Calcium in PDB 4lw9: Crystal Structure of Vibrio Cholera Major Pseudopilin Epsg

The structure of Crystal Structure of Vibrio Cholera Major Pseudopilin Epsg, PDB code: 4lw9 was solved by F.S.Vago, K.Raghunathan, J.C.Jens, W.J.Wedemeyer, M.Bagdasarian, J.S.Brunzelle, D.N.Arvidson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.54 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	88.610, 70.015, 131.544, 90.00, 103.29, 90.00
R / Rfree (%)	20.2 / 24.5

The structure of Crystal Structure of Vibrio Cholera Major Pseudopilin Epsg also contains other interesting chemical elements:

Zinc	(Zn)	32 atoms
Platinum	(Pt)	12 atoms
Chlorine	(Cl)	9 atoms
Sodium	(Na)	6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Vibrio Cholera Major Pseudopilin Epsg (pdb code 4lw9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 14 binding sites of Calcium where determined in the Crystal Structure of Vibrio Cholera Major Pseudopilin Epsg, PDB code: 4lw9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 14 in the Crystal Structure of Vibrio Cholera Major Pseudopilin Epsg


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 Vibrio Cholera Major Pseudopilin Epsg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:42.7 occ:1.00 O A:GLN118 2.3 48.2 1.0 OD1 A:ASP127 2.3 39.9 1.0 O A:GLY125 2.3 38.9 1.0 O A:GLY120 2.3 47.9 1.0 O A:LEU113 2.3 38.2 1.0 OD1 A:ASP116 2.6 47.9 1.0 CG A:ASP116 3.4 47.6 1.0 OD2 A:ASP116 3.4 46.7 1.0 C A:GLY120 3.4 50.0 1.0 CG A:ASP127 3.5 38.2 1.0 C A:LEU113 3.5 36.6 1.0 C A:GLN118 3.5 51.0 1.0 C A:GLY125 3.5 36.8 1.0 N A:GLY120 4.0 51.7 1.0 N A:ASP127 4.0 33.7 1.0 C A:GLU119 4.0 52.6 1.0 OD2 A:ASP127 4.1 39.9 1.0 C A:ALA126 4.1 34.3 1.0 N A:GLN118 4.2 50.6 1.0 CA A:LEU113 4.2 36.1 1.0 CA A:GLY120 4.3 50.5 1.0 CB A:LEU113 4.3 37.6 1.0 O A:GLU119 4.3 53.6 1.0 CA A:ALA126 4.4 34.5 1.0 N A:GLY121 4.4 50.0 1.0 CA A:GLN118 4.4 51.0 1.0 CA A:GLY125 4.4 37.2 1.0 N A:GLU119 4.4 51.6 1.0 N A:ALA126 4.4 35.3 1.0 CA A:GLU119 4.5 52.9 1.0 CA A:ASP127 4.5 34.0 1.0 N A:GLY114 4.5 35.6 1.0 CA A:GLY121 4.5 49.9 1.0 O A:ALA126 4.5 32.8 1.0 CB A:ASP127 4.6 36.1 1.0 CA A:GLY114 4.7 36.1 1.0 CB A:ASP116 4.8 47.9 1.0 CD2 A:LEU113 5.0 38.5 1.0

Calcium binding site 2 out of 14 in the Crystal Structure of Vibrio Cholera Major Pseudopilin Epsg


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 Vibrio Cholera Major Pseudopilin Epsg within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:34.8 occ:1.00 O B:LEU113 2.3 30.7 1.0 O B:GLN118 2.3 40.8 1.0 O B:GLY125 2.3 33.3 1.0 OD1 B:ASP127 2.3 32.6 1.0 OD1 B:ASP116 2.3 38.0 1.0 O B:GLY120 2.3 38.4 1.0 CG B:ASP116 3.1 39.8 1.0 OD2 B:ASP116 3.2 39.7 1.0 C B:LEU113 3.4 30.1 1.0 C B:GLY125 3.5 31.9 1.0 C B:GLN118 3.5 44.4 1.0 C B:GLY120 3.5 40.4 1.0 CG B:ASP127 3.5 34.0 1.0 N B:GLY120 4.0 41.3 1.0 N B:GLN118 4.0 45.1 1.0 N B:ASP127 4.1 29.8 1.0 CA B:LEU113 4.1 28.8 1.0 C B:GLU119 4.2 43.3 1.0 CA B:GLY125 4.2 32.6 1.0 OD2 B:ASP127 4.2 34.2 1.0 C B:ALA126 4.2 29.9 1.0 CB B:LEU113 4.3 31.0 1.0 CA B:GLY120 4.3 41.1 1.0 CA B:GLN118 4.4 45.1 1.0 N B:GLU119 4.4 43.8 1.0 CA B:GLU119 4.5 44.3 1.0 N B:GLY114 4.5 29.1 1.0 CA B:ASP127 4.5 28.5 1.0 O B:ALA126 4.5 28.6 1.0 N B:ALA126 4.5 31.0 1.0 N B:GLY121 4.5 41.4 1.0 CB B:ASP116 4.6 40.2 1.0 O B:GLU119 4.6 43.7 1.0 CB B:ASP127 4.6 30.3 1.0 CA B:GLY114 4.6 29.8 1.0 N B:GLY117 4.7 43.1 1.0 CA B:ALA126 4.7 30.6 1.0 CA B:GLY121 4.7 42.0 1.0 CG B:GLN118 4.8 48.5 1.0 N B:ASP116 4.9 39.5 1.0 C B:GLY114 4.9 31.1 1.0

Calcium binding site 3 out of 14 in the Crystal Structure of Vibrio Cholera Major Pseudopilin Epsg


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 Vibrio Cholera Major Pseudopilin Epsg within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca204 b:39.2 occ:1.00 O C:LEU113 2.3 36.6 1.0 OD1 C:ASP127 2.3 38.0 1.0 O C:GLY125 2.3 35.9 1.0 OD1 C:ASP116 2.3 43.3 1.0 O C:GLN118 2.3 46.8 1.0 O C:GLY120 2.3 44.5 1.0 CG C:ASP116 3.1 44.0 1.0 OD2 C:ASP116 3.2 43.7 1.0 C C:LEU113 3.4 34.0 1.0 CG C:ASP127 3.4 36.2 1.0 C C:GLY120 3.5 46.9 1.0 C C:GLY125 3.5 33.5 1.0 C C:GLN118 3.6 49.2 1.0 CA C:LEU113 4.0 32.3 1.0 OD2 C:ASP127 4.1 38.5 1.0 N C:GLY120 4.1 48.6 1.0 N C:ASP127 4.1 31.8 1.0 C C:GLU119 4.1 49.9 1.0 CB C:LEU113 4.2 33.4 1.0 N C:GLN118 4.2 48.8 1.0 CA C:GLY125 4.2 34.5 1.0 C C:ALA126 4.3 31.5 1.0 CA C:GLY120 4.4 47.5 1.0 N C:GLY121 4.4 47.0 1.0 O C:GLU119 4.4 49.1 1.0 N C:GLU119 4.4 49.9 1.0 CA C:ASP127 4.5 31.5 1.0 N C:GLY114 4.5 34.1 1.0 CA C:GLU119 4.5 50.7 1.0 CA C:GLN118 4.5 49.1 1.0 N C:ALA126 4.5 32.6 1.0 CB C:ASP127 4.5 34.0 1.0 CA C:GLY121 4.5 47.2 1.0 CB C:ASP116 4.6 43.9 1.0 CA C:GLY114 4.6 34.0 1.0 O C:ALA126 4.7 30.0 1.0 N C:GLY117 4.7 46.8 1.0 CA C:ALA126 4.7 32.5 1.0 N C:ASP116 4.8 42.1 1.0 C C:GLY114 5.0 35.0 1.0

Calcium binding site 4 out of 14 in the Crystal Structure of Vibrio Cholera Major Pseudopilin Epsg


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 Vibrio Cholera Major Pseudopilin Epsg within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca205 b:40.3 occ:1.00 O D:GLY125 2.3 38.3 1.0 O D:GLY120 2.3 46.8 1.0 O D:LEU113 2.3 37.9 1.0 O D:GLN118 2.3 46.3 1.0 OD1 D:ASP116 2.3 42.9 1.0 OD1 D:ASP127 2.3 36.8 1.0 CG D:ASP116 3.1 45.0 1.0 OD2 D:ASP116 3.2 43.3 1.0 C D:LEU113 3.4 36.0 1.0 C D:GLY120 3.5 49.3 1.0 C D:GLY125 3.5 37.9 1.0 C D:GLN118 3.5 49.1 1.0 CG D:ASP127 3.5 34.9 1.0 N D:GLY120 4.0 50.7 1.0 N D:ASP127 4.1 32.6 1.0 N D:GLN118 4.1 48.9 1.0 CA D:LEU113 4.1 35.9 1.0 C D:GLU119 4.2 51.6 1.0 C D:ALA126 4.2 34.2 1.0 OD2 D:ASP127 4.2 37.3 1.0 CB D:LEU113 4.3 37.7 1.0 CA D:GLY125 4.3 39.5 1.0 CA D:GLY120 4.3 49.6 1.0 N D:GLY114 4.4 36.1 1.0 N D:GLY121 4.4 48.9 1.0 CA D:GLN118 4.4 49.9 1.0 N D:ALA126 4.5 36.5 1.0 N D:GLU119 4.5 50.6 1.0 CA D:GLY114 4.5 36.9 1.0 CA D:GLY121 4.5 49.7 1.0 CA D:ASP127 4.5 31.3 1.0 CA D:ALA126 4.5 35.2 1.0 CA D:GLU119 4.6 51.6 1.0 O D:ALA126 4.6 35.0 1.0 O D:GLU119 4.6 53.7 1.0 CB D:ASP116 4.6 44.9 1.0 CB D:ASP127 4.6 32.8 1.0 C D:GLY114 4.8 38.1 1.0 N D:GLY117 4.9 48.0 1.0 N D:ASP116 4.9 44.5 1.0

Calcium binding site 5 out of 14 in the Crystal Structure of Vibrio Cholera Major Pseudopilin Epsg


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 Vibrio Cholera Major Pseudopilin Epsg within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca205 b:25.4 occ:1.00 O E:GLY125 2.3 26.3 1.0 O E:LEU113 2.3 25.3 1.0 O E:GLN118 2.3 28.8 1.0 OD1 E:ASP127 2.3 26.4 1.0 O E:GLY120 2.3 30.0 1.0 OD1 E:ASP116 2.3 25.6 1.0 CG E:ASP116 3.2 28.1 1.0 OD2 E:ASP116 3.3 27.9 1.0 C E:LEU113 3.4 24.8 1.0 C E:GLY125 3.5 26.2 1.0 CG E:ASP127 3.5 27.3 1.0 C E:GLN118 3.5 31.5 1.0 C E:GLY120 3.6 32.9 1.0 CA E:LEU113 4.0 25.8 1.0 OD2 E:ASP127 4.1 28.8 1.0 N E:ASP127 4.1 23.4 1.0 N E:GLN118 4.1 30.6 1.0 N E:GLY120 4.2 33.4 1.0 CB E:LEU113 4.2 28.9 1.0 O E:HOH351 4.2 37.5 1.0 C E:GLU119 4.2 33.6 1.0 CA E:GLY125 4.3 27.4 1.0 C E:ALA126 4.3 23.5 1.0 N E:GLY114 4.4 22.9 1.0 CA E:GLN118 4.4 32.2 1.0 CA E:GLY120 4.5 32.4 1.0 N E:GLU119 4.5 31.9 1.0 N E:GLY121 4.5 33.1 1.0 N E:ALA126 4.5 24.6 1.0 CA E:GLY121 4.5 35.1 1.0 CA E:GLU119 4.5 32.8 1.0 CA E:ASP127 4.6 22.6 1.0 O E:GLU119 4.6 32.9 1.0 CA E:GLY114 4.6 22.5 1.0 CA E:ALA126 4.6 24.7 1.0 CB E:ASP127 4.6 24.9 1.0 CB E:ASP116 4.6 27.6 1.0 CD2 E:LEU113 4.8 31.7 1.0 O E:ALA126 4.8 24.2 1.0 N E:GLY117 4.9 27.7 1.0 C E:GLY114 4.9 25.3 1.0 N E:ASP116 4.9 25.7 1.0

Calcium binding site 6 out of 14 in the Crystal Structure of Vibrio Cholera Major Pseudopilin Epsg


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 Vibrio Cholera Major Pseudopilin Epsg within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca202 b:54.8 occ:1.00 O F:GLY125 2.3 53.4 1.0 O F:GLN118 2.3 57.3 1.0 O F:GLY120 2.3 59.6 1.0 O F:LEU113 2.3 49.8 1.0 OD1 F:ASP127 2.5 44.8 1.0 OD1 F:ASP116 2.5 61.2 1.0 C F:LEU113 3.4 47.0 1.0 CG F:ASP116 3.4 61.2 1.0 C F:GLY125 3.5 53.1 1.0 C F:GLY120 3.5 61.2 1.0 C F:GLN118 3.5 58.8 1.0 OD2 F:ASP116 3.6 61.5 1.0 CG F:ASP127 3.7 45.0 1.0 N F:GLN118 3.9 59.0 1.0 CA F:LEU113 4.1 44.5 1.0 CA F:GLY121 4.2 61.9 1.0 CA F:GLY125 4.2 54.5 1.0 CB F:LEU113 4.2 44.3 1.0 N F:ASP127 4.2 44.7 1.0 OD2 F:ASP127 4.3 45.8 1.0 CA F:GLN118 4.3 58.8 1.0 N F:GLY121 4.3 61.7 1.0 C F:GLU119 4.3 60.3 1.0 C F:ALA126 4.3 47.0 1.0 N F:GLY120 4.4 60.6 1.0 O F:GLU119 4.5 61.2 1.0 N F:ALA126 4.5 51.1 1.0 N F:GLY114 4.5 48.9 1.0 N F:GLU119 4.5 59.4 1.0 CA F:GLY120 4.6 60.8 1.0 CA F:ALA126 4.6 49.4 1.0 CD1 F:LEU113 4.6 44.8 1.0 O F:ALA126 4.6 46.9 1.0 CA F:GLU119 4.7 59.8 1.0 CA F:ASP127 4.7 42.9 1.0 CB F:GLN118 4.7 59.0 1.0 N F:GLY117 4.7 59.7 1.0 CA F:GLY114 4.7 51.0 1.0 CB F:ASP127 4.8 43.8 1.0 CB F:ASP116 4.8 60.3 1.0 CG F:LEU113 4.8 44.5 1.0 C F:GLY117 4.9 59.2 1.0

Calcium binding site 7 out of 14 in the Crystal Structure of Vibrio Cholera Major Pseudopilin Epsg


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 Vibrio Cholera Major Pseudopilin Epsg within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca203 b:38.2 occ:1.00 N A:GLY26 2.2 42.9 1.0 OD1 F:ASP61 2.3 41.2 1.0 CG F:ASP61 3.0 41.5 1.0 OD2 F:ASP61 3.0 44.4 1.0 CA A:GLY26 3.0 43.6 1.0 O F:HOH325 4.1 36.9 1.0 OE1 A:GLU29 4.3 41.0 1.0 C A:GLY26 4.4 43.8 1.0 CB F:ASP61 4.4 40.7 1.0 O A:HOH353 4.7 50.2 1.0 O A:GLY26 4.8 42.8 1.0 N F:ASP61 4.9 36.7 1.0 CA F:ASP61 5.0 39.2 1.0 CG2 F:THR60 5.0 32.5 1.0

Calcium binding site 8 out of 14 in the Crystal Structure of Vibrio Cholera Major Pseudopilin Epsg


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 Vibrio Cholera Major Pseudopilin Epsg within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca204 b:45.1 occ:1.00 O I:GLY125 2.3 43.2 1.0 OD1 I:ASP127 2.3 41.1 1.0 O I:GLN118 2.3 49.4 1.0 O I:LEU113 2.3 43.2 1.0 O I:GLY120 2.3 50.9 1.0 OD1 I:ASP116 2.5 52.8 1.0 OD2 I:ASP116 3.2 52.7 1.0 CG I:ASP116 3.2 52.9 1.0 C I:LEU113 3.4 41.1 1.0 CG I:ASP127 3.5 39.3 1.0 C I:GLY125 3.5 43.2 1.0 C I:GLY120 3.5 53.3 1.0 C I:GLN118 3.5 52.5 1.0 N I:GLY120 3.9 54.1 1.0 C I:GLU119 4.0 54.5 1.0 N I:ASP127 4.1 37.8 1.0 CA I:LEU113 4.1 39.0 1.0 OD2 I:ASP127 4.1 39.2 1.0 N I:GLN118 4.2 53.1 1.0 CB I:LEU113 4.2 40.1 1.0 C I:ALA126 4.2 39.3 1.0 CA I:GLY120 4.3 53.5 1.0 CA I:GLY125 4.3 45.3 1.0 O I:GLU119 4.3 56.0 1.0 N I:GLU119 4.4 52.9 1.0 CA I:GLU119 4.4 53.5 1.0 CA I:GLN118 4.5 53.3 1.0 N I:GLY114 4.5 40.5 1.0 N I:ALA126 4.5 41.5 1.0 CA I:ASP127 4.5 37.0 1.0 N I:GLY121 4.6 53.5 1.0 O I:ALA126 4.6 40.5 1.0 CB I:ASP127 4.6 38.0 1.0 CA I:ALA126 4.7 40.8 1.0 CB I:ASP116 4.7 52.6 1.0 CA I:GLY114 4.7 41.8 1.0 CA I:GLY121 4.8 54.0 1.0 N I:GLY117 4.9 53.0 1.0 N I:ASP116 5.0 51.0 1.0

Calcium binding site 9 out of 14 in the Crystal Structure of Vibrio Cholera Major Pseudopilin Epsg


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Vibrio Cholera Major Pseudopilin Epsg within 5.0Å range: probe atom residue distance (Å) B Occ J:Ca203 b:28.5 occ:1.00 O J:LEU113 2.3 26.2 1.0 OD1 J:ASP127 2.3 27.9 1.0 O J:GLY125 2.3 27.0 1.0 O J:GLN118 2.3 32.9 1.0 O J:GLY120 2.3 31.9 1.0 OD1 J:ASP116 2.5 31.3 1.0 CG J:ASP116 3.3 33.1 1.0 OD2 J:ASP116 3.4 34.5 1.0 C J:LEU113 3.4 25.0 1.0 C J:GLY125 3.5 29.3 1.0 CG J:ASP127 3.5 29.2 1.0 C J:GLY120 3.5 34.7 1.0 C J:GLN118 3.5 35.0 1.0 N J:GLY120 4.0 35.6 1.0 C J:GLU119 4.1 36.5 1.0 N J:GLN118 4.1 33.7 1.0 CA J:LEU113 4.1 26.8 1.0 N J:ASP127 4.2 23.3 1.0 OD2 J:ASP127 4.2 27.7 1.0 CA J:GLY125 4.2 31.1 1.0 CA J:GLY120 4.3 34.6 1.0 C J:ALA126 4.3 25.2 1.0 CB J:LEU113 4.3 28.4 1.0 N J:GLU119 4.4 35.2 1.0 N J:GLY114 4.4 25.2 1.0 CA J:GLN118 4.4 34.7 1.0 CA J:GLU119 4.5 37.5 1.0 N J:ALA126 4.5 28.8 1.0 CA J:ASP127 4.5 25.1 1.0 O J:GLU119 4.5 36.0 1.0 N J:GLY121 4.5 35.4 1.0 CA J:GLY114 4.6 25.1 1.0 O J:HOH329 4.6 35.9 1.0 CB J:ASP127 4.6 25.8 1.0 O J:ALA126 4.6 25.7 1.0 CA J:GLY121 4.7 38.2 1.0 CA J:ALA126 4.7 27.5 1.0 CB J:ASP116 4.8 32.8 1.0 N J:GLY117 4.8 31.8 1.0 C J:GLY114 4.9 27.4 1.0 CD2 J:LEU113 4.9 31.7 1.0 N J:ASP116 5.0 32.3 1.0

Calcium binding site 10 out of 14 in the Crystal Structure of Vibrio Cholera Major Pseudopilin Epsg


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Vibrio Cholera Major Pseudopilin Epsg within 5.0Å range: probe atom residue distance (Å) B Occ K:Ca206 b:44.5 occ:1.00 O K:LEU113 2.2 38.5 1.0 O K:GLY120 2.3 49.2 1.0 O K:GLY125 2.3 40.7 1.0 OD1 K:ASP127 2.3 42.9 1.0 O K:GLN118 2.5 52.9 1.0 OD1 K:ASP116 2.6 49.7 1.0 OD2 K:ASP116 3.3 49.1 1.0 CG K:ASP116 3.3 48.4 1.0 C K:LEU113 3.3 37.8 1.0 CG K:ASP127 3.5 41.5 1.0 C K:GLY120 3.5 51.7 1.0 C K:GLY125 3.5 40.6 1.0 C K:GLN118 3.7 52.5 1.0 CA K:LEU113 4.0 37.3 1.0 N K:GLY120 4.1 52.7 1.0 OD2 K:ASP127 4.1 42.9 1.0 C K:GLU119 4.1 53.0 1.0 CB K:LEU113 4.2 38.9 1.0 N K:ASP127 4.2 38.4 1.0 C K:ALA126 4.3 38.1 1.0 N K:GLY114 4.3 36.9 1.0 CA K:GLY125 4.4 41.2 1.0 N K:GLN118 4.4 51.5 1.0 CA K:GLY121 4.4 51.9 1.0 N K:GLY121 4.4 51.8 1.0 CA K:GLY120 4.4 51.9 1.0 CA K:GLU119 4.4 53.0 1.0 O K:GLU119 4.5 54.4 1.0 N K:GLU119 4.5 52.4 1.0 N K:ALA126 4.5 39.4 1.0 CA K:GLY114 4.5 37.9 1.0 CA K:ASP127 4.6 37.3 1.0 CB K:ASP127 4.6 39.4 1.0 CA K:ALA126 4.7 39.1 1.0 CA K:GLN118 4.7 52.4 1.0 O K:ALA126 4.7 35.8 1.0 CB K:ASP116 4.7 47.4 1.0 CD1 K:LEU113 4.9 39.9 1.0 C K:GLY114 4.9 38.2 1.0

F.S.Vago, K.Raghunathan, J.C.Jens, W.J.Wedemeyer, M.Bagdasarian, J.S.Brunzelle, D.N.Arvidson. Crystal Structure of Vibrio Cholera Major Pseudopilin Epsg To Be Published.