Calcium in PDB 4xhe: Crystal Structure of A-Achbp in Complex with Pinnatoxin A

The structure of Crystal Structure of A-Achbp in Complex with Pinnatoxin A, PDB code: 4xhe was solved by Y.Bourne, G.Sulzenbacher, P.Marchot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.02 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	129.734, 144.231, 147.121, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 21.6

The structure of Crystal Structure of A-Achbp in Complex with Pinnatoxin A also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of A-Achbp in Complex with Pinnatoxin A (pdb code 4xhe). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of A-Achbp in Complex with Pinnatoxin A, PDB code: 4xhe:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of A-Achbp in Complex with Pinnatoxin A


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 A-Achbp in Complex with Pinnatoxin A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:39.5 occ:1.00 O B:ASN70 2.3 38.7 1.0 O B:HOH517 2.4 25.8 1.0 O B:LYS-6 2.4 44.0 1.0 OD1 B:ASP-2 2.4 52.3 1.0 O B:HOH487 2.5 23.7 1.0 OD1 B:ASP-3 2.6 41.4 1.0 OD2 B:ASP-3 2.7 42.3 1.0 CG B:ASP-3 3.0 43.3 1.0 C B:ASN70 3.3 38.2 1.0 CG B:ASP-2 3.4 52.5 1.0 C B:LYS-6 3.5 44.9 1.0 OD2 B:ASP-2 3.7 55.0 1.0 CA B:ASN70 4.0 39.4 1.0 CB B:LYS-6 4.2 44.1 1.0 N B:ASP-5 4.4 47.1 1.0 CA B:ASP-5 4.4 48.6 1.0 N B:ASP-2 4.4 48.4 1.0 N B:GLU71 4.4 37.4 1.0 CB B:ASN70 4.4 40.9 1.0 CA B:LYS-6 4.5 44.3 1.0 CB B:ASP-3 4.5 44.4 1.0 CB B:ASP-2 4.7 51.1 1.0 CA B:GLU71 4.7 38.2 1.0 N B:GLY73 4.8 34.3 1.0 CA B:ASP-2 4.9 50.2 1.0 C B:ASP-5 4.9 48.9 1.0 C B:GLU71 5.0 37.2 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of A-Achbp in Complex with Pinnatoxin A


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 A-Achbp in Complex with Pinnatoxin A within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca302 b:44.6 occ:1.00 O D:HOH552 2.3 34.8 1.0 O D:HOH553 2.4 35.0 1.0 O D:HOH554 2.5 34.7 1.0 O E:HOH555 2.6 28.4 1.0 O E:HOH448 2.7 19.4 1.0 OG D:SER166 2.8 26.6 1.0 CL E:CL302 2.9 63.5 1.0 CB D:SER166 4.0 28.5 1.0 O E:HOH532 4.3 35.9 1.0 O66 E:40P301 4.3 27.4 1.0 OG D:SER167 4.3 26.4 1.0 OD1 D:ASP164 4.4 29.9 1.0 C61 E:40P301 4.7 26.4 1.0 OD2 D:ASP164 4.8 28.2 1.0 O1 E:40P301 4.9 31.3 1.0 C D:SER166 4.9 27.8 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of A-Achbp in Complex with Pinnatoxin A


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 A-Achbp in Complex with Pinnatoxin A within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca302 b:36.8 occ:1.00 O I:HOH533 2.2 37.5 1.0 O I:HOH543 2.2 32.7 1.0 O J:HOH506 2.5 17.5 1.0 OG I:SER166 2.7 22.9 1.0 O J:HOH514 2.8 29.4 1.0 CL J:CL302 3.4 56.1 1.0 CB I:SER166 3.7 23.2 1.0 OD1 I:ASP164 4.3 32.9 1.0 OG I:SER167 4.3 25.8 1.0 O66 J:40P301 4.4 19.0 1.0 OD2 I:ASP164 4.7 26.5 1.0 C I:SER166 4.8 25.4 1.0 C61 J:40P301 4.8 18.6 1.0 CA I:SER166 4.8 24.1 1.0 O J:HOH570 4.9 40.3 1.0 O1 J:40P301 4.9 23.7 1.0 O I:SER166 4.9 27.0 1.0 CG I:ASP164 5.0 26.9 1.0

Y.Bourne, G.Sulzenbacher, Z.Radic, R.Araoz, M.Reynaud, E.Benoit, A.Zakarian, D.Servent, J.Molgo, P.Taylor, P.Marchot. Marine Macrocyclic Imines, Pinnatoxins A and G: Structural Determinants and Functional Properties to Distinguish Neuronal Alpha 7 From Muscle Alpha 12 Beta Gamma Delta Nachrs. Structure V. 23 1106 2015.
ISSN: ISSN 0969-2126
PubMed: 26004441
DOI: 10.1016/J.STR.2015.04.009