Calcium in PDB 9cse: Crystal Structure of Repeats-in-Toxin-Like Domain From Aeromonas Hydrophila

The structure of Crystal Structure of Repeats-in-Toxin-Like Domain From Aeromonas Hydrophila, PDB code: 9cse was solved by Q.Ye, T.D.R.Vance, P.L.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.75 / 1.95
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	67.603, 103.327, 95.71, 90, 90, 90
R / Rfree (%)	20.3 / 25.8

The binding sites of Calcium atom in the Crystal Structure of Repeats-in-Toxin-Like Domain From Aeromonas Hydrophila (pdb code 9cse). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Crystal Structure of Repeats-in-Toxin-Like Domain From Aeromonas Hydrophila, PDB code: 9cse:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in the Crystal Structure of Repeats-in-Toxin-Like Domain From Aeromonas Hydrophila


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 Repeats-in-Toxin-Like Domain From Aeromonas Hydrophila within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4506 b:27.1 occ:1.00 O A:GLY4288 2.3 24.8 1.0 OD2 A:ASP4290 2.3 22.7 1.0 O A:HOH4695 2.4 30.7 1.0 OE1 A:GLU4330 2.4 28.6 1.0 O A:ASP4328 2.5 26.6 1.0 O A:GLY4286 2.5 26.5 1.0 OE2 A:GLU4330 2.6 25.8 1.0 CD A:GLU4330 2.8 26.7 1.0 C A:GLY4288 3.5 27.7 1.0 CG A:ASP4290 3.5 22.5 1.0 C A:ASP4328 3.6 28.8 1.0 C A:GLY4286 3.8 28.9 1.0 C A:ALA4287 3.9 26.1 1.0 CB A:ASP4328 4.0 31.3 1.0 N A:GLY4288 4.0 28.7 1.0 O A:ALA4287 4.1 25.6 1.0 CB A:ASP4290 4.1 21.3 1.0 N A:ASP4290 4.2 20.9 1.0 CA A:ASP4328 4.2 26.6 1.0 O A:HOH4609 4.3 59.3 1.0 CG A:GLU4330 4.3 27.7 1.0 CA A:GLY4288 4.3 28.2 1.0 CA A:ALA4287 4.4 26.1 1.0 N A:THR4289 4.4 27.1 1.0 C A:GLY4285 4.4 30.9 1.0 OD1 A:ASP4290 4.5 21.1 1.0 N A:GLY4286 4.5 32.1 1.0 N A:ALA4287 4.5 25.6 1.0 O A:HOH4681 4.5 40.1 1.0 N A:ILE4329 4.6 25.0 1.0 O A:GLY4285 4.6 29.2 1.0 CA A:THR4289 4.6 26.4 1.0 CA A:GLY4285 4.7 26.5 1.0 CA A:GLY4286 4.8 32.6 1.0 CA A:ILE4329 4.8 25.6 1.0 CA A:ASP4290 4.8 20.2 1.0 C A:THR4289 4.8 23.4 1.0 CA A:CA4508 4.9 25.5 1.0 O A:HOH4783 4.9 35.0 1.0 N A:GLU4330 5.0 21.1 1.0

Calcium binding site 2 out of 9 in the Crystal Structure of Repeats-in-Toxin-Like Domain From Aeromonas Hydrophila


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 Repeats-in-Toxin-Like Domain From Aeromonas Hydrophila within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4507 b:25.8 occ:1.00 O A:GLY4247 2.2 33.3 1.0 O A:ALA4249 2.2 30.8 1.0 OD2 A:ASP4233 2.3 25.1 1.0 O A:GLY4231 2.3 25.1 1.0 O A:THR4229 2.4 28.9 1.0 OD1 A:ASP4252 2.4 23.7 1.0 CG A:ASP4252 3.0 24.1 1.0 OD2 A:ASP4252 3.1 25.0 1.0 CG A:ASP4233 3.3 27.5 1.0 C A:GLY4247 3.4 32.6 1.0 C A:THR4229 3.5 31.6 1.0 C A:ALA4249 3.5 25.1 1.0 C A:GLY4231 3.6 25.3 1.0 N A:THR4229 4.0 27.4 1.0 N A:GLY4231 4.1 30.6 1.0 C A:GLY4248 4.1 32.0 1.0 CB A:ASP4233 4.1 25.0 1.0 N A:ASP4233 4.1 25.9 1.0 C A:SER4230 4.1 30.3 1.0 O A:GLY4248 4.2 24.8 1.0 OD1 A:ASP4233 4.2 26.6 1.0 CA A:GLY4247 4.2 29.4 1.0 N A:ALA4249 4.2 25.1 1.0 CA A:THR4229 4.3 30.3 1.0 OG1 A:THR4229 4.4 26.8 1.0 N A:SER4230 4.4 30.6 1.0 N A:GLY4250 4.4 26.6 1.0 N A:GLY4248 4.4 30.4 1.0 CA A:GLY4250 4.4 27.1 1.0 CA A:GLY4231 4.5 26.2 1.0 CA A:SER4230 4.5 33.0 1.0 CB A:ASP4252 4.5 23.3 1.0 O A:SER4230 4.5 31.0 1.0 CA A:ALA4249 4.5 27.6 1.0 CA A:GLY4248 4.5 31.6 1.0 N A:ASN4232 4.5 26.8 1.0 O A:GLY4250 4.6 26.3 1.0 C A:GLY4250 4.6 27.9 1.0 CA A:ASN4232 4.7 24.7 1.0 CA A:CA4509 4.7 25.8 1.0 CA A:ASP4233 4.8 23.9 1.0 C A:ASN4232 4.8 23.8 1.0 C A:GLY4228 4.9 28.8 1.0

Calcium binding site 3 out of 9 in the Crystal Structure of Repeats-in-Toxin-Like Domain From Aeromonas Hydrophila


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 Repeats-in-Toxin-Like Domain From Aeromonas Hydrophila within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4508 b:25.5 occ:1.00 OD2 A:ASP4272 2.3 25.7 1.0 O A:ALA4287 2.3 25.6 1.0 OD1 A:ASP4290 2.4 21.1 1.0 O A:GLY4268 2.4 24.3 1.0 O A:GLY4285 2.4 29.2 1.0 O A:GLY4270 2.4 22.2 1.0 CG A:ASP4290 3.0 22.5 1.0 OD2 A:ASP4290 3.1 22.7 1.0 CG A:ASP4272 3.4 24.1 1.0 C A:GLY4285 3.5 30.9 1.0 C A:ALA4287 3.6 26.1 1.0 C A:GLY4270 3.6 27.1 1.0 C A:GLY4268 3.6 29.8 1.0 C A:GLY4286 3.9 28.9 1.0 C A:THR4269 3.9 24.8 1.0 O A:GLY4286 3.9 26.5 1.0 O A:THR4269 4.0 27.1 1.0 N A:GLY4270 4.1 23.8 1.0 N A:ALA4287 4.1 25.6 1.0 CB A:ASP4272 4.2 21.4 1.0 N A:ASP4272 4.2 20.9 1.0 CA A:GLY4286 4.3 32.6 1.0 CA A:THR4269 4.3 25.2 1.0 C A:GLY4267 4.3 30.2 1.0 N A:GLY4286 4.3 32.1 1.0 OD1 A:ASP4272 4.3 25.4 1.0 N A:GLY4268 4.4 28.4 1.0 N A:THR4269 4.4 26.2 1.0 CB A:ASP4290 4.4 21.3 1.0 CA A:GLY4270 4.4 29.4 1.0 N A:GLY4288 4.4 28.7 1.0 N A:ASN4271 4.5 29.8 1.0 CA A:GLY4285 4.5 26.5 1.0 CA A:ALA4287 4.5 26.1 1.0 O A:GLY4267 4.5 26.4 1.0 CA A:GLY4288 4.5 28.2 1.0 CA A:GLY4267 4.6 29.6 1.0 CA A:GLY4268 4.6 29.1 1.0 CA A:ASN4271 4.7 26.8 1.0 C A:GLY4288 4.8 27.7 1.0 CA A:CA4509 4.8 25.8 1.0 CA A:ASP4272 4.9 20.5 1.0 O A:GLY4288 4.9 24.8 1.0 CA A:CA4506 4.9 27.1 1.0 C A:ASN4271 4.9 23.4 1.0

Calcium binding site 4 out of 9 in the Crystal Structure of Repeats-in-Toxin-Like Domain From Aeromonas Hydrophila


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 Repeats-in-Toxin-Like Domain From Aeromonas Hydrophila within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4509 b:25.8 occ:1.00 OD2 A:ASP4252 2.2 25.0 1.0 O A:THR4269 2.2 27.1 1.0 O A:GLY4267 2.3 26.4 1.0 OD1 A:ASP4272 2.4 25.4 1.0 O A:GLY4250 2.4 26.3 1.0 O A:GLY4248 2.4 24.8 1.0 CG A:ASP4272 3.1 24.1 1.0 OD2 A:ASP4272 3.2 25.7 1.0 CG A:ASP4252 3.4 24.1 1.0 C A:GLY4267 3.5 30.2 1.0 C A:THR4269 3.5 24.8 1.0 C A:GLY4250 3.6 27.9 1.0 C A:GLY4248 3.6 32.0 1.0 C A:ALA4249 3.9 25.1 1.0 C A:GLY4268 4.0 29.8 1.0 O A:ALA4249 4.0 30.8 1.0 CB A:ASP4252 4.0 23.3 1.0 N A:GLY4250 4.1 26.6 1.0 N A:THR4269 4.1 26.2 1.0 O A:GLY4268 4.2 24.3 1.0 N A:ASP4252 4.2 23.0 1.0 C A:GLY4247 4.3 32.6 1.0 CA A:GLY4268 4.3 29.1 1.0 N A:GLY4268 4.3 28.4 1.0 OD1 A:ASP4252 4.3 23.7 1.0 CA A:ALA4249 4.3 27.6 1.0 N A:GLY4248 4.4 30.4 1.0 N A:GLY4270 4.4 23.8 1.0 CA A:GLY4270 4.4 29.4 1.0 O A:GLY4247 4.4 33.3 1.0 CA A:GLY4267 4.4 29.6 1.0 N A:ALA4249 4.4 25.1 1.0 CA A:GLY4250 4.4 27.1 1.0 CB A:ASP4272 4.5 21.4 1.0 CA A:THR4269 4.5 25.2 1.0 N A:ASN4251 4.6 30.0 1.0 C A:GLY4270 4.6 27.1 1.0 CA A:GLY4248 4.6 31.6 1.0 CA A:GLY4247 4.7 29.4 1.0 CA A:CA4507 4.7 25.8 1.0 CA A:ASN4251 4.7 27.0 1.0 CA A:ASP4252 4.7 21.1 1.0 O A:GLY4270 4.8 22.2 1.0 CA A:CA4508 4.8 25.5 1.0 C A:ASN4251 4.9 26.9 1.0

Calcium binding site 5 out of 9 in the Crystal Structure of Repeats-in-Toxin-Like Domain From Aeromonas Hydrophila


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 Repeats-in-Toxin-Like Domain From Aeromonas Hydrophila within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4510 b:32.9 occ:1.00 OD1 A:ASP4281 2.0 30.1 1.0 O A:GLY4257 2.1 37.1 1.0 O A:ALA4276 2.4 29.7 1.0 O A:LEU4278 2.4 43.2 1.0 OD2 A:ASP4263 2.4 35.8 1.0 O A:HOH4628 2.5 31.2 1.0 CG A:ASP4281 2.7 35.5 1.0 OD2 A:ASP4281 2.8 30.9 1.0 C A:GLY4257 3.4 34.5 1.0 CG A:ASP4263 3.5 36.3 1.0 C A:ALA4276 3.6 27.2 1.0 C A:LEU4278 3.6 40.1 1.0 N A:GLY4257 3.8 36.4 1.0 C A:GLY4277 3.9 30.0 1.0 O A:HOH4708 4.1 53.2 1.0 N A:LEU4278 4.1 32.5 1.0 CA A:GLY4277 4.1 28.7 1.0 O A:GLY4277 4.1 31.0 1.0 CB A:ASP4281 4.2 33.9 1.0 CA A:GLY4257 4.2 35.5 1.0 N A:ASP4263 4.2 38.5 1.0 CB A:ASP4263 4.3 31.9 1.0 N A:GLY4277 4.3 27.5 1.0 N A:ASN4258 4.4 41.0 1.0 C A:GLY4256 4.4 28.5 1.0 OD1 A:ASP4263 4.4 34.3 1.0 N A:GLY4279 4.5 35.2 1.0 CA A:LEU4278 4.5 36.4 1.0 O A:SER4259 4.5 51.6 1.0 CA A:ALA4276 4.6 27.1 1.0 CA A:GLY4256 4.6 28.8 1.0 CA A:GLY4279 4.6 36.5 1.0 CA A:ASN4258 4.7 42.6 1.0 C A:GLY4279 4.9 35.3 1.0 CA A:ASP4263 4.9 31.7 1.0 O A:SER4261 4.9 43.4 1.0 O A:GLY4279 5.0 40.6 1.0

Calcium binding site 6 out of 9 in the Crystal Structure of Repeats-in-Toxin-Like Domain From Aeromonas Hydrophila


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 Repeats-in-Toxin-Like Domain From Aeromonas Hydrophila within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4511 b:45.4 occ:1.00 O A:HOH4632 1.8 32.9 1.0 OD1 A:ASP4370 2.2 45.0 1.0 OD2 A:ASP4370 2.3 34.4 1.0 OD1 A:ASP4368 2.5 43.4 1.0 CG A:ASP4370 2.5 43.7 1.0 O A:HOH4735 2.6 49.7 1.0 OG A:SER4372 2.6 37.5 1.0 OD2 A:ASP4368 2.7 50.5 1.0 O A:HOH4675 2.7 44.4 1.0 CG A:ASP4368 2.9 51.8 1.0 CB A:SER4372 3.7 38.3 1.0 CB A:ASP4370 4.1 45.9 1.0 CA A:CA4513 4.3 51.0 1.0 OE1 A:GLU4445 4.3 54.5 1.0 CB A:ASP4368 4.4 50.6 1.0 OE2 A:GLU4445 4.5 46.6 1.0 N A:SER4372 4.7 38.7 1.0 CA A:SER4372 4.7 41.9 1.0 N A:ASP4370 4.8 41.4 1.0 O A:HOH4635 4.8 35.7 1.0 CA A:ASP4370 4.9 41.6 1.0 CD A:GLU4445 4.9 51.7 1.0

Calcium binding site 7 out of 9 in the Crystal Structure of Repeats-in-Toxin-Like Domain From Aeromonas Hydrophila


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 Repeats-in-Toxin-Like Domain From Aeromonas Hydrophila within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4512 b:50.2 occ:1.00 OD1 A:ASP4243 2.3 40.5 1.0 OD2 A:ASP4218 2.4 47.5 1.0 O A:THR4220 2.5 73.0 1.0 O A:GLY4240 2.5 59.5 1.0 OD2 A:ASP4224 2.6 39.4 1.0 OD2 A:ASP4243 2.8 35.6 1.0 CG A:ASP4243 2.8 41.1 1.0 O A:THR4222 3.2 51.4 1.0 CG A:ASP4218 3.3 38.7 1.0 CB A:ASP4218 3.5 43.1 1.0 C A:THR4220 3.5 68.8 1.0 CG A:ASP4224 3.5 40.6 1.0 C A:GLY4240 3.7 51.9 1.0 N A:THR4220 4.1 63.9 1.0 OG A:SER4237 4.2 44.0 1.0 CB A:ASP4224 4.2 44.1 1.0 C A:LYS4239 4.2 62.1 1.0 N A:THR4222 4.2 52.4 1.0 CB A:LYS4239 4.2 66.6 1.0 OG1 A:THR4220 4.2 66.6 1.0 N A:GLY4240 4.3 57.6 1.0 OD1 A:ASP4224 4.3 50.8 1.0 N A:THR4221 4.3 57.7 1.0 CA A:THR4221 4.3 51.8 1.0 O A:LYS4239 4.3 63.0 1.0 CB A:ASP4243 4.3 41.6 1.0 CA A:THR4220 4.4 60.8 1.0 C A:THR4222 4.4 47.9 1.0 C A:THR4221 4.5 54.7 1.0 N A:SER4219 4.5 53.0 1.0 OD1 A:ASP4218 4.5 43.8 1.0 CA A:GLY4240 4.6 50.8 1.0 N A:GLY4241 4.6 50.5 1.0 CA A:LYS4239 4.7 64.3 1.0 N A:ASP4224 4.7 50.6 1.0 CA A:ASP4218 4.8 44.6 1.0 CA A:GLY4241 4.8 43.6 1.0 C A:SER4219 4.9 60.3 1.0 N A:LYS4239 4.9 54.3 1.0 CG A:LYS4239 5.0 72.9 1.0 CB A:THR4220 5.0 65.7 1.0 CA A:THR4222 5.0 56.6 1.0

Calcium binding site 8 out of 9 in the Crystal Structure of Repeats-in-Toxin-Like Domain From Aeromonas Hydrophila


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 Repeats-in-Toxin-Like Domain From Aeromonas Hydrophila within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4513 b:51.0 occ:1.00 OD2 A:ASP4368 2.1 50.5 1.0 OE2 A:GLU4445 2.4 46.6 1.0 OE2 A:GLU4373 2.5 46.5 1.0 O A:VAL4169 2.6 59.1 1.0 O A:HOH4675 3.1 44.4 1.0 OD1 A:ASP4171 3.1 56.6 1.0 CG A:ASP4368 3.2 51.8 1.0 CD A:GLU4445 3.3 51.7 1.0 CD A:GLU4373 3.5 44.0 1.0 C A:VAL4169 3.6 68.4 1.0 O A:HOH4691 3.6 47.9 1.0 CG A:ASP4171 3.7 47.6 1.0 CB A:ASP4368 3.7 50.6 1.0 N A:ASP4171 3.8 43.8 1.0 CG A:GLU4373 3.9 43.9 1.0 O A:HOH4632 3.9 32.9 1.0 OE1 A:GLU4445 3.9 54.5 1.0 CA A:ALA4170 4.1 51.1 1.0 OD2 A:ASP4171 4.1 68.0 1.0 N A:ALA4170 4.2 60.2 1.0 CA A:CA4511 4.3 45.4 1.0 CG A:GLU4445 4.3 58.8 1.0 C A:ALA4170 4.3 44.0 1.0 OD1 A:ASP4368 4.3 43.4 1.0 CB A:ASP4171 4.4 47.6 1.0 N A:VAL4169 4.4 65.3 1.0 OE1 A:GLU4373 4.6 45.4 1.0 CA A:VAL4169 4.7 69.7 1.0 OG A:SER4372 4.7 37.5 1.0 CA A:ASP4171 4.7 43.1 1.0 C A:ALA4168 5.0 70.0 1.0

Calcium binding site 9 out of 9 in the Crystal Structure of Repeats-in-Toxin-Like Domain From Aeromonas Hydrophila


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 Repeats-in-Toxin-Like Domain From Aeromonas Hydrophila within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4514 b:83.8 occ:1.00 OD1 A:ASP4263 2.5 34.3 1.0 OG A:SER4237 2.5 44.0 1.0 O A:HOH4708 2.7 53.2 1.0 N A:GLY4242 3.2 49.1 1.0 CB A:SER4237 3.2 41.0 1.0 CA A:GLY4240 3.3 50.8 1.0 N A:GLY4257 3.3 36.4 1.0 C A:GLY4240 3.3 51.9 1.0 OD2 A:ASP4243 3.4 35.6 1.0 CG A:ASP4263 3.5 36.3 1.0 N A:GLY4241 3.5 50.5 1.0 CA A:GLY4257 3.6 35.5 1.0 N A:ASP4243 3.6 45.5 1.0 CA A:GLY4242 3.7 42.1 1.0 OD2 A:ASP4263 3.7 35.8 1.0 O A:GLY4240 3.8 59.5 1.0 CG A:ASP4243 3.9 41.1 1.0 C A:GLY4242 4.2 49.9 1.0 N A:GLY4240 4.2 57.6 1.0 C A:GLY4241 4.3 45.9 1.0 CB A:ASP4243 4.3 41.6 1.0 C A:GLY4257 4.4 34.5 1.0 C A:GLY4256 4.4 28.5 1.0 CA A:GLY4241 4.5 43.6 1.0 OD1 A:ASP4243 4.5 40.5 1.0 CA A:ASP4243 4.6 42.0 1.0 CA A:SER4237 4.6 37.6 1.0 O A:HOH4628 4.7 31.2 1.0 OG A:SER4259 4.8 56.0 1.0 CA A:GLY4256 4.8 28.8 1.0 O A:GLY4257 4.8 37.1 1.0 CB A:ASP4263 4.8 31.9 1.0

Q.Ye, R.Eves, T.D.R.Vance, T.Hansen, A.P.Sage, A.Petkovic, B.Bradley, C.Escobedo, L.A.Graham, J.S.Allingham, P.L.Davies. Aeromonas Hydrophila Rtx Adhesin Has Three Ligand-Binding Domains That Give the Bacterium the Potential to Adhere to and Aggregate A Wide Variety of Cell Types. Mbio 15824 2025.
ISSN: ESSN 2150-7511
PubMed: 40243363
DOI: 10.1128/MBIO.03158-24