Calcium in PDB 5lob: Structure of the CA2+-Bound RABPHILIN3A C2B- SNAP25 Complex (C2 Space Group)

The structure of Structure of the CA2+-Bound RABPHILIN3A C2B- SNAP25 Complex (C2 Space Group), PDB code: 5lob 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)	42.53 / 3.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	153.970, 58.754, 125.311, 90.00, 103.24, 90.00
R / Rfree (%)	24 / 28.6

The binding sites of Calcium atom in the Structure of the CA2+-Bound RABPHILIN3A C2B- SNAP25 Complex (C2 Space Group) (pdb code 5lob). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of the CA2+-Bound RABPHILIN3A C2B- SNAP25 Complex (C2 Space Group), PDB code: 5lob:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Structure of the CA2+-Bound RABPHILIN3A C2B- SNAP25 Complex (C2 Space Group)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the CA2+-Bound RABPHILIN3A C2B- SNAP25 Complex (C2 Space Group) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:46.8 occ:1.00 OD1 A:ASP633 2.5 0.6 1.0 OD2 A:ASP571 2.5 55.2 1.0 OD1 A:ASP571 2.6 57.4 1.0 O4 A:SO4703 2.7 0.2 1.0 OD2 A:ASP577 2.7 65.5 1.0 O A:TYR632 2.8 94.4 1.0 CG A:ASP571 2.9 56.8 1.0 OD1 A:ASP631 2.9 58.9 1.0 OD2 A:ASP631 3.0 61.5 1.0 CG A:ASP631 3.2 58.8 1.0 S A:SO4703 3.5 1.0 1.0 C A:TYR632 3.7 85.8 1.0 O3 A:SO4703 3.7 0.5 1.0 CG A:ASP633 3.7 0.4 1.0 CG A:ASP577 3.7 65.3 1.0 CA A:CA702 3.7 58.6 1.0 O2 A:SO4703 3.7 0.1 1.0 CB A:ASP577 4.1 65.2 1.0 CA A:ASP633 4.1 95.6 1.0 N A:ASP633 4.2 93.2 1.0 N A:ASP577 4.2 66.8 1.0 CB A:ASP571 4.4 56.9 1.0 N A:TYR632 4.5 61.5 1.0 C A:ASP631 4.5 53.1 1.0 CB A:ASP633 4.5 99.8 1.0 O A:ASP631 4.6 50.1 1.0 OD2 A:ASP633 4.6 0.5 1.0 CB A:ASP631 4.6 54.0 1.0 CA A:TYR632 4.7 70.0 1.0 CA A:ASP577 4.8 67.2 1.0 OD1 A:ASP577 4.9 65.5 1.0 O1 A:SO4703 4.9 0.2 1.0

Calcium binding site 2 out of 6 in the Structure of the CA2+-Bound RABPHILIN3A C2B- SNAP25 Complex (C2 Space Group)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the CA2+-Bound RABPHILIN3A C2B- SNAP25 Complex (C2 Space Group) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:58.6 occ:1.00 OD1 A:ASP633 2.6 0.6 1.0 OD1 A:ASP571 2.6 57.4 1.0 O A:MET570 2.6 64.1 1.0 OD2 A:ASP631 2.8 61.5 1.0 OD2 A:ASP633 2.8 0.5 1.0 CG A:ASP633 3.0 0.4 1.0 OD2 A:ASP639 3.0 90.7 1.0 C A:MET570 3.7 67.4 1.0 CA A:CA701 3.7 46.8 1.0 CG A:ASP571 3.8 56.8 1.0 CE A:LYS636 3.8 97.5 1.0 NZ A:LYS636 4.0 95.3 1.0 CG A:ASP631 4.0 58.8 1.0 CG A:ASP639 4.1 85.1 1.0 CA A:ASP571 4.3 62.3 1.0 N A:ASP571 4.4 71.0 1.0 CB A:MET570 4.4 82.5 1.0 O3 A:SO4703 4.4 0.5 1.0 CB A:ASP633 4.5 99.8 1.0 OD2 A:ASP571 4.6 55.2 1.0 CB A:ASP571 4.7 56.9 1.0 CB A:ASP639 4.7 78.5 1.0 CA A:MET570 4.7 73.4 1.0 OD1 A:ASP631 4.8 58.9 1.0 CB A:ASP631 4.8 54.0 1.0 O A:ASP631 5.0 50.1 1.0

Calcium binding site 3 out of 6 in the Structure of the CA2+-Bound RABPHILIN3A C2B- SNAP25 Complex (C2 Space Group)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the CA2+-Bound RABPHILIN3A C2B- SNAP25 Complex (C2 Space Group) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca701 b:53.6 occ:1.00 OD1 B:ASP571 2.4 98.1 1.0 OD2 B:ASP571 2.5 98.8 1.0 OD2 B:ASP577 2.5 66.2 1.0 O B:TYR632 2.6 83.2 1.0 OD1 B:ASP633 2.6 79.2 1.0 OD1 B:ASP631 2.7 48.2 1.0 CG B:ASP571 2.8 91.5 1.0 OD2 B:ASP631 3.1 47.0 1.0 CG B:ASP631 3.2 50.2 1.0 C B:TYR632 3.6 81.2 1.0 CG B:ASP577 3.6 68.3 1.0 CG B:ASP633 3.9 77.6 1.0 CB B:ASP577 4.0 47.1 1.0 CA B:CA702 4.0 57.9 1.0 CA B:ASP633 4.2 81.0 1.0 N B:ASP633 4.2 80.9 1.0 N B:ASP577 4.3 67.2 1.0 CB B:ASP571 4.3 79.8 1.0 N B:TYR632 4.3 73.7 1.0 C B:ASP631 4.6 74.5 1.0 CA B:TYR632 4.6 78.6 1.0 CB B:ASP633 4.6 79.2 1.0 CB B:ASP631 4.6 53.7 1.0 OD1 B:ASP577 4.7 74.2 1.0 OD2 B:ASP633 4.7 77.4 1.0 CA B:ASP577 4.8 68.7 1.0 O B:ASP631 4.8 85.5 1.0

Calcium binding site 4 out of 6 in the Structure of the CA2+-Bound RABPHILIN3A C2B- SNAP25 Complex (C2 Space Group)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the CA2+-Bound RABPHILIN3A C2B- SNAP25 Complex (C2 Space Group) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca702 b:57.9 occ:1.00 OD2 B:ASP639 2.5 76.5 1.0 O B:MET570 2.6 62.8 1.0 OD1 B:ASP571 2.6 98.1 1.0 OD1 B:ASP633 2.8 79.2 1.0 OD2 B:ASP633 2.9 77.4 1.0 OD2 B:ASP631 3.0 47.0 1.0 CG B:ASP633 3.2 77.6 1.0 C B:MET570 3.5 64.0 1.0 CG B:ASP639 3.6 74.7 1.0 CG B:ASP571 3.7 91.5 1.0 CA B:ASP571 3.9 70.6 1.0 NZ B:LYS636 4.0 54.6 1.0 CA B:CA701 4.0 53.6 1.0 N B:ASP571 4.1 66.6 1.0 CG B:ASP631 4.2 50.2 1.0 CE B:LYS636 4.3 55.7 1.0 CB B:ASP571 4.4 79.8 1.0 OD1 B:ASP639 4.4 81.7 1.0 CB B:MET570 4.5 62.9 1.0 CB B:ASP639 4.5 70.9 1.0 CB B:ASP633 4.6 79.2 1.0 CA B:MET570 4.6 61.4 1.0 OD2 B:ASP571 4.7 98.8 1.0 OD1 B:ASP631 4.9 48.2 1.0

Calcium binding site 5 out of 6 in the Structure of the CA2+-Bound RABPHILIN3A C2B- SNAP25 Complex (C2 Space Group)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the CA2+-Bound RABPHILIN3A C2B- SNAP25 Complex (C2 Space Group) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca701 b:56.5 occ:1.00 O2 C:SO4703 2.3 0.9 1.0 OD1 C:ASP571 2.4 60.2 1.0 OD1 C:ASP633 2.5 51.1 1.0 O C:TYR632 2.5 89.0 1.0 OD2 C:ASP571 2.5 62.6 1.0 OD1 C:ASP631 2.8 93.3 1.0 CG C:ASP571 2.8 59.8 1.0 OD2 C:ASP631 3.0 98.8 1.0 OD2 C:ASP577 3.1 65.7 1.0 CG C:ASP631 3.2 95.3 1.0 C C:TYR632 3.5 82.6 1.0 CA C:CA702 3.6 56.8 1.0 S C:SO4703 3.7 0.3 1.0 CG C:ASP633 3.8 57.0 1.0 CA C:ASP633 4.0 73.3 1.0 CG C:ASP577 4.0 69.4 1.0 N C:ASP633 4.0 80.6 1.0 N C:ASP577 4.1 56.6 1.0 O3 C:SO4703 4.1 0.3 1.0 CB C:ASP577 4.2 70.5 1.0 N C:TYR632 4.3 75.5 1.0 CB C:ASP571 4.3 61.4 1.0 C C:ASP631 4.4 75.4 1.0 O1 C:SO4703 4.4 0.2 1.0 CB C:ASP633 4.5 61.2 1.0 CA C:TYR632 4.5 78.4 1.0 CB C:ASP631 4.5 93.1 1.0 O C:ASP631 4.6 74.5 1.0 O4 C:SO4703 4.6 0.5 1.0 OD2 C:ASP633 4.7 56.4 1.0 CA C:ASP577 4.7 67.5 1.0 CA C:SER576 4.9 63.3 1.0 C C:SER576 4.9 55.4 1.0 O C:MET570 4.9 52.5 1.0 CA C:ASP631 5.0 81.9 1.0

Calcium binding site 6 out of 6 in the Structure of the CA2+-Bound RABPHILIN3A C2B- SNAP25 Complex (C2 Space Group)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the CA2+-Bound RABPHILIN3A C2B- SNAP25 Complex (C2 Space Group) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca702 b:56.8 occ:1.00 O C:MET570 2.4 52.5 1.0 OD1 C:ASP633 2.4 51.1 1.0 OD1 C:ASP571 2.5 60.2 1.0 OD2 C:ASP639 2.5 0.6 1.0 OD2 C:ASP631 2.7 98.8 1.0 OD2 C:ASP633 2.8 56.4 1.0 CG C:ASP633 3.0 57.0 1.0 C C:MET570 3.5 57.7 1.0 CA C:CA701 3.6 56.5 1.0 CG C:ASP571 3.6 59.8 1.0 CG C:ASP639 3.7 0.1 1.0 CG C:ASP631 3.8 95.3 1.0 CA C:ASP571 4.0 65.2 1.0 N C:ASP571 4.2 59.3 1.0 CB C:MET570 4.4 62.0 1.0 CB C:ASP571 4.4 61.4 1.0 CB C:ASP633 4.4 61.2 1.0 OD2 C:ASP571 4.5 62.6 1.0 CB C:ASP639 4.5 0.0 1.0 OD1 C:ASP639 4.5 0.2 1.0 CA C:MET570 4.6 63.6 1.0 OD1 C:ASP631 4.6 93.3 1.0 CB C:ASP631 4.6 93.1 1.0 O2 C:SO4703 4.9 0.9 1.0 O C:ASP631 4.9 74.5 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