Calcium in PDB 8jc7: Cryo-Em Structure of Vibrio Campbellii Alpha-Hemolysin

The structure of Cryo-Em Structure of Vibrio Campbellii Alpha-Hemolysin also contains other interesting chemical elements:

Potassium

(K)

7 atoms

The binding sites of Calcium atom in the Cryo-Em Structure of Vibrio Campbellii Alpha-Hemolysin (pdb code 8jc7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Cryo-Em Structure of Vibrio Campbellii Alpha-Hemolysin, PDB code: 8jc7:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Cryo-Em Structure of Vibrio Campbellii Alpha-Hemolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of Vibrio Campbellii Alpha-Hemolysin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:95.0 occ:1.00 NE2 A:HIS137 2.3 71.0 1.0 O A:HOH977 2.4 84.4 1.0 O A:HOH978 2.4 92.2 1.0 O A:HOH980 2.5 90.0 1.0 OE1 A:GLU185 2.5 72.3 1.0 O A:HOH979 3.2 87.4 1.0 O A:HOH934 3.3 75.4 1.0 CE1 A:HIS137 3.3 71.0 1.0 CD2 A:HIS137 3.3 71.0 1.0 CD A:GLU185 3.6 72.3 1.0 O A:HOH981 3.6 86.6 1.0 O A:HOH936 4.1 77.5 1.0 OE2 A:GLU185 4.1 72.3 1.0 ND1 A:HIS137 4.4 71.0 1.0 NH1 A:ARG204 4.4 71.0 1.0 CG A:HIS137 4.4 71.0 1.0 CD2 A:LEU135 4.4 74.7 1.0 CG A:GLU185 4.6 72.3 1.0

Calcium binding site 2 out of 7 in the Cryo-Em Structure of Vibrio Campbellii Alpha-Hemolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of Vibrio Campbellii Alpha-Hemolysin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:95.3 occ:1.00 NE2 B:HIS137 2.3 70.8 1.0 O B:HOH980 2.4 86.0 1.0 O B:HOH981 2.4 93.2 1.0 O B:HOH983 2.5 90.7 1.0 OE1 B:GLU185 2.5 72.6 1.0 O B:HOH982 3.2 85.5 1.0 O B:HOH936 3.2 75.7 1.0 CE1 B:HIS137 3.3 70.8 1.0 CD2 B:HIS137 3.3 70.8 1.0 CD B:GLU185 3.5 72.6 1.0 O B:HOH984 3.7 86.2 1.0 O B:HOH937 4.1 77.1 1.0 OE2 B:GLU185 4.1 72.6 1.0 ND1 B:HIS137 4.4 70.8 1.0 NH1 B:ARG204 4.4 72.3 1.0 CG B:HIS137 4.4 70.8 1.0 CD2 B:LEU135 4.5 73.8 1.0 CG B:GLU185 4.6 72.6 1.0

Calcium binding site 3 out of 7 in the Cryo-Em Structure of Vibrio Campbellii Alpha-Hemolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of Vibrio Campbellii Alpha-Hemolysin within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca802 b:95.0 occ:1.00 NE2 C:HIS137 2.3 70.5 1.0 O C:HOH981 2.4 86.3 1.0 O C:HOH982 2.4 94.3 1.0 O C:HOH984 2.5 91.8 1.0 OE1 C:GLU185 2.5 72.2 1.0 O C:HOH983 3.2 87.3 1.0 O C:HOH936 3.2 75.3 1.0 CE1 C:HIS137 3.3 70.5 1.0 CD2 C:HIS137 3.3 70.5 1.0 CD C:GLU185 3.6 72.2 1.0 O C:HOH985 3.6 86.2 1.0 O C:HOH937 4.1 78.8 1.0 OE2 C:GLU185 4.1 72.2 1.0 ND1 C:HIS137 4.4 70.5 1.0 NH1 C:ARG204 4.4 71.0 1.0 CG C:HIS137 4.4 70.5 1.0 CD2 C:LEU135 4.5 74.8 1.0 CG C:GLU185 4.6 72.2 1.0

Calcium binding site 4 out of 7 in the Cryo-Em Structure of Vibrio Campbellii Alpha-Hemolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of Vibrio Campbellii Alpha-Hemolysin within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca802 b:96.8 occ:1.00 NE2 D:HIS137 2.3 70.6 1.0 O D:HOH980 2.4 85.5 1.0 O D:HOH981 2.4 91.5 1.0 O D:HOH983 2.5 89.6 1.0 OE1 D:GLU185 2.5 72.5 1.0 O D:HOH982 3.1 87.0 1.0 CE1 D:HIS137 3.3 70.6 1.0 O D:HOH935 3.3 74.6 1.0 CD2 D:HIS137 3.3 70.6 1.0 CD D:GLU185 3.5 72.5 1.0 O D:HOH984 3.6 82.4 1.0 OE2 D:GLU185 4.1 72.5 1.0 O D:HOH938 4.1 76.9 1.0 ND1 D:HIS137 4.4 70.6 1.0 NH1 D:ARG204 4.4 70.8 1.0 CG D:HIS137 4.4 70.6 1.0 CD2 D:LEU135 4.4 74.3 1.0 CG D:GLU185 4.6 72.5 1.0

Calcium binding site 5 out of 7 in the Cryo-Em Structure of Vibrio Campbellii Alpha-Hemolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cryo-Em Structure of Vibrio Campbellii Alpha-Hemolysin within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca802 b:95.9 occ:1.00 NE2 E:HIS137 2.3 71.0 1.0 O E:HOH982 2.4 84.8 1.0 O E:HOH983 2.4 91.7 1.0 O E:HOH985 2.5 92.1 1.0 OE1 E:GLU185 2.5 72.5 1.0 O E:HOH984 3.2 87.0 1.0 O E:HOH934 3.2 76.6 1.0 CE1 E:HIS137 3.3 71.0 1.0 CD2 E:HIS137 3.3 71.0 1.0 O E:HOH986 3.6 86.2 1.0 CD E:GLU185 3.6 72.5 1.0 O E:HOH936 4.1 78.9 1.0 OE2 E:GLU185 4.1 72.5 1.0 ND1 E:HIS137 4.4 71.0 1.0 NH1 E:ARG204 4.4 70.5 1.0 CG E:HIS137 4.4 71.0 1.0 CD2 E:LEU135 4.5 75.4 1.0 CG E:GLU185 4.6 72.5 1.0

Calcium binding site 6 out of 7 in the Cryo-Em Structure of Vibrio Campbellii Alpha-Hemolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cryo-Em Structure of Vibrio Campbellii Alpha-Hemolysin within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca802 b:94.9 occ:1.00 NE2 F:HIS137 2.3 71.2 1.0 O F:HOH980 2.4 85.0 1.0 O F:HOH981 2.4 92.5 1.0 O F:HOH983 2.5 89.8 1.0 OE1 F:GLU185 2.5 72.1 1.0 O F:HOH982 3.2 86.1 1.0 O F:HOH936 3.2 76.8 1.0 CE1 F:HIS137 3.3 71.2 1.0 CD2 F:HIS137 3.3 71.2 1.0 CD F:GLU185 3.5 72.1 1.0 O F:HOH984 3.6 83.7 1.0 O F:HOH930 4.1 77.1 1.0 OE2 F:GLU185 4.1 72.1 1.0 ND1 F:HIS137 4.4 71.2 1.0 NH1 F:ARG204 4.4 71.3 1.0 CG F:HIS137 4.4 71.2 1.0 CD2 F:LEU135 4.5 74.9 1.0 CG F:GLU185 4.6 72.1 1.0

Calcium binding site 7 out of 7 in the Cryo-Em Structure of Vibrio Campbellii Alpha-Hemolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Cryo-Em Structure of Vibrio Campbellii Alpha-Hemolysin within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca802 b:94.4 occ:1.00 NE2 G:HIS137 2.3 70.5 1.0 O G:HOH983 2.4 83.3 1.0 O G:HOH984 2.4 90.5 1.0 O G:HOH986 2.5 87.8 1.0 OE1 G:GLU185 2.5 73.0 1.0 O G:HOH985 3.2 84.9 1.0 CE1 G:HIS137 3.3 70.5 1.0 O G:HOH939 3.3 74.9 1.0 CD2 G:HIS137 3.3 70.5 1.0 CD G:GLU185 3.6 73.0 1.0 O G:HOH987 3.6 81.3 1.0 OE2 G:GLU185 4.1 73.0 1.0 O G:HOH940 4.1 76.8 1.0 ND1 G:HIS137 4.4 70.5 1.0 NH1 G:ARG204 4.4 70.8 1.0 CG G:HIS137 4.4 70.5 1.0 CD2 G:LEU135 4.5 74.2 1.0 CG G:GLU185 4.6 73.0 1.0

Y.C.Chiu, M.K.Yeh, C.H.Wang, Y.A.Chen, H.Chang, C.H.Yu, H.Y.Lin, M.C.Ho, S.M.Lin. Structural Basis For Calcium-Stimulating Pore Formation of Vibrio Alpha-Hemolysin To Be Published.