Calcium in PDB 2yn5: Structural Insight Into the Giant Calcium-Binding Adhesin Siie: Implications For the Adhesion of Salmonella Enterica to Polarized Epithelial Cells

The structure of Structural Insight Into the Giant Calcium-Binding Adhesin Siie: Implications For the Adhesion of Salmonella Enterica to Polarized Epithelial Cells, PDB code: 2yn5 was solved by M.H.Griessl, B.Schmid, K.Kassler, C.Braunsmann, R.Ritter, B.Barlag, K.U.Sturm, C.Danzer, C.Wagner, T.E.Schaeffer, H.Sticht, M.Hensel, Y.A.Muller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.00 / 1.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	129.400, 69.040, 67.260, 90.00, 90.92, 90.00
R / Rfree (%)	20.643 / 24.626

The binding sites of Calcium atom in the Structural Insight Into the Giant Calcium-Binding Adhesin Siie: Implications For the Adhesion of Salmonella Enterica to Polarized Epithelial Cells (pdb code 2yn5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Structural Insight Into the Giant Calcium-Binding Adhesin Siie: Implications For the Adhesion of Salmonella Enterica to Polarized Epithelial Cells, PDB code: 2yn5:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in the Structural Insight Into the Giant Calcium-Binding Adhesin Siie: Implications For the Adhesion of Salmonella Enterica to Polarized Epithelial Cells


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural Insight Into the Giant Calcium-Binding Adhesin Siie: Implications For the Adhesion of Salmonella Enterica to Polarized Epithelial Cells within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca6361 b:12.7 occ:1.00 O A:HOH2084 2.4 17.3 1.0 O A:HOH2085 2.5 10.2 1.0 O A:ASN5205 2.5 12.9 1.0 C A:ASN5205 3.7 13.2 1.0 CB A:ASN5205 4.2 13.2 1.0 OG1 A:THR5207 4.5 15.0 1.0 O A:HOH2087 4.6 26.2 1.0 CA A:ASN5205 4.6 12.7 1.0 N A:GLY5206 4.6 12.5 1.0 CA A:GLY5206 4.7 12.8 1.0 N A:THR5207 4.9 12.8 1.0 O A:ILE5204 4.9 12.4 1.0 C A:GLY5206 5.0 12.1 1.0

Calcium binding site 2 out of 9 in the Structural Insight Into the Giant Calcium-Binding Adhesin Siie: Implications For the Adhesion of Salmonella Enterica to Polarized Epithelial Cells


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural Insight Into the Giant Calcium-Binding Adhesin Siie: Implications For the Adhesion of Salmonella Enterica to Polarized Epithelial Cells within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca6362 b:15.9 occ:1.00 OD1 A:ASP5157 2.2 16.3 1.0 O A:ILE5158 2.3 15.2 1.0 O A:GLU5136 2.3 15.6 1.0 OD2 A:ASP5240 2.4 15.6 1.0 OD2 A:ASP5196 2.4 16.5 1.0 O A:HOH2044 2.5 16.7 1.0 C A:GLU5136 3.4 16.2 1.0 CG A:ASP5157 3.4 17.4 1.0 CG A:ASP5196 3.4 16.8 1.0 CG A:ASP5240 3.5 17.0 1.0 C A:ILE5158 3.5 15.0 1.0 OD1 A:ASP5196 3.7 18.5 1.0 CB A:ASP5240 4.0 16.6 1.0 N A:ILE5158 4.0 14.3 1.0 OD2 A:ASP5157 4.0 18.6 1.0 ND2 A:ASN5244 4.1 15.1 1.0 O A:HOH2053 4.1 17.2 1.0 C A:ASP5157 4.2 15.2 1.0 CA A:GLU5136 4.3 16.9 1.0 N A:GLY5137 4.3 15.6 1.0 CA A:ILE5158 4.3 14.6 1.0 CA A:GLY5137 4.3 14.6 1.0 N A:MET5159 4.3 16.0 1.0 CB A:MET5159 4.4 18.4 1.0 CA A:MET5159 4.4 17.9 1.0 OD1 A:ASP5240 4.5 18.9 1.0 CB A:GLU5136 4.5 18.1 1.0 CB A:ASP5157 4.6 16.5 1.0 C A:GLY5137 4.6 14.7 1.0 CA A:ASP5157 4.6 15.5 1.0 O A:ASP5157 4.7 16.2 1.0 CB A:ASP5196 4.8 18.1 1.0 CG A:MET5159 4.8 21.2 1.0 OE1 A:GLU5194 4.9 17.9 1.0 O A:GLY5137 4.9 14.6 1.0 OH A:TYR5133 4.9 16.0 1.0 CG A:LYS5138 5.0 17.3 1.0

Calcium binding site 3 out of 9 in the Structural Insight Into the Giant Calcium-Binding Adhesin Siie: Implications For the Adhesion of Salmonella Enterica to Polarized Epithelial Cells


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structural Insight Into the Giant Calcium-Binding Adhesin Siie: Implications For the Adhesion of Salmonella Enterica to Polarized Epithelial Cells within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca6363 b:15.8 occ:1.00 OD1 A:ASP5172 2.3 25.3 1.0 O A:ILE5180 2.3 12.6 1.0 O A:HOH2069 2.3 16.9 1.0 O A:SER5173 2.3 15.9 1.0 O A:THR5175 2.4 22.1 1.0 OD1 A:ASP5178 2.4 17.4 1.0 CG A:ASP5178 3.4 18.3 1.0 C A:ILE5180 3.5 13.9 1.0 CG A:ASP5172 3.5 25.4 1.0 C A:SER5173 3.5 17.0 1.0 C A:THR5175 3.6 22.6 1.0 OD2 A:ASP5178 3.7 19.0 1.0 N A:SER5173 4.0 18.3 1.0 N A:ILE5180 4.0 15.6 1.0 C A:ASP5172 4.0 20.3 1.0 N A:THR5175 4.1 19.9 1.0 OD2 A:ASP5172 4.1 26.8 1.0 C A:GLY5174 4.2 19.3 1.0 CA A:ILE5180 4.2 14.2 1.0 O A:ASP5172 4.3 21.5 1.0 CB A:ILE5180 4.3 15.2 1.0 CA A:THR5175 4.4 21.7 1.0 CA A:SER5173 4.4 17.2 1.0 O A:GLY5174 4.4 20.9 1.0 N A:GLY5174 4.5 16.8 1.0 N A:THR5181 4.5 13.2 1.0 N A:VAL5176 4.6 24.2 1.0 CA A:ASP5172 4.6 21.8 1.0 CA A:GLY5174 4.6 18.4 1.0 N A:ASP5178 4.6 21.5 1.0 CB A:ASP5172 4.6 23.5 1.0 CA A:VAL5176 4.6 26.2 1.0 O A:ARG5344 4.7 18.5 1.0 CA A:THR5181 4.7 13.0 1.0 CB A:THR5175 4.7 21.2 1.0 CB A:ASP5178 4.8 19.8 1.0 N A:GLY5177 4.8 25.9 1.0 OG A:SER5173 4.8 15.2 1.0 N A:ASN5179 4.9 18.3 1.0

Calcium binding site 4 out of 9 in the Structural Insight Into the Giant Calcium-Binding Adhesin Siie: Implications For the Adhesion of Salmonella Enterica to Polarized Epithelial Cells


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structural Insight Into the Giant Calcium-Binding Adhesin Siie: Implications For the Adhesion of Salmonella Enterica to Polarized Epithelial Cells within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca6364 b:17.4 occ:1.00 OD2 A:ASP5343 2.3 16.6 1.0 O A:HOH2106 2.3 25.5 1.0 O A:HOH2108 2.4 18.6 1.0 O A:THR5258 2.4 17.7 1.0 OD1 A:ASP5256 2.4 15.4 1.0 OD2 A:ASP5256 2.5 15.7 1.0 OD2 A:ASP5296 2.5 20.7 1.0 CG A:ASP5256 2.8 15.0 1.0 CG A:ASP5343 3.4 17.7 1.0 CG A:ASP5296 3.5 23.2 1.0 C A:THR5258 3.6 19.2 1.0 OD1 A:ASP5296 3.8 26.4 1.0 CB A:ASP5343 4.0 19.0 1.0 ND2 A:ASN5347 4.2 16.6 1.0 OD1 A:ASP5343 4.4 18.3 1.0 CB A:ASP5256 4.4 14.6 1.0 N A:THR5258 4.4 21.0 1.0 CA A:THR5258 4.5 21.5 1.0 N A:LEU5259 4.6 17.6 1.0 CA A:LEU5259 4.6 17.5 1.0 CB A:LEU5259 4.7 17.1 1.0 O A:HOH2091 4.8 26.3 1.0 CB A:THR5258 4.9 23.2 1.0 CB A:ASP5296 4.9 22.9 1.0 CD1 A:LEU5259 4.9 15.5 1.0

Calcium binding site 5 out of 9 in the Structural Insight Into the Giant Calcium-Binding Adhesin Siie: Implications For the Adhesion of Salmonella Enterica to Polarized Epithelial Cells


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structural Insight Into the Giant Calcium-Binding Adhesin Siie: Implications For the Adhesion of Salmonella Enterica to Polarized Epithelial Cells within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca6365 b:26.9 occ:1.00 O A:SER5275 2.3 42.2 1.0 O A:ASN5272 2.3 32.5 1.0 O A:VAL5280 2.3 29.2 1.0 OD1 A:ASP5271 2.4 30.9 1.0 OD1 A:ASP5278 2.4 28.7 1.0 C A:ASN5272 3.4 34.5 1.0 N A:ASN5272 3.5 33.3 1.0 C A:SER5275 3.5 46.1 1.0 C A:VAL5280 3.5 29.3 1.0 CG A:ASP5278 3.5 31.9 1.0 CG A:ASP5271 3.6 30.6 1.0 C A:ASP5271 3.6 32.6 1.0 N A:VAL5280 3.9 28.5 1.0 OD2 A:ASP5278 3.9 30.9 1.0 CA A:ASN5272 3.9 32.9 1.0 O A:ASP5271 4.0 34.4 1.0 N A:SER5275 4.0 49.0 1.0 CA A:VAL5280 4.1 28.6 1.0 CA A:ASP5271 4.2 31.1 1.0 CA A:SER5275 4.2 48.0 1.0 CB A:VAL5280 4.3 28.6 1.0 OD2 A:ASP5271 4.4 29.7 1.0 CB A:ASP5271 4.5 30.0 1.0 N A:ASP5276 4.5 43.2 1.0 N A:GLY5273 4.6 37.0 1.0 N A:THR5281 4.6 27.1 1.0 N A:ASN5279 4.7 28.9 1.0 CB A:SER5275 4.7 48.5 1.0 N A:ASP5278 4.7 31.9 1.0 CA A:ASP5276 4.7 41.1 1.0 N A:ALA5274 4.8 46.5 1.0 CB A:ASP5278 4.9 30.7 1.0 CA A:THR5281 4.9 27.1 1.0 CA A:GLY5273 4.9 40.1 1.0 OD1 A:ASN5272 4.9 32.9 1.0 C A:ASN5279 5.0 28.0 1.0

Calcium binding site 6 out of 9 in the Structural Insight Into the Giant Calcium-Binding Adhesin Siie: Implications For the Adhesion of Salmonella Enterica to Polarized Epithelial Cells


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structural Insight Into the Giant Calcium-Binding Adhesin Siie: Implications For the Adhesion of Salmonella Enterica to Polarized Epithelial Cells within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca6362 b:14.2 occ:1.00 O B:SER5173 2.3 15.1 1.0 O B:ILE5180 2.3 11.2 1.0 O B:THR5175 2.3 22.0 1.0 OD1 B:ASP5172 2.4 19.8 1.0 OD1 B:ASP5178 2.4 14.6 1.0 O B:HOH2069 2.5 14.1 1.0 CG B:ASP5178 3.4 14.5 1.0 C B:ILE5180 3.5 11.5 1.0 C B:SER5173 3.5 16.1 1.0 C B:THR5175 3.5 23.4 1.0 CG B:ASP5172 3.5 20.7 1.0 OD2 B:ASP5178 3.7 15.1 1.0 N B:SER5173 3.9 16.1 1.0 N B:ILE5180 4.0 12.3 1.0 C B:ASP5172 4.0 16.6 1.0 N B:THR5175 4.1 20.7 1.0 OD2 B:ASP5172 4.2 24.0 1.0 CA B:ILE5180 4.2 11.2 1.0 C B:GLY5174 4.2 18.6 1.0 CA B:THR5175 4.3 24.6 1.0 CA B:SER5173 4.3 16.0 1.0 O B:ASP5172 4.4 16.6 1.0 CB B:ILE5180 4.4 11.6 1.0 N B:VAL5176 4.5 25.6 1.0 N B:THR5181 4.5 10.8 1.0 N B:GLY5174 4.5 15.5 1.0 CA B:ASP5172 4.6 17.3 1.0 CA B:THR5181 4.6 10.6 1.0 CA B:VAL5176 4.6 24.4 1.0 O B:GLY5174 4.6 19.8 1.0 CB B:THR5175 4.6 26.5 1.0 CB B:ASP5172 4.6 18.4 1.0 CA B:GLY5174 4.6 18.0 1.0 N B:ASP5178 4.7 15.2 1.0 CB B:ASP5178 4.8 14.8 1.0 O B:ARG5344 4.8 14.9 1.0 N B:ASN5179 4.9 14.2 1.0 N B:GLY5177 4.9 20.8 1.0 OG B:SER5173 4.9 13.4 1.0 CB B:THR5181 5.0 10.5 1.0

Calcium binding site 7 out of 9 in the Structural Insight Into the Giant Calcium-Binding Adhesin Siie: Implications For the Adhesion of Salmonella Enterica to Polarized Epithelial Cells


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structural Insight Into the Giant Calcium-Binding Adhesin Siie: Implications For the Adhesion of Salmonella Enterica to Polarized Epithelial Cells within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca6363 b:11.3 occ:1.00 O B:HOH2112 2.2 11.6 1.0 OD2 B:ASP5343 2.3 12.4 1.0 O B:HOH2115 2.3 15.3 1.0 O B:THR5258 2.3 12.2 1.0 OD2 B:ASP5296 2.4 15.3 1.0 OD2 B:ASP5256 2.5 13.1 1.0 OD1 B:ASP5256 2.5 12.1 1.0 CG B:ASP5256 2.9 11.9 1.0 CG B:ASP5296 3.4 17.5 1.0 CG B:ASP5343 3.4 13.8 1.0 C B:THR5258 3.6 13.0 1.0 OD1 B:ASP5296 3.6 19.8 1.0 CB B:ASP5343 4.0 13.1 1.0 ND2 B:ASN5347 4.0 12.9 1.0 O B:HOH2113 4.2 28.0 1.0 OD1 B:ASP5343 4.4 13.7 1.0 CB B:ASP5256 4.4 11.4 1.0 N B:LEU5259 4.5 12.0 1.0 N B:THR5258 4.5 13.2 1.0 CA B:THR5258 4.5 13.2 1.0 CA B:LEU5259 4.5 12.5 1.0 CB B:LEU5259 4.6 12.3 1.0 O B:HOH2103 4.7 12.5 1.0 CB B:ASP5296 4.8 16.7 1.0 CB B:THR5258 4.8 13.8 1.0 CD1 B:LEU5259 4.9 11.7 1.0 OD2 B:ASP5294 5.0 16.5 1.0

Calcium binding site 8 out of 9 in the Structural Insight Into the Giant Calcium-Binding Adhesin Siie: Implications For the Adhesion of Salmonella Enterica to Polarized Epithelial Cells


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structural Insight Into the Giant Calcium-Binding Adhesin Siie: Implications For the Adhesion of Salmonella Enterica to Polarized Epithelial Cells within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca6364 b:25.9 occ:1.00 OD1 B:ASP5271 2.3 25.7 1.0 OD1 B:ASP5278 2.3 30.0 1.0 O B:VAL5280 2.3 24.8 1.0 O B:ASN5272 2.4 34.2 1.0 O B:SER5275 2.4 47.1 1.0 C B:SER5275 3.4 49.9 1.0 C B:VAL5280 3.4 25.7 1.0 CG B:ASP5278 3.4 30.0 1.0 C B:ASN5272 3.4 33.3 1.0 CG B:ASP5271 3.5 25.7 1.0 N B:ASN5272 3.5 27.7 1.0 C B:ASP5271 3.7 27.7 1.0 N B:VAL5280 3.7 25.6 1.0 N B:SER5275 3.8 48.7 1.0 OD2 B:ASP5278 3.9 32.4 1.0 CA B:SER5275 3.9 49.6 1.0 CA B:ASN5272 4.0 30.5 1.0 CA B:VAL5280 4.0 26.2 1.0 O B:ASP5271 4.0 27.8 1.0 CB B:SER5275 4.1 51.1 1.0 CB B:VAL5280 4.2 26.2 1.0 OD2 B:ASP5271 4.2 25.0 1.0 CA B:ASP5271 4.3 24.9 1.0 N B:ASP5276 4.5 45.4 1.0 CB B:ASP5271 4.5 25.5 1.0 N B:ASP5278 4.5 32.1 1.0 N B:ASN5279 4.5 27.2 1.0 N B:THR5281 4.6 22.9 1.0 N B:GLY5273 4.6 36.2 1.0 OG B:SER5275 4.6 50.1 1.0 CB B:ASP5278 4.7 32.1 1.0 N B:ALA5274 4.7 41.2 1.0 C B:ASN5279 4.8 25.0 1.0 CA B:ASP5276 4.9 44.4 1.0 C B:GLY5273 4.9 39.2 1.0 CA B:THR5281 4.9 23.3 1.0 CA B:ASP5278 4.9 31.0 1.0 N B:SER5277 4.9 35.5 1.0 C B:ASP5278 4.9 28.4 1.0 C B:ALA5274 4.9 46.3 1.0 OD1 B:ASN5272 5.0 29.8 1.0 CA B:GLY5273 5.0 38.0 1.0

Calcium binding site 9 out of 9 in the Structural Insight Into the Giant Calcium-Binding Adhesin Siie: Implications For the Adhesion of Salmonella Enterica to Polarized Epithelial Cells


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structural Insight Into the Giant Calcium-Binding Adhesin Siie: Implications For the Adhesion of Salmonella Enterica to Polarized Epithelial Cells within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca6365 b:11.4 occ:1.00 OD1 B:ASP5157 2.3 13.6 1.0 OD2 B:ASP5240 2.3 13.2 1.0 O B:ILE5158 2.4 11.0 1.0 O B:GLU5136 2.4 12.7 1.0 OD2 B:ASP5196 2.4 11.8 1.0 O B:HOH2043 2.5 12.2 1.0 CG B:ASP5196 3.4 12.6 1.0 C B:GLU5136 3.4 12.7 1.0 C B:ILE5158 3.5 11.3 1.0 CG B:ASP5240 3.5 12.8 1.0 CG B:ASP5157 3.5 14.1 1.0 OD1 B:ASP5196 3.7 12.3 1.0 O B:HOH2050 3.9 13.4 1.0 CB B:ASP5240 4.0 12.7 1.0 OD2 B:ASP5157 4.0 14.2 1.0 N B:ILE5158 4.1 11.5 1.0 ND2 B:ASN5244 4.2 12.7 1.0 CA B:GLU5136 4.3 14.1 1.0 C B:ASP5157 4.3 12.0 1.0 N B:MET5159 4.3 12.1 1.0 CB B:MET5159 4.3 14.3 1.0 CA B:MET5159 4.3 13.9 1.0 N B:GLY5137 4.3 12.1 1.0 CA B:ILE5158 4.4 11.2 1.0 CA B:GLY5137 4.5 11.0 1.0 CB B:GLU5136 4.5 15.7 1.0 OD1 B:ASP5240 4.5 12.2 1.0 CB B:ASP5157 4.7 13.8 1.0 O B:ASP5157 4.7 13.3 1.0 C B:GLY5137 4.7 11.1 1.0 CA B:ASP5157 4.7 13.6 1.0 CB B:ASP5196 4.8 13.0 1.0 O B:GLY5137 4.8 10.2 1.0 CG B:MET5159 4.8 16.3 1.0 CG B:LYS5138 4.8 14.6 1.0 OE1 B:GLU5194 4.8 14.5 1.0 OH B:TYR5133 4.9 12.7 1.0

M.H.Griessl, B.Schmid, K.Kassler, C.Braunsmann, R.Ritter, B.Barlag, Y.Stierhof, K.U.Sturm, C.Danzer, C.Wagner, T.E.Schaffer, H.Sticht, M.Hensel, Y.A.Muller. Structural Insight Into the Giant Ca(2+)-Binding Adhesin Siie: Implications For the Adhesion of Salmonella Enterica to Polarized Epithelial Cells. Structure V. 21 741 2013.
ISSN: ISSN 0969-2126
PubMed: 23562396
DOI: 10.1016/J.STR.2013.02.020