Calcium in PDB 5lo8: The C2B Domain of Rabphilin 3A in Complex with Pi(4,5)P2

The structure of The C2B Domain of Rabphilin 3A in Complex with Pi(4,5)P2, PDB code: 5lo8 was solved by C.Ferrer-Orta, N.Verdaguer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.42 / 2.50
Space group	P 4
Cell size a, b, c (Å), α, β, γ (°)	92.520, 92.520, 40.020, 90.00, 90.00, 90.00
R / Rfree (%)	25.2 / 26.5

The binding sites of Calcium atom in the The C2B Domain of Rabphilin 3A in Complex with Pi(4,5)P2 (pdb code 5lo8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the The C2B Domain of Rabphilin 3A in Complex with Pi(4,5)P2, PDB code: 5lo8:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the The C2B Domain of Rabphilin 3A in Complex with Pi(4,5)P2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The C2B Domain of Rabphilin 3A in Complex with Pi(4,5)P2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:22.0 occ:1.00 OD1 A:ASP571 2.4 22.2 1.0 OD2 A:ASP631 2.6 20.7 1.0 OD2 A:ASP633 2.7 22.8 1.0 OD1 A:ASP633 2.7 22.6 1.0 OD1 A:ASP639 2.7 23.4 1.0 O A:MET570 2.8 25.4 1.0 CG A:ASP639 3.0 22.3 1.0 CG A:ASP633 3.1 22.7 1.0 OD2 A:ASP639 3.3 22.9 1.0 CG A:ASP571 3.5 22.1 1.0 C A:MET570 3.6 23.9 1.0 CG A:ASP631 3.8 20.6 1.0 CA A:CA702 3.8 24.6 1.0 CB A:ASP639 3.9 21.5 1.0 CA A:ASP571 4.0 22.3 1.0 N A:ASP571 4.1 22.1 1.0 CB A:MET570 4.2 22.0 1.0 O3 A:SO4707 4.3 28.9 1.0 CB A:ASP571 4.4 22.3 1.0 OD2 A:ASP571 4.4 22.0 1.0 O A:HOH804 4.4 24.0 1.0 OD1 A:ASP631 4.5 20.6 1.0 CA A:MET570 4.5 24.1 1.0 CB A:ASP633 4.6 22.8 1.0 CB A:ASP631 4.9 20.4 1.0

Calcium binding site 2 out of 4 in the The C2B Domain of Rabphilin 3A in Complex with Pi(4,5)P2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The C2B Domain of Rabphilin 3A in Complex with Pi(4,5)P2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:24.6 occ:1.00 OD2 A:ASP577 2.4 20.1 1.0 OD1 A:ASP633 2.5 22.6 1.0 OD2 A:ASP571 2.5 22.0 1.0 OD1 A:ASP571 2.5 22.2 1.0 O A:TYR632 2.6 19.9 1.0 OD1 A:ASP631 2.8 20.6 1.0 CG A:ASP571 2.8 22.1 1.0 OD2 A:ASP631 3.2 20.7 1.0 O3 A:SO4707 3.3 28.9 1.0 CG A:ASP631 3.4 20.6 1.0 C A:TYR632 3.4 19.9 1.0 CG A:ASP577 3.5 19.0 1.0 CG A:ASP633 3.6 22.7 1.0 O4 A:SO4707 3.8 26.1 1.0 CA A:CA701 3.8 22.0 1.0 CA A:ASP633 3.9 22.7 1.0 N A:ASP633 4.0 22.5 1.0 CB A:ASP577 4.1 18.8 1.0 S A:SO4707 4.2 26.7 1.0 CB A:ASP571 4.3 22.3 1.0 CB A:ASP633 4.3 22.8 1.0 N A:ASP577 4.4 18.7 1.0 N A:TYR632 4.4 20.5 1.0 OD1 A:ASP577 4.4 20.0 1.0 OD2 A:ASP633 4.5 22.8 1.0 CA A:TYR632 4.5 19.8 1.0 C A:ASP631 4.6 20.4 1.0 CB A:ASP631 4.8 20.4 1.0 CA A:ASP577 4.9 18.6 1.0 O A:ASP631 4.9 20.5 1.0

Calcium binding site 3 out of 4 in the The C2B Domain of Rabphilin 3A in Complex with Pi(4,5)P2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The C2B Domain of Rabphilin 3A in Complex with Pi(4,5)P2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca701 b:17.8 occ:1.00 O B:TYR632 2.4 23.3 1.0 OD1 B:ASP571 2.4 24.1 1.0 OD2 B:ASP571 2.4 25.2 1.0 OD1 B:ASP631 2.5 26.9 1.0 OD1 B:ASP633 2.5 25.8 1.0 CG B:ASP571 2.7 24.3 1.0 OD2 B:ASP577 2.9 20.9 1.0 CG B:ASP633 3.0 25.9 1.0 OD2 B:ASP633 3.0 25.1 1.0 OD2 B:ASP631 3.2 26.6 1.0 CG B:ASP631 3.2 26.6 1.0 CG B:ASP577 3.3 22.7 1.0 N B:ASP577 3.4 24.2 1.0 C B:TYR632 3.5 23.3 1.0 CB B:ASP577 3.7 23.7 1.0 OD1 B:ASP577 4.0 21.2 1.0 CA B:ASP577 4.2 24.9 1.0 C B:SER576 4.2 24.2 1.0 CB B:ASP633 4.2 22.6 1.0 CA B:CA702 4.2 28.2 1.0 CB B:ASP571 4.2 24.3 1.0 CA B:SER576 4.3 25.1 1.0 CA B:ASP633 4.3 27.6 1.0 N B:TYR632 4.3 23.2 1.0 N B:ASP633 4.3 22.6 1.0 CA B:TYR632 4.5 23.2 1.0 CB B:ASP631 4.6 25.0 1.0 C B:ASP631 4.6 23.6 1.0

Calcium binding site 4 out of 4 in the The C2B Domain of Rabphilin 3A in Complex with Pi(4,5)P2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The C2B Domain of Rabphilin 3A in Complex with Pi(4,5)P2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca702 b:28.2 occ:1.00 OD1 B:ASP571 2.5 24.1 1.0 OD2 B:ASP639 2.6 32.1 1.0 OD2 B:ASP633 2.7 25.1 1.0 OD2 B:ASP631 2.7 26.6 1.0 O B:MET570 2.9 22.5 1.0 C B:MET570 3.1 26.1 1.0 CB B:MET570 3.5 31.8 1.0 N B:ASP571 3.5 27.4 1.0 CA B:ASP571 3.6 28.1 1.0 CG B:ASP571 3.6 24.3 1.0 CG B:ASP633 3.7 25.9 1.0 CG B:ASP639 3.7 31.7 1.0 CG B:ASP631 3.9 26.6 1.0 CA B:MET570 3.9 29.8 1.0 OD1 B:ASP633 4.0 25.8 1.0 CA B:CA701 4.2 17.8 1.0 CB B:ASP571 4.2 24.3 1.0 CB B:ASP639 4.3 32.6 1.0 OD1 B:ASP631 4.6 26.9 1.0 O2 B:GOL705 4.6 33.2 1.0 OD2 B:ASP571 4.7 25.2 1.0 OD1 B:ASP639 4.7 32.1 1.0 CG B:MET570 4.8 33.2 1.0 C B:ASP571 4.8 29.6 1.0 CB B:ASP633 4.9 22.6 1.0 CB B:ASP631 5.0 25.0 1.0

C.Ferrer-Orta, M.D.Perez-Sanchez, T.Coronado-Parra, C.Silva, D.Lopez-Martinez, J.Baltanas-Copado, J.C.Gomez-Fernandez, S.Corbalan-Garcia, N.Verdaguer. Structural Characterization of the Rabphilin-3A-SNAP25 Interaction. Proc. Natl. Acad. Sci. V. 114 E5343 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28634303
DOI: 10.1073/PNAS.1702542114