Calcium in PDB 2cm6: Crystal Structure of the C2B Domain of RABPHILIN3A

The structure of Crystal Structure of the C2B Domain of RABPHILIN3A, PDB code: 2cm6 was solved by C.Schlicker, P.Montaville, G.M.Sheldrick, S.Becker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.76 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.069, 59.606, 66.385, 90.00, 103.89, 90.00
R / Rfree (%)	19.48 / 26.75

The binding sites of Calcium atom in the Crystal Structure of the C2B Domain of RABPHILIN3A (pdb code 2cm6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the C2B Domain of RABPHILIN3A, PDB code: 2cm6:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the C2B Domain of RABPHILIN3A


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 the C2B Domain of RABPHILIN3A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1679 b:18.5 occ:1.00 OD2 A:ASP571 2.2 28.1 1.0 OD1 A:ASP633 2.2 23.5 1.0 O A:TYR632 2.2 18.4 1.0 OD2 A:ASP577 2.3 20.9 1.0 OD1 A:ASP631 2.4 16.1 1.0 O A:HOH2004 2.4 20.4 1.0 OD1 A:ASP571 2.8 22.9 1.0 CG A:ASP571 2.8 15.6 1.0 CG A:ASP631 3.2 25.9 1.0 OD2 A:ASP631 3.3 26.2 1.0 C A:TYR632 3.3 25.5 1.0 CG A:ASP577 3.4 29.7 1.0 CG A:ASP633 3.4 17.4 1.0 CA A:CA1680 3.8 18.3 1.0 CB A:ASP577 3.9 19.8 1.0 CA A:ASP633 3.9 25.6 1.0 N A:ASP633 4.0 22.8 1.0 N A:ASP577 4.1 16.6 1.0 CB A:ASP633 4.2 19.9 1.0 CB A:ASP571 4.3 21.1 1.0 OD2 A:ASP633 4.3 18.3 1.0 N A:TYR632 4.3 19.5 1.0 C A:ASP631 4.4 23.0 1.0 CA A:TYR632 4.4 20.3 1.0 OD1 A:ASP577 4.5 22.6 1.0 O A:HOH2010 4.6 29.5 1.0 CB A:ASP631 4.6 16.9 1.0 OE2 A:GLU530 4.6 33.8 1.0 O A:ASP631 4.6 19.2 1.0 CA A:ASP577 4.7 20.8 1.0 C A:SER576 4.8 14.5 1.0 CG A:GLU530 4.9 27.2 1.0 CA A:SER576 5.0 15.0 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the C2B Domain of RABPHILIN3A


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 the C2B Domain of RABPHILIN3A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1680 b:18.3 occ:1.00 OD1 A:ASP571 2.1 22.9 1.0 OD2 A:ASP639 2.2 20.2 1.0 O A:MET570 2.2 21.7 1.0 OD2 A:ASP633 2.2 18.3 1.0 O A:GLU530 2.3 23.6 1.0 OD2 A:ASP631 2.3 26.2 1.0 OD1 A:ASP633 2.5 23.5 1.0 CG A:ASP633 2.7 17.4 1.0 C A:MET570 3.3 22.7 1.0 C A:GLU530 3.3 24.3 1.0 CG A:ASP639 3.3 29.1 1.0 CG A:ASP571 3.3 15.6 1.0 CG A:ASP631 3.5 25.9 1.0 CA A:CA1679 3.8 18.5 1.0 CA A:GLU530 3.9 24.4 1.0 CB A:MET570 4.0 22.8 1.0 CB A:ASP639 4.0 20.6 1.0 OD2 A:ASP571 4.1 28.1 1.0 OD1 A:ASP631 4.1 16.1 1.0 N A:ASP571 4.1 21.8 1.0 O A:HOH2031 4.1 32.0 1.0 CB A:GLU530 4.1 28.5 1.0 CA A:ASP571 4.1 21.9 1.0 CB A:ASP633 4.2 19.9 1.0 OD1 A:ASP639 4.2 21.7 1.0 CA A:MET570 4.2 23.9 1.0 CB A:ASP571 4.3 21.1 1.0 N A:GLN531 4.4 21.9 1.0 NZ A:LYS636 4.5 22.4 1.0 CB A:ASP631 4.6 16.9 1.0 CA A:GLN531 4.8 23.2 1.0 O A:HOH2004 4.9 20.4 1.0 O A:ASP631 4.9 19.2 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the C2B Domain of RABPHILIN3A


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 the C2B Domain of RABPHILIN3A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2679 b:21.5 occ:1.00 O B:TYR1632 2.2 19.1 1.0 O B:HOH2004 2.3 32.1 1.0 OD2 B:ASP1577 2.3 20.0 1.0 OD1 B:ASP1633 2.4 26.6 1.0 OD1 B:ASP1631 2.4 23.3 1.0 OD2 B:ASP1571 2.5 20.0 1.0 OD1 B:ASP1571 2.8 27.8 1.0 CG B:ASP1571 3.1 23.3 1.0 CG B:ASP1631 3.2 29.2 1.0 OD2 B:ASP1631 3.3 23.6 1.0 C B:TYR1632 3.3 23.2 1.0 CG B:ASP1577 3.4 26.8 1.0 CG B:ASP1633 3.5 23.0 1.0 CA B:CA2680 3.9 20.2 1.0 CB B:ASP1577 4.0 17.0 1.0 CA B:ASP1633 4.0 17.2 1.0 N B:ASP1633 4.1 24.0 1.0 N B:ASP1577 4.2 22.9 1.0 N B:TYR1632 4.3 23.8 1.0 CB B:ASP1633 4.4 21.1 1.0 CA B:TYR1632 4.4 24.1 1.0 OD2 B:ASP1633 4.4 16.2 1.0 OD1 B:ASP1577 4.4 23.6 1.0 C B:ASP1631 4.4 19.9 1.0 O B:HOH2010 4.4 22.9 1.0 CB B:ASP1571 4.6 23.9 1.0 CB B:ASP1631 4.6 11.8 1.0 O B:ASP1631 4.6 23.6 1.0 CG B:GLU1530 4.6 29.0 1.0 OE2 B:GLU1530 4.6 27.6 1.0 CA B:ASP1577 4.7 18.1 1.0 CD B:GLU1530 4.9 31.2 1.0 O B:HOH2003 4.9 47.8 1.0 C B:SER1576 4.9 22.5 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the C2B Domain of RABPHILIN3A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the C2B Domain of RABPHILIN3A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2680 b:20.2 occ:1.00 OD1 B:ASP1639 2.1 22.1 1.0 OD2 B:ASP1633 2.3 16.2 1.0 O B:GLU1530 2.3 24.4 1.0 OD2 B:ASP1631 2.3 23.6 1.0 O B:MET1570 2.5 30.0 1.0 OD1 B:ASP1571 2.5 27.8 1.0 OD1 B:ASP1633 2.6 26.6 1.0 CG B:ASP1633 2.8 23.0 1.0 CG B:ASP1639 3.3 34.6 1.0 C B:GLU1530 3.4 26.9 1.0 C B:MET1570 3.4 27.5 1.0 CG B:ASP1631 3.5 29.2 1.0 CG B:ASP1571 3.7 23.3 1.0 CA B:GLU1530 3.9 22.0 1.0 CA B:CA2679 3.9 21.5 1.0 CB B:ASP1639 4.0 23.3 1.0 CB B:GLU1530 4.0 29.6 1.0 N B:ASP1571 4.1 18.8 1.0 OD1 B:ASP1631 4.2 23.3 1.0 CB B:MET1570 4.2 26.7 1.0 CA B:ASP1571 4.2 23.8 1.0 OD2 B:ASP1639 4.3 24.9 1.0 CB B:ASP1633 4.3 21.1 1.0 CA B:MET1570 4.5 27.3 1.0 NZ B:LYS1636 4.5 19.5 1.0 OD2 B:ASP1571 4.5 20.0 1.0 N B:GLN1531 4.5 27.5 1.0 CE B:LYS1636 4.6 27.4 1.0 CB B:ASP1571 4.6 23.9 1.0 CB B:ASP1631 4.7 11.8 1.0 CA B:GLN1531 4.7 28.3 1.0 CG B:GLU1530 4.8 29.0 1.0 O B:ASP1631 4.9 23.6 1.0 O B:HOH2004 4.9 32.1 1.0

P.Montaville, C.Schlicker, A.Leonov, M.Zweckstetter, G.M.Sheldrick, S.Becker. The C2A-C2B Linker Defines the High Affinity CA2+ Binding Mode of Rabphilin-3A. J.Biol.Chem. V. 282 5015 2007.
ISSN: ISSN 0021-9258
PubMed: 17166855
DOI: 10.1074/JBC.M606746200