Calcium in PDB 5low: Structure of the CA2+-Bound Rabphilin 3A C2B Domain SNAP25 Complex (P21 Space Group)

The structure of Structure of the CA2+-Bound Rabphilin 3A C2B Domain SNAP25 Complex (P21 Space Group), PDB code: 5low was solved by N.Verdaguer, C.Ferrer-Orta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.03 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.080, 239.496, 71.487, 90.00, 114.92, 90.00
R / Rfree (%)	23.8 / 26.9

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>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Structure of the CA2+-Bound Rabphilin 3A C2B Domain SNAP25 Complex (P21 Space Group) (pdb code 5low). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Structure of the CA2+-Bound Rabphilin 3A C2B Domain SNAP25 Complex (P21 Space Group), PDB code: 5low:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in the Structure of the CA2+-Bound Rabphilin 3A C2B Domain SNAP25 Complex (P21 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 Rabphilin 3A C2B Domain SNAP25 Complex (P21 Space Group) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:64.1 occ:1.00 O A:TYR632 2.4 47.8 1.0 OD1 A:ASP633 2.7 47.5 1.0 OD2 A:ASP571 2.9 51.7 1.0 OD2 A:ASP577 3.0 47.5 1.0 OD1 A:ASP631 3.2 49.6 1.0 OD1 A:ASP571 3.3 52.2 1.0 CG A:ASP571 3.5 52.2 1.0 OD2 A:ASP631 3.5 48.0 1.0 CG A:ASP633 3.5 47.9 1.0 C A:TYR632 3.6 48.4 1.0 CG A:ASP577 3.6 47.8 1.0 CG A:ASP631 3.7 48.9 1.0 CB A:ASP577 3.7 48.1 1.0 N A:ASP577 3.9 48.3 1.0 OD2 A:ASP633 4.0 48.6 1.0 CA A:ASP633 4.3 47.6 1.0 N A:ASP633 4.4 47.9 1.0 CA A:CA703 4.4 59.3 1.0 CA A:ASP577 4.4 48.3 1.0 CB A:ASP633 4.5 47.6 1.0 N A:TYR632 4.5 48.4 1.0 OD1 A:ASP577 4.6 47.5 1.0 CA A:TYR632 4.6 48.5 1.0 C A:SER576 4.7 48.8 1.0 CA A:SER576 4.8 49.0 1.0 C A:ASP631 4.8 48.2 1.0 CB A:ASP571 4.9 52.3 1.0 O A:ASP577 5.0 47.8 1.0

Calcium binding site 2 out of 12 in the Structure of the CA2+-Bound Rabphilin 3A C2B Domain SNAP25 Complex (P21 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 Rabphilin 3A C2B Domain SNAP25 Complex (P21 Space Group) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:59.3 occ:1.00 OD2 A:ASP631 2.4 48.0 1.0 OD2 A:ASP633 2.4 48.6 1.0 OD1 A:ASP571 2.4 52.2 1.0 O A:MET570 2.5 53.0 1.0 OD2 A:ASP639 2.5 47.9 1.0 C A:MET570 3.4 53.1 1.0 CG A:ASP633 3.4 47.9 1.0 CG A:ASP639 3.5 48.3 1.0 OD1 A:ASP633 3.6 47.5 1.0 CG A:ASP571 3.6 52.2 1.0 CG A:ASP631 3.6 48.9 1.0 CB A:ASP639 3.8 47.8 1.0 NZ A:LYS636 3.8 45.6 1.0 CB A:MET570 3.8 52.6 1.0 N A:ASP571 4.2 53.2 1.0 CA A:MET570 4.2 53.1 1.0 OD2 A:ASP571 4.4 51.7 1.0 CA A:ASP571 4.4 52.8 1.0 CA A:CA702 4.4 64.1 1.0 OD1 A:ASP631 4.5 49.6 1.0 CB A:ASP631 4.5 48.8 1.0 CB A:ASP571 4.6 52.3 1.0 OD1 A:ASP639 4.6 49.3 1.0 CB A:ASP633 4.8 47.6 1.0 CE A:LYS636 4.8 45.5 1.0 O A:ASP631 4.9 48.0 1.0 N A:ASP639 5.0 47.3 1.0 CA A:ASP639 5.0 47.7 1.0

Calcium binding site 3 out of 12 in the Structure of the CA2+-Bound Rabphilin 3A C2B Domain SNAP25 Complex (P21 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 Rabphilin 3A C2B Domain SNAP25 Complex (P21 Space Group) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca702 b:55.7 occ:1.00 O B:MET570 2.4 47.7 1.0 OD2 B:ASP631 2.4 42.3 1.0 O B:HOH806 2.4 32.2 1.0 OD2 B:ASP639 2.5 41.0 1.0 OD2 B:ASP633 2.9 43.6 1.0 OD1 B:ASP633 2.9 44.2 1.0 CG B:ASP633 3.3 43.8 1.0 OD1 B:ASP571 3.5 49.3 1.0 C B:MET570 3.6 47.7 1.0 CG B:ASP639 3.6 41.0 1.0 CG B:ASP631 3.6 42.2 1.0 CG B:ASP571 3.6 48.3 1.0 CA B:CA703 3.6 58.9 1.0 OD2 B:ASP571 3.7 47.5 1.0 CB B:ASP639 4.1 41.2 1.0 CA B:ASP571 4.1 47.9 1.0 N B:ASP571 4.3 47.9 1.0 OD1 B:ASP631 4.3 42.3 1.0 NZ B:LYS636 4.4 43.5 1.0 CB B:ASP571 4.5 48.1 1.0 CB B:MET570 4.6 47.3 1.0 CB B:ASP631 4.7 42.3 1.0 OD1 B:ASP639 4.7 40.6 1.0 CA B:MET570 4.7 47.5 1.0 CB B:ASP633 4.8 43.8 1.0 CE B:LYS636 4.8 43.5 1.0 O B:ASP631 4.9 42.2 1.0 O B:TYR632 4.9 44.2 1.0

Calcium binding site 4 out of 12 in the Structure of the CA2+-Bound Rabphilin 3A C2B Domain SNAP25 Complex (P21 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 Rabphilin 3A C2B Domain SNAP25 Complex (P21 Space Group) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca703 b:58.9 occ:1.00 O B:TYR632 2.4 44.2 1.0 OD1 B:ASP633 2.5 44.2 1.0 OD2 B:ASP571 2.6 47.5 1.0 OD2 B:ASP577 2.6 47.5 1.0 CG B:ASP571 3.3 48.3 1.0 OD1 B:ASP631 3.4 42.3 1.0 OD2 B:ASP631 3.4 42.3 1.0 OD1 B:ASP571 3.4 49.3 1.0 C B:TYR632 3.5 44.2 1.0 CG B:ASP577 3.5 47.8 1.0 CG B:ASP633 3.6 43.8 1.0 CA B:CA702 3.6 55.7 1.0 CG B:ASP631 3.7 42.2 1.0 CB B:ASP577 3.8 47.5 1.0 CA B:ASP633 4.2 43.8 1.0 N B:ASP633 4.3 44.3 1.0 OD2 B:ASP633 4.3 43.6 1.0 CB B:ASP633 4.5 43.8 1.0 N B:TYR632 4.5 43.4 1.0 N B:ASP577 4.5 47.6 1.0 CA B:TYR632 4.6 44.0 1.0 OD1 B:ASP577 4.6 47.9 1.0 C B:ASP631 4.7 42.8 1.0 CB B:ASP571 4.8 48.1 1.0 CA B:ASP577 4.8 47.4 1.0 O B:ASP631 4.9 42.2 1.0

Calcium binding site 5 out of 12 in the Structure of the CA2+-Bound Rabphilin 3A C2B Domain SNAP25 Complex (P21 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 Rabphilin 3A C2B Domain SNAP25 Complex (P21 Space Group) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca702 b:55.8 occ:1.00 OD2 C:ASP631 2.4 45.3 1.0 O C:MET570 2.4 44.5 1.0 O C:HOH806 2.5 9.6 1.0 OD1 C:ASP571 2.5 44.3 1.0 OD2 C:ASP639 2.5 48.6 1.0 OD2 C:ASP633 2.9 47.9 1.0 OD1 C:ASP633 3.2 48.2 1.0 CG C:ASP633 3.4 48.3 1.0 C C:MET570 3.5 45.0 1.0 CG C:ASP639 3.6 48.5 1.0 CG C:ASP631 3.7 44.9 1.0 CG C:ASP571 3.7 44.5 1.0 CB C:ASP639 4.1 48.4 1.0 CB C:MET570 4.2 45.5 1.0 N C:ASP571 4.3 45.0 1.0 CA C:ASP571 4.3 44.8 1.0 OD1 C:ASP631 4.5 44.8 1.0 CA C:CA703 4.5 65.3 1.0 CA C:MET570 4.5 45.2 1.0 OD2 C:ASP571 4.5 44.1 1.0 CB C:ASP631 4.6 44.6 1.0 CB C:ASP571 4.6 44.6 1.0 OD1 C:ASP639 4.7 48.5 1.0 CB C:ASP633 4.9 48.3 1.0

Calcium binding site 6 out of 12 in the Structure of the CA2+-Bound Rabphilin 3A C2B Domain SNAP25 Complex (P21 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 Rabphilin 3A C2B Domain SNAP25 Complex (P21 Space Group) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca703 b:65.3 occ:1.00 OD1 C:ASP633 2.5 48.2 1.0 O C:TYR632 2.7 46.8 1.0 OD1 C:ASP577 2.9 41.4 1.0 O C:HOH805 3.0 10.3 1.0 OD2 C:ASP571 3.1 44.1 1.0 OD1 C:ASP631 3.1 44.8 1.0 OD1 C:ASP571 3.2 44.3 1.0 CG C:ASP571 3.5 44.5 1.0 OD2 C:ASP631 3.5 45.3 1.0 C C:TYR632 3.6 47.1 1.0 CG C:ASP631 3.6 44.9 1.0 CG C:ASP577 3.7 41.8 1.0 CG C:ASP633 3.7 48.3 1.0 CA C:ASP633 4.1 48.4 1.0 CB C:ASP577 4.1 42.2 1.0 N C:ASP633 4.2 47.9 1.0 N C:ASP577 4.4 43.0 1.0 CB C:ASP633 4.4 48.3 1.0 CA C:CA702 4.5 55.8 1.0 OD2 C:ASP577 4.5 41.9 1.0 N C:TYR632 4.6 45.6 1.0 OD2 C:ASP633 4.6 47.9 1.0 CA C:TYR632 4.7 46.8 1.0 C C:ASP631 4.8 45.0 1.0 CB C:ASP571 4.9 44.6 1.0 CA C:ASP577 4.9 42.5 1.0 O C:ASP631 5.0 45.0 1.0

Calcium binding site 7 out of 12 in the Structure of the CA2+-Bound Rabphilin 3A C2B Domain SNAP25 Complex (P21 Space Group)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of the CA2+-Bound Rabphilin 3A C2B Domain SNAP25 Complex (P21 Space Group) within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca701 b:52.6 occ:1.00 OD1 H:ASP631 2.4 55.3 1.0 OD1 H:ASP633 2.4 53.0 1.0 O H:HOH802 2.5 41.5 1.0 O H:TYR632 2.8 55.3 1.0 OD2 H:ASP577 2.8 49.6 1.0 OD1 H:ASP571 2.9 51.5 1.0 OD2 H:ASP571 3.1 51.2 1.0 CG H:ASP571 3.4 51.4 1.0 C H:TYR632 3.4 55.4 1.0 CG H:ASP631 3.6 54.8 1.0 CG H:ASP633 3.6 53.6 1.0 CG H:ASP577 3.7 50.3 1.0 CB H:ASP577 3.9 50.8 1.0 N H:ASP633 3.9 55.2 1.0 CA H:ASP633 4.0 55.1 1.0 N H:TYR632 4.1 55.3 1.0 OD2 H:ASP631 4.1 54.5 1.0 N H:ASP577 4.2 51.1 1.0 CA H:TYR632 4.4 55.5 1.0 CB H:ASP633 4.4 54.3 1.0 OD2 H:ASP633 4.5 52.8 1.0 O H:MET570 4.6 51.9 1.0 CA H:ASP577 4.7 51.1 1.0 CB H:ASP631 4.7 54.6 1.0 OD1 H:ASP577 4.9 50.0 1.0 CB H:ASP571 4.9 51.6 1.0

Calcium binding site 8 out of 12 in the Structure of the CA2+-Bound Rabphilin 3A C2B Domain SNAP25 Complex (P21 Space Group)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of the CA2+-Bound Rabphilin 3A C2B Domain SNAP25 Complex (P21 Space Group) within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca702 b:72.9 occ:1.00 OD2 H:ASP639 2.5 55.2 1.0 OD2 H:ASP633 2.5 52.8 1.0 O H:MET570 2.6 51.9 1.0 O H:HOH803 2.6 21.0 1.0 CG H:ASP633 3.5 53.6 1.0 C H:MET570 3.6 51.7 1.0 CG H:ASP639 3.7 55.5 1.0 OD1 H:ASP633 3.9 53.0 1.0 OD1 H:ASP639 4.2 55.5 1.0 OD1 H:ASP571 4.2 51.5 1.0 CB H:MET570 4.3 51.3 1.0 N H:ASP571 4.4 51.8 1.0 CA H:MET570 4.4 51.4 1.0 CA H:ASP571 4.5 51.9 1.0 CB H:ASP639 4.9 55.2 1.0 CB H:ASP633 4.9 54.3 1.0

Calcium binding site 9 out of 12 in the Structure of the CA2+-Bound Rabphilin 3A C2B Domain SNAP25 Complex (P21 Space Group)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of the CA2+-Bound Rabphilin 3A C2B Domain SNAP25 Complex (P21 Space Group) within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca701 b:58.2 occ:1.00 O I:TYR632 2.4 48.3 1.0 OD1 I:ASP633 2.6 45.8 1.0 OD2 I:ASP577 2.6 46.4 1.0 OD1 I:ASP571 3.0 48.6 1.0 OD1 I:ASP631 3.2 47.7 1.0 OD2 I:ASP571 3.2 48.9 1.0 CG I:ASP571 3.5 48.8 1.0 OD2 I:ASP631 3.5 47.8 1.0 C I:TYR632 3.5 48.0 1.0 CG I:ASP577 3.5 47.1 1.0 CG I:ASP631 3.7 47.5 1.0 CG I:ASP633 3.8 46.1 1.0 CB I:ASP577 3.8 47.2 1.0 CA I:CA702 3.9 54.1 1.0 N I:ASP577 4.2 47.5 1.0 CA I:ASP633 4.2 46.9 1.0 N I:ASP633 4.2 47.4 1.0 N I:TYR632 4.5 47.2 1.0 CA I:TYR632 4.6 47.8 1.0 CB I:ASP633 4.6 46.6 1.0 OD1 I:ASP577 4.6 47.5 1.0 OD2 I:ASP633 4.7 45.9 1.0 CA I:ASP577 4.7 47.4 1.0 C I:ASP631 4.7 47.2 1.0 CB I:ASP571 4.9 48.8 1.0 C I:SER576 5.0 47.7 1.0 O I:ASP631 5.0 47.0 1.0

Calcium binding site 10 out of 12 in the Structure of the CA2+-Bound Rabphilin 3A C2B Domain SNAP25 Complex (P21 Space Group)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of the CA2+-Bound Rabphilin 3A C2B Domain SNAP25 Complex (P21 Space Group) within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca702 b:54.1 occ:1.00 OD1 I:ASP571 2.4 48.6 1.0 OD2 I:ASP639 2.4 52.4 1.0 O I:MET570 2.5 50.8 1.0 OD2 I:ASP631 2.8 47.8 1.0 OD1 I:ASP633 3.0 45.8 1.0 OD2 I:ASP633 3.2 45.9 1.0 CG I:ASP633 3.5 46.1 1.0 C I:MET570 3.6 50.6 1.0 CG I:ASP639 3.7 52.2 1.0 CG I:ASP571 3.7 48.8 1.0 CA I:CA701 3.9 58.2 1.0 CG I:ASP631 4.0 47.5 1.0 CA I:ASP571 4.1 49.2 1.0 N I:ASP571 4.3 49.8 1.0 CB I:ASP639 4.4 52.2 1.0 CB I:ASP571 4.5 48.8 1.0 OD1 I:ASP639 4.5 52.6 1.0 OD2 I:ASP571 4.6 48.9 1.0 OD1 I:ASP631 4.6 47.7 1.0 CB I:MET570 4.7 51.8 1.0 CA I:MET570 4.8 51.2 1.0 NZ I:LYS636 4.8 50.4 1.0 CB I:ASP631 5.0 47.4 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