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Calcium in PDB 6rim: Crystal Structure of the Catalytic Domain of the Weissela Oryzae Botulinum Like Toxin

Enzymatic activity of Crystal Structure of the Catalytic Domain of the Weissela Oryzae Botulinum Like Toxin

All present enzymatic activity of Crystal Structure of the Catalytic Domain of the Weissela Oryzae Botulinum Like Toxin:
3.4.24.69;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of the Weissela Oryzae Botulinum Like Toxin, PDB code: 6rim was solved by S.Kosenina, G.Masuyer, P.Stenmark, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.63 / 1.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 57.908, 105.208, 179.621, 101.71, 90.00, 90.00
R / Rfree (%) 15.1 / 20.2

Other elements in 6rim:

The structure of Crystal Structure of the Catalytic Domain of the Weissela Oryzae Botulinum Like Toxin also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Catalytic Domain of the Weissela Oryzae Botulinum Like Toxin (pdb code 6rim). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of the Catalytic Domain of the Weissela Oryzae Botulinum Like Toxin, PDB code: 6rim:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6rim

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Calcium binding site 1 out of 8 in the Crystal Structure of the Catalytic Domain of the Weissela Oryzae Botulinum Like Toxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Catalytic Domain of the Weissela Oryzae Botulinum Like Toxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:47.1
occ:1.00
 O A:HOH951 2.1 44.6 1.0
O A:HOH757 2.4 38.2 1.0
OE2 A:GLU198 2.5 46.0 1.0
O A:HOH604 2.5 63.3 1.0
O A:HOH601 2.9 73.2 1.0
CD A:GLU198 3.3 47.3 1.0
OE1 A:GLU198 3.4 57.6 1.0
OD2 A:ASP85 4.4 37.0 1.0
O A:ALA199 4.6 25.4 1.0
OD1 A:ASP85 4.7 32.8 1.0
CG A:GLU198 4.7 36.2 1.0
N A:ALA199 4.7 22.2 1.0
CA A:GLU198 4.9 26.3 1.0
CG A:ASP85 5.0 32.8 1.0

Calcium binding site 2 out of 8 in 6rim

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Calcium binding site 2 out of 8 in the Crystal Structure of the Catalytic Domain of the Weissela Oryzae Botulinum Like Toxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Catalytic Domain of the Weissela Oryzae Botulinum Like Toxin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:51.7
occ:1.00
 O B:HOH910 2.3 54.1 1.0
O B:HOH988 2.3 59.0 1.0
OE2 B:GLU198 2.5 41.5 1.0
O B:HOH653 2.7 56.1 1.0
O B:HOH683 2.7 49.8 1.0
O B:HOH943 3.0 61.6 1.0
CD B:GLU198 3.5 44.3 1.0
O B:HOH659 3.6 47.9 1.0
OE1 B:GLU198 3.9 55.7 1.0
O B:ALA199 4.5 28.3 1.0
N B:ALA199 4.6 22.5 1.0
OD1 B:ASP85 4.7 37.0 1.0
OD2 B:ASP85 4.7 40.8 1.0
CG B:GLU198 4.8 33.7 1.0
CA B:GLU198 4.9 26.5 1.0

Calcium binding site 3 out of 8 in 6rim

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Calcium binding site 3 out of 8 in the Crystal Structure of the Catalytic Domain of the Weissela Oryzae Botulinum Like Toxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Catalytic Domain of the Weissela Oryzae Botulinum Like Toxin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:50.3
occ:1.00
 O C:HOH922 2.0 51.5 1.0
O C:HOH626 2.4 61.9 1.0
O C:HOH671 2.5 67.7 1.0
OE1 C:GLU198 2.5 43.6 1.0
O C:HOH739 2.5 39.9 1.0
CD C:GLU198 3.4 43.0 1.0
OE2 C:GLU198 3.6 60.6 1.0
OD2 C:ASP85 4.5 35.2 1.0
O C:ALA199 4.6 26.4 1.0
OD1 C:ASP85 4.6 30.9 1.0
N C:ALA199 4.7 21.0 1.0
CG C:GLU198 4.8 34.8 1.0
CA C:GLU198 4.9 25.1 1.0

Calcium binding site 4 out of 8 in 6rim

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Calcium binding site 4 out of 8 in the Crystal Structure of the Catalytic Domain of the Weissela Oryzae Botulinum Like Toxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Catalytic Domain of the Weissela Oryzae Botulinum Like Toxin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:55.4
occ:1.00
 O D:HOH650 2.4 48.3 1.0
OE2 D:GLU198 2.5 47.4 1.0
O D:HOH936 2.5 70.7 1.0
O D:HOH691 2.5 60.4 1.0
O D:HOH972 2.9 62.7 1.0
O D:HOH626 3.3 64.0 1.0
CD D:GLU198 3.6 43.0 1.0
OE1 D:GLU198 4.0 53.6 1.0
O D:ALA199 4.6 26.1 1.0
N D:ALA199 4.7 23.2 1.0
OD1 D:ASP85 4.7 36.0 1.0
OD2 D:ASP85 4.7 40.2 1.0
CG D:GLU198 4.9 33.5 1.0
CA D:GLU198 4.9 26.5 1.0

Calcium binding site 5 out of 8 in 6rim

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Calcium binding site 5 out of 8 in the Crystal Structure of the Catalytic Domain of the Weissela Oryzae Botulinum Like Toxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Catalytic Domain of the Weissela Oryzae Botulinum Like Toxin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca502

b:46.3
occ:1.00
 O E:HOH1034 2.2 57.1 1.0
O E:HOH708 2.3 47.6 1.0
O E:HOH734 2.4 38.0 1.0
OE1 E:GLU198 2.5 39.5 1.0
O E:HOH842 2.5 54.1 1.0
O E:HOH971 2.6 59.9 1.0
O E:HOH601 3.1 73.2 1.0
CD E:GLU198 3.5 42.1 1.0
OE2 E:GLU198 3.8 57.2 1.0
O E:ALA199 4.5 24.2 1.0
OD2 E:ASP85 4.6 32.2 1.0
N E:ALA199 4.7 25.3 1.0
OD1 E:ASP85 4.8 31.2 1.0
CG E:GLU198 4.8 33.6 1.0
CA E:GLU198 4.9 23.8 1.0
OH E:TYR412 4.9 45.7 1.0

Calcium binding site 6 out of 8 in 6rim

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Calcium binding site 6 out of 8 in the Crystal Structure of the Catalytic Domain of the Weissela Oryzae Botulinum Like Toxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Catalytic Domain of the Weissela Oryzae Botulinum Like Toxin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca502

b:52.5
occ:1.00
 O F:HOH857 2.2 53.6 1.0
O F:HOH1016 2.3 53.7 1.0
O F:HOH835 2.3 60.4 1.0
O F:HOH949 2.4 71.9 1.0
O F:HOH674 2.4 48.6 1.0
OE1 F:GLU198 2.7 40.3 1.0
O F:HOH929 2.7 50.5 1.0
CD F:GLU198 3.6 42.0 1.0
OE2 F:GLU198 3.9 57.7 1.0
O F:ALA199 4.6 24.2 1.0
OD2 F:ASP85 4.6 44.6 1.0
N F:ALA199 4.6 27.2 1.0
OD1 F:ASP85 4.7 42.3 1.0
CA F:GLU198 5.0 28.8 1.0
CG F:GLU198 5.0 36.3 1.0

Calcium binding site 7 out of 8 in 6rim

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Calcium binding site 7 out of 8 in the Crystal Structure of the Catalytic Domain of the Weissela Oryzae Botulinum Like Toxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of the Catalytic Domain of the Weissela Oryzae Botulinum Like Toxin within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca502

b:43.4
occ:1.00
 O G:HOH613 2.3 61.5 1.0
O G:HOH820 2.4 44.0 1.0
O G:HOH972 2.4 63.4 1.0
O G:HOH646 2.5 43.7 1.0
OE1 G:GLU198 2.5 35.1 1.0
O G:HOH964 2.7 51.6 1.0
CD G:GLU198 3.5 44.0 1.0
OE2 G:GLU198 4.0 58.2 1.0
O G:ALA199 4.5 21.2 1.0
N G:ALA199 4.6 19.0 1.0
OD2 G:ASP85 4.7 34.1 1.0
OD1 G:ASP85 4.8 33.3 1.0
CG G:GLU198 4.8 35.4 1.0
OH G:TYR412 4.9 49.2 1.0
CA G:GLU198 4.9 23.4 1.0

Calcium binding site 8 out of 8 in 6rim

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Calcium binding site 8 out of 8 in the Crystal Structure of the Catalytic Domain of the Weissela Oryzae Botulinum Like Toxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of the Catalytic Domain of the Weissela Oryzae Botulinum Like Toxin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca502

b:48.8
occ:1.00
 O H:HOH1016 2.2 57.9 1.0
O H:HOH879 2.3 56.8 1.0
O H:HOH756 2.4 44.1 1.0
O H:HOH936 2.4 53.5 1.0
O H:HOH818 2.4 43.9 1.0
OE2 H:GLU198 2.7 38.9 1.0
O H:HOH602 2.7 49.1 1.0
CD H:GLU198 3.6 44.4 1.0
OE1 H:GLU198 3.9 52.1 1.0
O H:ALA199 4.6 23.6 1.0
OD2 H:ASP85 4.6 42.0 1.0
N H:ALA199 4.7 25.4 1.0
OD1 H:ASP85 4.9 40.3 1.0

Reference:

S.Kosenina, G.Masuyer, S.Zhang, M.Dong, P.Stenmark. Crystal Structure of the Catalytic Domain of the Weissella Oryzae Botulinum-Like Toxin. Febs Lett. V. 593 1403 2019.
ISSN: ISSN 0014-5793
PubMed: 31111466
DOI: 10.1002/1873-3468.13446
Page generated: Tue Jul 16 14:21:54 2024

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