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

Protein crystallography data

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

Calcium Binding Sites:

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 8dml

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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 8dml

Go back to Calcium Binding Sites List in 8dml
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 8dml

Go back to Calcium Binding Sites List in 8dml
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 8dml

Go back to Calcium Binding Sites List in 8dml
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

Reference:

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
Page generated: Thu Jul 10 03:58:18 2025

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