 3.2 30.9 1.0
N3B A:ANP301 3.4 35.6 1.0
PB A:ANP301 3.5 32.5 1.0
O2G A:ANP301 3.7 39.0 1.0
OD1 A:ASP145 3.8 45.0 0.5
O2A A:ANP301 3.8 32.2 1.0
OD2 A:ASP145 3.9 45.0 0.5
OD1 A:ASP145 4.0 45.4 0.5
NH2 B:ARG226 4.1 35.9 1.0
CG2 A:THR53 4.1 31.4 1.0
OD2 A:ASP145 4.1 44.1 0.5
N A:THR53 4.2 29.8 1.0
CA A:THR53 4.2 30.3 1.0
O3G A:ANP301 4.3 38.3 1.0
OE2 A:GLU78 4.3 55.9 1.0
CG A:ASP145 4.3 45.2 0.5
CG A:ASP145 4.4 44.6 0.5
NE B:ARG226 4.5 36.1 1.0
O2B A:ANP301 4.5 33.0 1.0
O3A A:ANP301 4.5 33.1 1.0
CZ B:ARG226 4.6 36.7 1.0
PA A:ANP301 4.6 32.7 1.0

Magnesium binding site 2 out of 6 in 5yz8

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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:40.2
occ:1.00
 O1G B:ANP301 1.8 33.6 1.0
OG1 B:THR53 2.0 33.6 1.0
O B:HOH403 2.0 24.5 1.0
O B:HOH401 2.3 15.8 1.0
O1B B:ANP301 2.5 30.4 1.0
PG B:ANP301 3.2 33.2 1.0
CB B:THR53 3.3 32.8 1.0
PB B:ANP301 3.7 29.6 1.0
N3B B:ANP301 3.7 31.1 1.0
O3G B:ANP301 3.8 33.1 1.0
OD1 B:ASP145 3.9 40.8 0.5
OD2 B:ASP145 4.1 36.6 0.5
O2A B:ANP301 4.1 28.9 1.0
CG2 B:THR53 4.2 33.1 1.0
N B:THR53 4.2 31.7 1.0
OD1 B:ASP145 4.2 37.1 0.5
OD2 B:ASP145 4.3 40.8 0.5
CA B:THR53 4.3 32.9 1.0
O2G B:ANP301 4.3 32.0 1.0
NH2 C:ARG226 4.4 34.1 1.0
CG B:ASP145 4.5 40.4 0.5
NE C:ARG226 4.5 33.0 1.0
CG B:ASP145 4.6 37.8 0.5
O2B B:ANP301 4.7 28.3 1.0
O3A B:ANP301 4.7 30.2 1.0
PA B:ANP301 4.8 29.3 1.0
CZ C:ARG226 4.8 33.7 1.0

Magnesium binding site 3 out of 6 in 5yz8

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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:Mg302

b:26.6
occ:1.00
 O2G C:ANP301 1.9 37.0 1.0
O2B C:ANP301 2.0 31.3 1.0
OG1 C:THR53 2.1 27.2 1.0
O C:HOH401 2.2 28.4 1.0
O C:HOH403 2.2 25.9 1.0
PG C:ANP301 3.1 37.2 1.0
PB C:ANP301 3.2 30.8 1.0
N3B C:ANP301 3.3 33.5 1.0
CB C:THR53 3.3 27.3 1.0
O2A C:ANP301 3.4 30.4 1.0
O1G C:ANP301 3.9 36.3 1.0
N C:THR53 4.1 26.6 1.0
OD1 C:ASP145 4.1 48.2 0.5
OD2 C:ASP145 4.1 42.5 0.5
O3A C:ANP301 4.2 30.8 1.0
OD2 C:ASP145 4.2 47.5 0.5
CA C:THR53 4.2 27.5 1.0
NH2 D:ARG226 4.3 35.5 1.0
OE1 C:GLU78 4.3 53.4 1.0
O3G C:ANP301 4.3 36.1 1.0
O1B C:ANP301 4.3 31.8 1.0
CG2 C:THR53 4.3 27.0 1.0
PA C:ANP301 4.3 29.8 1.0
OD1 C:ASP145 4.4 44.1 0.5
NE D:ARG226 4.5 34.5 1.0
CG C:ASP145 4.5 47.7 0.5
CG C:ASP145 4.6 44.1 0.5
CZ D:ARG226 4.8 35.0 1.0
O1A C:ANP301 5.0 29.6 1.0

Magnesium binding site 4 out of 6 in 5yz8

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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:19.9
occ:1.00
 O3G D:ANP301 1.8 42.4 1.0
OG1 D:THR53 1.9 31.2 1.0
O D:HOH401 2.1 26.3 1.0
O D:HOH406 2.2 19.0 1.0
O2B D:ANP301 2.2 33.2 1.0
PG D:ANP301 3.1 40.7 1.0
CB D:THR53 3.3 29.5 1.0
PB D:ANP301 3.4 33.0 1.0
N3B D:ANP301 3.5 37.2 1.0
OD1 D:ASP145 3.8 37.6 0.5
O1G D:ANP301 3.8 39.6 1.0
OD2 D:ASP145 3.9 33.9 0.5
NH2 E:ARG226 4.0 36.5 1.0
O D:HOH404 4.1 27.7 1.0
N D:THR53 4.1 27.5 1.0
O2A D:ANP301 4.1 33.8 1.0
OD1 D:ASP145 4.2 34.8 0.5
CG2 D:THR53 4.2 29.4 1.0
CA D:THR53 4.2 29.0 1.0
O2G D:ANP301 4.2 41.4 1.0
OD2 D:ASP145 4.3 37.9 0.5
CG D:ASP145 4.4 35.4 0.5
CG D:ASP145 4.4 37.6 0.5
O1B D:ANP301 4.4 32.5 1.0
NE E:ARG226 4.5 36.5 1.0
O3A D:ANP301 4.6 34.5 1.0
CZ E:ARG226 4.6 36.6 1.0
PA D:ANP301 4.7 35.2 1.0
O1A D:ANP301 5.0 35.2 1.0

Magnesium binding site 5 out of 6 in 5yz8

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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:33.4
occ:1.00
 O2G E:ANP301 1.9 35.6 1.0
OG1 E:THR53 2.0 36.9 1.0
O E:HOH405 2.0 33.5 1.0
O E:HOH401 2.3 18.8 1.0
O2B E:ANP301 2.5 32.4 1.0
PG E:ANP301 3.1 35.3 1.0
CB E:THR53 3.4 35.1 1.0
N3B E:ANP301 3.6 33.1 1.0
PB E:ANP301 3.6 31.4 1.0
OD1 E:ASP145 3.6 40.5 0.5
OD2 E:ASP145 3.6 41.1 0.5
O3G E:ANP301 3.6 34.6 1.0
OD2 E:ASP145 4.0 40.9 0.5
O1A E:ANP301 4.0 34.9 1.0
OD1 E:ASP145 4.2 42.5 0.5
CG E:ASP145 4.2 41.2 0.5
N E:THR53 4.2 32.3 1.0
CG E:ASP145 4.2 41.6 0.5
CG2 E:THR53 4.2 34.9 1.0
CA E:THR53 4.3 33.9 1.0
O1G E:ANP301 4.4 34.2 1.0
NH2 F:ARG226 4.6 42.8 1.0
O1B E:ANP301 4.6 31.3 1.0
NE F:ARG226 4.7 39.5 1.0
O3A E:ANP301 4.7 33.1 1.0
PA E:ANP301 4.8 33.4 1.0
CZ F:ARG226 4.9 41.9 1.0

Magnesium binding site 6 out of 6 in 5yz8

Go back to Magnesium Binding Sites List in 5yz8
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:53.0
occ:1.00
 O3G F:ANP301 1.9 44.7 1.0
OG1 F:THR53 2.0 34.9 1.0
O F:HOH403 2.2 27.9 1.0
O F:HOH402 2.4 35.2 1.0
O1B F:ANP301 2.5 35.1 1.0
PG F:ANP301 3.2 43.9 1.0
CB F:THR53 3.3 33.9 1.0
OD1 F:ASP145 3.5 52.2 0.5
OD1 F:ASP145 3.6 51.0 0.5
PB F:ANP301 3.7 35.5 1.0
N3B F:ANP301 3.7 39.3 1.0
O2G F:ANP301 3.9 43.5 1.0
OD2 F:ASP145 3.9 49.5 0.5
OD2 F:ASP145 3.9 50.9 0.5
CG F:ASP145 4.1 51.6 0.5
N F:THR53 4.1 32.4 1.0
CG F:ASP145 4.1 50.9 0.5
CG2 F:THR53 4.2 33.5 1.0
O1A F:ANP301 4.2 40.1 1.0
CA F:THR53 4.2 33.6 1.0
NH2 A:ARG226 4.2 33.2 1.0
O1G F:ANP301 4.4 42.9 1.0
NE A:ARG226 4.5 33.1 1.0
CZ A:ARG226 4.7 32.9 1.0
O3A F:ANP301 4.7 37.8 1.0
O2B F:ANP301 4.7 33.4 1.0
PA F:ANP301 4.8 39.6 1.0
O2A F:ANP301 4.9 39.1 1.0

Reference:

A.Mukaiyama, Y.Furuike, J.Abe, E.Yamashita, T.Kondo, S.Akiyama. Conformational Rearrangements of the C1 Ring in Kaic Measure the Timing of Assembly with Kaib. Sci Rep V. 8 8803 2018.
ISSN: ESSN 2045-2322
PubMed: 29892030
DOI: 10.1038/S41598-018-27131-8
Page generated: Mon Sep 30 11:40:21 2024

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