Calcium in PDB 3ded: C-Terminal Domain of Probable Hemolysin From Chromobacterium Violaceum

The structure of C-Terminal Domain of Probable Hemolysin From Chromobacterium Violaceum, PDB code: 3ded was solved by C.Chang, X.Xu, H.Cui, A.Savchenko, A.Edwards, A.Joachimiak, Midwest Centerfor Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.14
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.144, 55.312, 93.734, 90.00, 94.34, 90.00
R / Rfree (%)	18.6 / 23.5

The binding sites of Calcium atom in the C-Terminal Domain of Probable Hemolysin From Chromobacterium Violaceum (pdb code 3ded). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the C-Terminal Domain of Probable Hemolysin From Chromobacterium Violaceum, PDB code: 3ded:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in the C-Terminal Domain of Probable Hemolysin From Chromobacterium Violaceum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of C-Terminal Domain of Probable Hemolysin From Chromobacterium Violaceum within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:20.5 occ:1.00 OD1 A:ASP412 2.4 21.6 1.0 O B:HOH510 2.4 17.3 1.0 O A:MSE413 2.4 22.7 1.0 OD1 A:ASP414 2.5 26.2 1.0 O A:HOH509 2.5 24.4 1.0 OD2 B:ASP419 2.5 21.2 1.0 O B:HOH514 2.5 18.9 1.0 OD2 A:ASP412 2.9 25.4 1.0 CG A:ASP412 3.0 21.5 1.0 CG B:ASP419 3.4 22.1 1.0 C A:MSE413 3.5 23.7 1.0 CG A:ASP414 3.6 26.6 1.0 OD1 B:ASP419 3.7 21.9 1.0 CA A:CA505 3.8 20.2 1.0 O B:HOH512 3.8 17.6 1.0 CA A:ASP414 4.1 24.9 1.0 N A:ASP414 4.2 24.0 1.0 NZ B:LYS420 4.2 22.0 1.0 N A:MSE413 4.3 23.6 1.0 OD2 A:ASP414 4.4 26.7 1.0 CB A:ASP412 4.4 21.5 1.0 O A:HOH517 4.5 23.8 1.0 O B:HOH574 4.5 27.0 1.0 CB A:ASP414 4.5 25.3 1.0 OD2 B:ASP354 4.5 32.4 1.0 O A:HOH544 4.6 36.5 1.0 O B:HOH576 4.6 22.3 1.0 CA A:MSE413 4.6 23.6 1.0 OD2 B:ASP414 4.7 23.3 1.0 CB B:ASP419 4.8 23.0 1.0 O B:ASP419 4.8 22.3 1.0 CE B:LYS420 4.9 23.5 1.0 C A:ASP412 4.9 22.3 1.0 CA A:ASP412 5.0 22.2 1.0

Calcium binding site 2 out of 9 in the C-Terminal Domain of Probable Hemolysin From Chromobacterium Violaceum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of C-Terminal Domain of Probable Hemolysin From Chromobacterium Violaceum within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:20.2 occ:1.00 OD2 A:ASP412 2.3 25.4 1.0 OD2 B:ASP412 2.3 28.2 1.0 OD2 A:ASP414 2.4 26.7 1.0 OD2 A:ASP419 2.4 22.0 1.0 OD2 B:ASP419 2.5 21.2 1.0 OD2 B:ASP414 2.5 23.3 1.0 OD1 B:ASP414 2.6 24.3 1.0 OD1 A:ASP414 2.8 26.2 1.0 CG B:ASP414 2.9 24.0 1.0 CG A:ASP414 2.9 26.6 1.0 CG A:ASP419 3.3 23.4 1.0 CG B:ASP419 3.3 22.1 1.0 CG A:ASP412 3.4 21.5 1.0 CG B:ASP412 3.4 23.1 1.0 CA B:CA506 3.7 22.4 1.0 CA A:CA504 3.8 20.5 1.0 CB A:ASP419 3.8 24.7 1.0 CB B:ASP419 3.9 23.0 1.0 OD1 B:ASP412 4.0 19.1 1.0 OD1 A:ASP412 4.1 21.6 1.0 OD1 A:ASP419 4.2 22.7 1.0 OD1 B:ASP419 4.3 21.9 1.0 CB B:ASP414 4.4 21.5 1.0 CB A:ASP414 4.4 25.3 1.0 CB A:ASP412 4.4 21.5 1.0 CB B:ASP412 4.6 23.1 1.0 O A:HOH512 4.7 25.3 1.0 O B:HOH510 4.7 17.3 1.0 O A:MSE413 4.8 22.7 1.0 O B:MSE413 4.8 21.2 1.0 NH2 B:ARG417 4.9 21.2 1.0 NH2 A:ARG417 5.0 33.7 1.0

Calcium binding site 3 out of 9 in the C-Terminal Domain of Probable Hemolysin From Chromobacterium Violaceum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of C-Terminal Domain of Probable Hemolysin From Chromobacterium Violaceum within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca506 b:22.4 occ:1.00 O B:MSE413 2.4 21.2 1.0 OD1 B:ASP412 2.4 19.1 1.0 OD1 B:ASP414 2.4 24.3 1.0 O A:HOH510 2.5 20.6 1.0 O A:HOH512 2.5 25.3 1.0 OD2 A:ASP419 2.5 22.0 1.0 O B:HOH518 2.5 22.3 1.0 CG B:ASP412 3.1 23.1 1.0 OD2 B:ASP412 3.1 28.2 1.0 CG A:ASP419 3.4 23.4 1.0 C B:MSE413 3.5 22.0 1.0 OD1 A:ASP419 3.5 22.7 1.0 CA A:CA505 3.7 20.2 1.0 CG B:ASP414 3.7 24.0 1.0 O A:HOH506 3.9 14.5 1.0 CA B:ASP414 4.1 21.9 1.0 N B:ASP414 4.2 22.1 1.0 N B:MSE413 4.3 22.9 1.0 O B:HOH509 4.4 19.4 1.0 CB B:ASP414 4.5 21.5 1.0 OD2 B:ASP414 4.6 23.3 1.0 CB B:ASP412 4.6 23.1 1.0 OD1 A:ASP354 4.6 24.3 0.5 CA B:MSE413 4.6 22.6 1.0 OD1 A:ASP354 4.6 23.7 0.5 O A:ASP419 4.7 25.4 1.0 CB A:ASP419 4.7 24.7 1.0 OD2 A:ASP414 4.7 26.7 1.0 CE A:LYS420 4.7 23.4 1.0 NZ A:LYS420 4.8 24.4 1.0 C B:ASP412 4.9 23.0 1.0

Calcium binding site 4 out of 9 in the C-Terminal Domain of Probable Hemolysin From Chromobacterium Violaceum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of C-Terminal Domain of Probable Hemolysin From Chromobacterium Violaceum within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca507 b:23.5 occ:1.00 OD2 C:ASP419 2.3 21.6 1.0 OD2 D:ASP412 2.3 32.8 1.0 OD2 C:ASP412 2.4 29.1 1.0 OD2 C:ASP414 2.4 29.7 1.0 OD2 D:ASP419 2.4 22.7 1.0 OD2 D:ASP414 2.4 30.5 1.0 OD1 D:ASP414 2.6 24.4 1.0 OD1 C:ASP414 2.7 31.3 1.0 CG D:ASP414 2.9 28.0 1.0 CG C:ASP414 2.9 31.2 1.0 CG C:ASP419 3.3 26.0 1.0 CG D:ASP419 3.3 25.8 1.0 CG C:ASP412 3.4 28.9 1.0 CG D:ASP412 3.5 29.9 1.0 CA C:CA508 3.7 26.8 1.0 CA D:CA509 3.7 28.2 1.0 CB C:ASP419 3.8 26.9 1.0 CB D:ASP419 3.8 25.8 1.0 OD1 C:ASP412 4.0 30.3 1.0 OD1 D:ASP412 4.1 29.4 1.0 OD1 D:ASP419 4.2 29.1 1.0 OD1 C:ASP419 4.3 24.9 1.0 CB D:ASP414 4.4 29.2 1.0 CB C:ASP414 4.4 29.6 1.0 CB C:ASP412 4.5 28.3 1.0 CB D:ASP412 4.6 28.4 1.0 O D:HOH517 4.6 27.6 1.0 O C:HOH516 4.7 30.8 1.0 NH2 C:ARG417 4.7 38.1 1.0 O C:MSE413 4.8 28.6 1.0 NH2 D:ARG417 4.8 27.1 1.0 O D:MSE413 4.9 28.8 1.0

Calcium binding site 5 out of 9 in the C-Terminal Domain of Probable Hemolysin From Chromobacterium Violaceum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of C-Terminal Domain of Probable Hemolysin From Chromobacterium Violaceum within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca508 b:26.8 occ:1.00 OD1 C:ASP414 2.3 31.3 1.0 OD1 C:ASP412 2.3 30.3 1.0 O D:HOH517 2.4 27.6 1.0 O C:MSE413 2.4 28.6 1.0 OD2 D:ASP419 2.4 22.7 1.0 O D:HOH519 2.5 28.5 1.0 O C:HOH560 2.5 28.0 1.0 OD2 C:ASP412 2.9 29.1 1.0 CG C:ASP412 3.0 28.9 1.0 CG D:ASP419 3.4 25.8 1.0 C C:MSE413 3.5 29.0 1.0 CG C:ASP414 3.6 31.2 1.0 OD1 D:ASP419 3.6 29.1 1.0 CA C:CA507 3.7 23.5 1.0 O D:HOH513 3.9 26.9 1.0 CA C:ASP414 4.2 30.0 1.0 O C:HOH526 4.2 38.6 1.0 N C:ASP414 4.3 29.5 1.0 NZ D:LYS420 4.3 32.5 1.0 N C:MSE413 4.3 28.9 1.0 OD2 C:ASP414 4.4 29.7 1.0 CB C:ASP412 4.4 28.3 1.0 CB C:ASP414 4.5 29.6 1.0 O C:HOH515 4.5 27.6 1.0 OD2 D:ASP354 4.6 32.9 1.0 CA C:MSE413 4.6 29.2 1.0 CB D:ASP419 4.7 25.8 1.0 O D:HOH532 4.8 40.1 1.0 O D:ASP419 4.8 27.9 1.0 OD2 D:ASP414 4.8 30.5 1.0 CE D:LYS420 4.8 27.7 1.0 C C:ASP412 4.9 28.7 1.0 CA C:ASP412 5.0 28.8 1.0

Calcium binding site 6 out of 9 in the C-Terminal Domain of Probable Hemolysin From Chromobacterium Violaceum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of C-Terminal Domain of Probable Hemolysin From Chromobacterium Violaceum within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca509 b:28.2 occ:1.00 OD1 D:ASP412 2.3 29.4 1.0 O C:HOH521 2.3 28.1 1.0 OD1 D:ASP414 2.4 24.4 1.0 O C:HOH516 2.4 30.8 1.0 O D:MSE413 2.5 28.8 1.0 O D:HOH515 2.5 21.9 1.0 OD2 C:ASP419 2.5 21.6 1.0 OD2 D:ASP412 3.0 32.8 1.0 CG D:ASP412 3.0 29.9 1.0 CG C:ASP419 3.4 26.0 1.0 C D:MSE413 3.5 28.9 1.0 CG D:ASP414 3.6 28.0 1.0 OD1 C:ASP419 3.7 24.9 1.0 CA C:CA507 3.7 23.5 1.0 O C:HOH513 3.9 22.6 1.0 CA D:ASP414 4.1 29.1 1.0 N D:ASP414 4.2 28.8 1.0 O D:HOH537 4.3 31.3 1.0 N D:MSE413 4.3 29.0 1.0 OD2 D:ASP414 4.4 30.5 1.0 CB D:ASP414 4.4 29.2 1.0 CB D:ASP412 4.5 28.4 1.0 OD2 C:ASP354 4.5 39.0 1.0 CA D:MSE413 4.6 28.9 1.0 O C:ASP419 4.7 28.7 1.0 CB C:ASP419 4.7 26.9 1.0 NZ C:LYS420 4.7 30.6 1.0 CE C:LYS420 4.8 27.2 1.0 OD2 C:ASP414 4.8 29.7 1.0 C D:ASP412 4.9 27.8 1.0 CA D:ASP412 5.0 28.0 1.0

Calcium binding site 7 out of 9 in the C-Terminal Domain of Probable Hemolysin From Chromobacterium Violaceum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of C-Terminal Domain of Probable Hemolysin From Chromobacterium Violaceum within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca501 b:24.2 occ:1.00 O E:HOH513 2.3 23.4 1.0 O F:HOH545 2.3 20.4 1.0 OD1 E:ASP412 2.3 22.9 1.0 O F:HOH550 2.3 29.0 1.0 O E:MSE413 2.4 24.7 1.0 OD1 E:ASP414 2.5 25.9 1.0 OD2 F:ASP419 2.6 21.3 1.0 CG E:ASP412 3.1 24.8 1.0 OD2 E:ASP412 3.2 27.4 1.0 CG F:ASP419 3.4 22.5 1.0 C E:MSE413 3.5 24.7 1.0 OD1 F:ASP419 3.6 22.2 1.0 CG E:ASP414 3.7 25.6 1.0 O F:HOH539 3.8 20.6 1.0 CA E:CA502 3.8 21.4 1.0 CA E:ASP414 4.2 24.8 1.0 N E:ASP414 4.2 24.4 1.0 N E:MSE413 4.3 25.4 1.0 CB E:ASP412 4.5 22.6 1.0 CB E:ASP414 4.5 25.1 1.0 CA E:MSE413 4.5 25.1 1.0 OD1 F:ASP354 4.6 34.8 1.0 OD2 E:ASP414 4.6 24.5 1.0 CE F:LYS420 4.6 20.2 1.0 NZ F:LYS420 4.7 23.6 1.0 O F:ASP419 4.7 21.1 1.0 CB F:ASP419 4.8 21.0 1.0 OD2 F:ASP414 4.9 16.8 1.0 C E:ASP412 4.9 24.3 1.0 CA E:ASP412 5.0 24.1 1.0

Calcium binding site 8 out of 9 in the C-Terminal Domain of Probable Hemolysin From Chromobacterium Violaceum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of C-Terminal Domain of Probable Hemolysin From Chromobacterium Violaceum within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca502 b:21.4 occ:1.00 OD2 E:ASP412 2.2 27.4 1.0 OD2 E:ASP419 2.3 24.9 1.0 OD2 F:ASP419 2.3 21.3 1.0 OD2 F:ASP414 2.3 16.8 1.0 OD2 F:ASP412 2.3 22.0 1.0 OD2 E:ASP414 2.5 24.5 1.0 OD1 E:ASP414 2.5 25.9 1.0 OD1 F:ASP414 2.7 20.9 1.0 CG E:ASP414 2.9 25.6 1.0 CG F:ASP414 2.9 19.3 1.0 CG E:ASP419 3.2 26.4 1.0 CG F:ASP419 3.3 22.5 1.0 CG E:ASP412 3.4 24.8 1.0 CG F:ASP412 3.5 17.6 1.0 CA F:CA503 3.7 24.5 1.0 CA E:CA501 3.8 24.2 1.0 CB E:ASP419 3.8 24.8 1.0 CB F:ASP419 3.8 21.0 1.0 OD1 E:ASP412 4.0 22.9 1.0 OD1 F:ASP412 4.1 16.6 1.0 OD1 E:ASP419 4.1 23.6 1.0 OD1 F:ASP419 4.3 22.2 1.0 CB E:ASP414 4.4 25.1 1.0 CB F:ASP414 4.4 20.0 1.0 CB F:ASP412 4.5 18.3 1.0 CB E:ASP412 4.5 22.6 1.0 O F:HOH550 4.7 29.0 1.0 O E:HOH512 4.8 20.8 1.0 NH2 E:ARG417 4.8 32.3 1.0 O F:MSE413 4.9 18.1 1.0 O E:MSE413 4.9 24.7 1.0

Calcium binding site 9 out of 9 in the C-Terminal Domain of Probable Hemolysin From Chromobacterium Violaceum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of C-Terminal Domain of Probable Hemolysin From Chromobacterium Violaceum within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca503 b:24.5 occ:1.00 OD1 F:ASP414 2.3 20.9 1.0 OD2 E:ASP419 2.4 24.9 1.0 OD1 F:ASP412 2.5 16.6 1.0 O F:HOH536 2.5 18.6 1.0 O F:MSE413 2.5 18.1 1.0 O E:HOH519 2.5 27.4 1.0 O E:HOH512 2.6 20.8 1.0 OD2 F:ASP412 2.9 22.0 1.0 CG F:ASP412 3.1 17.6 1.0 CG E:ASP419 3.3 26.4 1.0 OD1 E:ASP419 3.5 23.6 1.0 CG F:ASP414 3.5 19.3 1.0 C F:MSE413 3.5 19.2 1.0 CA E:CA502 3.7 21.4 1.0 O E:HOH514 3.8 22.2 1.0 CA F:ASP414 4.2 20.2 1.0 N F:ASP414 4.2 19.9 1.0 N F:MSE413 4.3 19.1 1.0 OD2 F:ASP414 4.3 16.8 1.0 O E:HOH533 4.3 35.7 1.0 O F:HOH617 4.4 25.2 1.0 NZ E:LYS420 4.4 25.5 1.0 CB F:ASP414 4.4 20.0 1.0 OD2 E:ASP354 4.5 34.3 1.0 CB F:ASP412 4.5 18.3 1.0 O F:HOH558 4.5 25.0 1.0 CA F:MSE413 4.6 20.2 1.0 CB E:ASP419 4.6 24.8 1.0 O E:ASP419 4.7 25.8 1.0 OD2 E:ASP414 4.7 24.5 1.0 CE E:LYS420 4.9 22.8 1.0 OD2 E:ASP412 4.9 27.4 1.0 C F:ASP412 4.9 18.9 1.0

C.Chang, X.Xu, H.Cui, A.Savchenko, A.Edwards, A.Joachimiak. Crystal Structure of C-Terminal Domain of Probable Hemolysin From Chromobacterium Violaceum To Be Published.