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Chlorine 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:

Magnesium (Mg) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of N-Terminal C1 Domain of Kaic, PDB code: 5yz8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5yz8

Go back to Chlorine Binding Sites List in 5yz8
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl303

b:40.0
occ:1.00
 NE A:ARG218 3.5 24.2 1.0
CE B:LYS232 3.8 35.0 1.0
CD A:ARG218 3.9 24.6 1.0
N A:ILE239 4.0 34.3 1.0
CG2 A:THR238 4.0 32.5 1.0
CB A:THR238 4.0 31.7 1.0
CA A:THR238 4.1 31.4 1.0
CG A:ARG218 4.6 25.1 1.0
C A:THR238 4.6 32.6 1.0
CZ A:ARG218 4.6 24.6 1.0
NZ B:LYS232 4.7 35.8 1.0
O A:ILE239 4.8 42.4 1.0
NH1 A:ARG218 4.8 24.7 1.0
CG B:LYS232 4.9 32.9 1.0
CD B:LYS232 4.9 33.2 1.0
CA A:ILE239 4.9 36.2 1.0

Chlorine binding site 2 out of 6 in 5yz8

Go back to Chlorine Binding Sites List in 5yz8
Chlorine 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 Chlorine with other atoms in the Cl 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
A:Cl304

b:46.3
occ:1.00
 NZ A:LYS232 3.3 40.2 1.0
NE F:ARG218 3.7 29.0 1.0
N F:ILE239 3.9 35.9 1.0
CD F:ARG218 4.1 29.3 1.0
CB F:THR238 4.2 36.4 1.0
CA F:THR238 4.2 35.8 1.0
CE A:LYS232 4.4 39.2 1.0
O F:ILE239 4.4 39.3 1.0
CG2 F:THR238 4.4 37.5 1.0
C F:THR238 4.7 35.9 1.0
CG A:LYS232 4.8 37.2 1.0
CZ F:ARG218 4.8 28.3 1.0
CD A:LYS232 4.8 37.8 1.0
CG F:ARG218 4.9 29.5 1.0
CA F:ILE239 4.9 37.1 1.0
CB F:ILE239 5.0 36.0 1.0

Chlorine binding site 3 out of 6 in 5yz8

Go back to Chlorine Binding Sites List in 5yz8
Chlorine 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 Chlorine with other atoms in the Cl 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
B:Cl303

b:39.4
occ:1.00
 CB B:THR238 3.7 31.6 1.0
CG2 B:THR238 3.9 33.0 1.0
NE B:ARG218 4.0 24.2 1.0
CA B:THR238 4.0 31.1 1.0
N B:ILE239 4.1 33.6 1.0
CE C:LYS232 4.1 37.3 1.0
CD B:ARG218 4.3 24.8 1.0
O B:ILE239 4.5 37.4 1.0
C B:THR238 4.6 32.2 1.0
CG B:ARG218 4.8 25.1 1.0
CG C:LYS232 5.0 34.6 1.0
CD C:LYS232 5.0 35.9 1.0
CZ B:ARG218 5.0 23.9 1.0

Chlorine binding site 4 out of 6 in 5yz8

Go back to Chlorine Binding Sites List in 5yz8
Chlorine 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 Chlorine with other atoms in the Cl 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
C:Cl303

b:44.4
occ:1.00
 NE C:ARG218 3.8 27.5 1.0
CB C:THR238 3.9 28.4 1.0
CG2 C:THR238 3.9 28.7 1.0
N C:ILE239 4.0 31.9 1.0
CA C:THR238 4.0 29.0 1.0
CD C:ARG218 4.3 27.2 1.0
NZ D:LYS232 4.5 31.4 1.0
CE D:LYS232 4.5 30.3 1.0
C C:THR238 4.6 30.6 1.0
O C:ILE239 4.7 34.4 1.0
CZ C:ARG218 4.8 27.9 1.0
NH1 C:ARG218 4.8 28.4 1.0
CG C:ARG218 4.8 27.5 1.0
O C:PHE237 5.0 26.4 1.0

Chlorine binding site 5 out of 6 in 5yz8

Go back to Chlorine Binding Sites List in 5yz8
Chlorine 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 Chlorine with other atoms in the Cl 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
D:Cl303

b:39.4
occ:1.00
 NZ E:LYS232 3.6 35.9 1.0
NE D:ARG218 3.8 29.9 1.0
CB D:THR238 4.0 32.1 1.0
CG2 D:THR238 4.1 33.0 1.0
N D:ILE239 4.2 31.9 1.0
CA D:THR238 4.3 31.1 1.0
CD D:ARG218 4.3 29.7 1.0
CE E:LYS232 4.3 34.6 1.0
O D:ILE239 4.6 33.5 1.0
C D:THR238 4.8 31.0 1.0
CZ D:ARG218 4.8 29.6 1.0
CG D:ARG218 4.8 29.7 1.0
NH1 D:ARG218 4.9 29.5 1.0
CG E:LYS232 4.9 31.5 1.0

Chlorine binding site 6 out of 6 in 5yz8

Go back to Chlorine Binding Sites List in 5yz8
Chlorine 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 Chlorine with other atoms in the Cl 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
E:Cl303

b:48.8
occ:1.00
 CG2 E:THR238 3.7 29.5 1.0
NE E:ARG218 3.7 25.6 1.0
CB E:THR238 3.9 28.8 1.0
N E:ILE239 3.9 30.9 1.0
CA E:THR238 4.0 28.6 1.0
CD E:ARG218 4.1 25.7 1.0
NZ F:LYS232 4.1 37.5 1.0
C E:THR238 4.5 29.3 1.0
O E:ILE239 4.7 34.5 1.0
CG E:ARG218 4.7 26.0 1.0
CE F:LYS232 4.8 36.2 1.0
O E:PHE237 4.8 26.6 1.0
CZ E:ARG218 4.8 25.4 1.0
NH1 E:ARG218 5.0 25.3 1.0
CA E:ILE239 5.0 32.5 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: Fri Jul 26 21:36:44 2024

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