Calcium in PDB 8dml: Vibrio Parahaemolyticus Vtra/Vtrc Complex Bound to the Bile Salt Chenodeoxycholate

The structure of Vibrio Parahaemolyticus Vtra/Vtrc Complex Bound to the Bile Salt Chenodeoxycholate, PDB code: 8dml was solved by D.R.Tomchick, K.Orth, A.J.Zou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.78 / 2.08
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	142.603, 41.763, 168.956, 90, 91.57, 90
R / Rfree (%)	18.8 / 22.4

The binding sites of Calcium atom in the Vibrio Parahaemolyticus Vtra/Vtrc Complex Bound to the Bile Salt Chenodeoxycholate (pdb code 8dml). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Vibrio Parahaemolyticus Vtra/Vtrc Complex Bound to the Bile Salt Chenodeoxycholate, PDB code: 8dml:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Vibrio Parahaemolyticus Vtra/Vtrc Complex Bound to the Bile Salt Chenodeoxycholate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Vibrio Parahaemolyticus Vtra/Vtrc Complex Bound to the Bile Salt Chenodeoxycholate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca204 b:34.8 occ:1.00 OE2 B:GLU120 2.3 55.1 1.0 O B:HOH336 2.3 38.8 1.0 O B:ILE104 2.4 19.4 1.0 OD1 B:ASP105 2.4 19.1 1.0 OD1 B:ASN103 2.5 23.3 1.0 CD B:GLU120 3.1 54.7 1.0 O B:HOH356 3.1 43.9 1.0 C B:ILE104 3.3 22.4 1.0 H B:ILE104 3.3 25.8 1.0 HD21 B:ASN103 3.3 32.4 1.0 HA B:ASP105 3.4 23.4 1.0 CG B:ASN103 3.4 27.2 1.0 OE1 B:GLU120 3.5 52.0 1.0 CG B:ASP105 3.7 24.5 1.0 ND2 B:ASN103 3.7 26.9 1.0 N B:ILE104 3.9 21.5 1.0 N B:ASP105 4.0 16.1 1.0 CA B:ASP105 4.1 19.5 1.0 CA B:ILE104 4.3 22.3 1.0 CG B:GLU120 4.3 48.5 1.0 HG3 B:GLU120 4.4 58.2 1.0 HG2 B:GLU120 4.5 58.2 1.0 CB B:ASP105 4.5 18.4 1.0 OD2 B:ASP105 4.5 29.9 1.0 HD22 B:ASN103 4.6 32.4 1.0 HA B:ASN103 4.6 33.3 1.0 O B:HOH327 4.6 32.4 1.0 O B:HOH331 4.7 31.5 1.0 H B:ASP105 4.7 19.3 1.0 CB B:ASN103 4.8 26.7 1.0 HB B:ILE104 4.8 27.6 1.0 C B:ASN103 4.9 20.2 1.0 HA B:ILE104 5.0 26.9 1.0 CA B:ASN103 5.0 27.7 1.0

Calcium binding site 2 out of 4 in the Vibrio Parahaemolyticus Vtra/Vtrc Complex Bound to the Bile Salt Chenodeoxycholate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Vibrio Parahaemolyticus Vtra/Vtrc Complex Bound to the Bile Salt Chenodeoxycholate within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca204 b:31.6 occ:1.00 O D:ILE104 2.4 24.8 1.0 OE2 D:GLU120 2.4 48.6 1.0 OD1 D:ASN103 2.4 26.7 1.0 OD1 D:ASP105 2.4 23.3 1.0 OE1 D:GLU120 2.9 51.5 1.0 CD D:GLU120 2.9 53.1 1.0 H D:ILE104 3.3 25.3 1.0 C D:ILE104 3.3 22.2 1.0 HA D:ASP105 3.3 29.0 1.0 HD21 D:ASN103 3.4 28.9 1.0 CG D:ASN103 3.4 25.4 1.0 CG D:ASP105 3.7 26.2 1.0 ND2 D:ASN103 3.8 24.1 1.0 N D:ILE104 3.9 21.0 1.0 N D:ASP105 3.9 20.6 1.0 CA D:ASP105 4.0 24.1 1.0 CA D:ILE104 4.3 24.0 1.0 CG D:GLU120 4.4 51.2 1.0 CB D:ASP105 4.4 22.2 1.0 HG2 D:GLU120 4.5 61.5 1.0 HD11 D:ILE128 4.5 45.2 1.0 OD2 D:ASP105 4.6 25.3 1.0 O D:HOH309 4.6 29.8 1.0 HA D:ASN103 4.6 26.4 1.0 H D:ASP105 4.7 24.9 1.0 HD22 D:ASN103 4.7 28.9 1.0 HD13 D:ILE128 4.7 45.2 1.0 HG3 D:GLU120 4.7 61.5 1.0 HB D:ILE104 4.8 26.5 1.0 CB D:ASN103 4.8 23.2 1.0 C D:ASN103 4.9 24.8 1.0 HA D:ILE104 5.0 28.9 1.0 HB3 D:ASP105 5.0 26.2 1.0

Calcium binding site 3 out of 4 in the Vibrio Parahaemolyticus Vtra/Vtrc Complex Bound to the Bile Salt Chenodeoxycholate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Vibrio Parahaemolyticus Vtra/Vtrc Complex Bound to the Bile Salt Chenodeoxycholate within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca203 b:70.7 occ:1.00 OE1 F:GLU120 2.4 91.2 1.0 OD1 F:ASP105 2.5 69.5 1.0 OD1 F:ASN103 2.5 69.0 1.0 O F:HOH310 2.6 58.1 1.0 O F:ILE104 2.7 67.2 1.0 CD F:GLU120 3.3 103.6 1.0 HD21 F:ASN103 3.5 84.7 1.0 OE2 F:GLU120 3.5 107.2 1.0 CG F:ASN103 3.5 68.7 1.0 H F:ILE104 3.6 77.4 1.0 C F:ILE104 3.7 65.8 1.0 CG F:ASP105 3.7 69.1 1.0 HA F:ASP105 3.8 79.7 1.0 ND2 F:ASN103 3.9 70.5 1.0 N F:ILE104 4.2 64.8 1.0 N F:ASP105 4.4 65.4 1.0 CA F:ASP105 4.4 66.7 1.0 OD2 F:ASP105 4.5 71.2 1.0 CA F:ILE104 4.6 65.2 1.0 CG F:GLU120 4.7 98.4 1.0 HA F:ASN103 4.7 79.9 1.0 CB F:ASP105 4.7 68.0 1.0 HB3 F:GLU120 4.7 110.0 1.0 HD22 F:ASN103 4.7 84.7 1.0 HG2 F:GLU120 4.8 118.2 1.0 CB F:ASN103 4.9 67.7 1.0 HD11 F:ILE128 5.0 111.9 1.0

Calcium binding site 4 out of 4 in the Vibrio Parahaemolyticus Vtra/Vtrc Complex Bound to the Bile Salt Chenodeoxycholate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Vibrio Parahaemolyticus Vtra/Vtrc Complex Bound to the Bile Salt Chenodeoxycholate within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca203 b:92.7 occ:1.00 OE2 H:GLU120 2.2 114.7 1.0 OD1 H:ASN103 2.3 79.8 1.0 OD1 H:ASP105 2.4 82.7 1.0 O H:ILE104 2.8 74.3 1.0 HD21 H:ASN103 3.1 90.2 1.0 CG H:ASN103 3.3 72.4 1.0 CD H:GLU120 3.5 123.5 1.0 ND2 H:ASN103 3.6 75.1 1.0 CG H:ASP105 3.6 72.2 1.0 H H:ILE104 3.7 83.0 1.0 C H:ILE104 3.7 67.2 1.0 HA H:ASP105 3.8 79.5 1.0 N H:ILE104 4.3 69.1 1.0 OE1 H:GLU120 4.3 121.9 1.0 OD2 H:ASP105 4.3 78.9 1.0 HG2 H:GLU120 4.4 154.3 1.0 CA H:ASP105 4.4 66.2 1.0 HD22 H:ASN103 4.4 90.2 1.0 N H:ASP105 4.4 66.5 1.0 CG H:GLU120 4.5 128.5 1.0 HG3 H:GLU120 4.5 154.3 1.0 CB H:ASP105 4.6 71.0 1.0 CB H:ASN103 4.7 69.8 1.0 CA H:ILE104 4.7 69.2 1.0 HD11 H:ILE128 4.7 127.0 1.0 HD13 H:ILE128 4.7 127.0 1.0 HA H:ASN103 4.8 85.2 1.0 HB2 H:ASN103 4.9 83.8 1.0

A.J.Zou, L.Kinch, S.Chimalapati, N.Garcia, D.R.Tomchick, K.Orth. Molecular Determinants For Differential Activation of the Bile Acid Receptor From the Pathogen Vibrio Parahaemolyticus. J.Biol.Chem. V. 299 04591 2023.
ISSN: ESSN 1083-351X
PubMed: 36894018
DOI: 10.1016/J.JBC.2023.104591