Calcium in PDB 4ldc: Crystal Structure of DOC2B C2B Domain

The structure of Crystal Structure of DOC2B C2B Domain, PDB code: 4ldc was solved by M.Giladi, L.Almagor, J.A.Hirsch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.45 / 1.26
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.802, 40.091, 36.922, 90.00, 105.47, 90.00
R / Rfree (%)	12.7 / 14.4

The binding sites of Calcium atom in the Crystal Structure of DOC2B C2B Domain (pdb code 4ldc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of DOC2B C2B Domain, PDB code: 4ldc:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of DOC2B C2B Domain


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 DOC2B C2B Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:3.4 occ:1.00 OD2 A:ASP357 2.3 4.5 1.0 OD2 A:ASP365 2.3 3.8 1.0 O A:MET296 2.4 2.3 1.0 OD2 A:ASP359 2.4 6.0 1.0 OD1 A:ASP297 2.4 3.5 1.0 OD1 A:ASP359 2.6 3.2 1.0 CG A:ASP359 2.8 4.4 1.0 C A:MET296 3.3 2.8 1.0 HA A:ASP297 3.4 4.1 1.0 HZ2 A:LYS362 3.4 9.7 1.0 HB3 A:MET296 3.4 3.0 0.5 CG A:ASP357 3.5 3.0 1.0 CG A:ASP365 3.5 4.2 1.0 HB3 A:MET296 3.5 4.3 0.6 CG A:ASP297 3.6 2.6 1.0 HB2 A:ASP365 3.6 4.0 1.0 HB2 A:MET296 3.8 4.3 0.6 CA A:CA502 3.8 2.4 1.0 HB2 A:MET296 3.9 3.0 0.5 CB A:MET296 4.0 2.5 0.5 CB A:MET296 4.0 3.6 0.6 OD1 A:ASP357 4.0 2.7 1.0 CA A:ASP297 4.0 3.4 1.0 N A:ASP297 4.1 2.5 1.0 CB A:ASP365 4.1 3.4 1.0 HD3 A:LYS362 4.2 9.6 1.0 NZ A:LYS362 4.3 8.1 1.0 CA A:MET296 4.3 2.1 0.5 CA A:MET296 4.3 2.5 0.6 CB A:ASP359 4.3 4.0 1.0 H A:ASP365 4.3 4.2 1.0 HB3 A:ASP357 4.4 2.9 1.0 OD1 A:ASP365 4.4 5.4 1.0 CB A:ASP297 4.4 2.7 1.0 OD2 A:ASP297 4.5 3.1 1.0 HZ1 A:LYS362 4.6 9.7 1.0 CB A:ASP357 4.6 2.4 1.0 HB3 A:ASP359 4.6 4.8 1.0 HZ3 A:LYS362 4.7 9.7 1.0 HB3 A:ASP365 4.7 4.0 1.0 HB2 A:ASP359 4.7 4.8 1.0 HE3 A:LYS362 4.8 10.6 1.0 O A:HOH602 4.8 5.8 1.0 O A:ASP357 4.8 2.7 1.0 HE3 A:MET296 4.8 1.6 0.6 H A:ASP297 4.8 3.0 1.0 HA A:MET296 4.9 3.0 0.5 CE A:LYS362 4.9 8.8 1.0 HB3 A:ASP297 4.9 3.2 1.0 CD A:LYS362 5.0 8.0 1.0 N A:ASP365 5.0 3.5 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of DOC2B C2B Domain


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 DOC2B C2B Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:2.4 occ:1.00 OD1 A:ASP359 2.3 3.2 1.0 OD2 A:ASP303 2.4 3.0 1.0 O A:TYR358 2.4 2.5 1.0 OD1 A:ASP357 2.4 2.7 1.0 O A:HOH602 2.4 5.8 1.0 OD2 A:ASP297 2.4 3.1 1.0 OD1 A:ASP297 2.5 3.5 1.0 CG A:ASP297 2.8 2.6 1.0 CG A:ASP357 3.2 3.0 1.0 HB2 A:ASP303 3.4 2.8 1.0 HA A:ASP359 3.4 4.6 1.0 OD2 A:ASP357 3.4 4.5 1.0 CG A:ASP303 3.4 2.4 1.0 C A:TYR358 3.4 2.6 1.0 H A:ASP303 3.5 1.9 1.0 CG A:ASP359 3.5 4.4 1.0 CA A:CA501 3.8 3.4 1.0 CB A:ASP303 3.9 2.3 1.0 N A:ASP303 4.0 1.6 1.0 CA A:ASP359 4.0 3.9 1.0 N A:ASP359 4.1 2.9 1.0 HA A:SER302 4.1 2.5 1.0 O A:HOH631 4.3 10.3 1.0 CB A:ASP297 4.3 2.7 1.0 CB A:ASP359 4.4 4.0 1.0 C A:ASP357 4.4 2.4 1.0 N A:TYR358 4.4 2.2 1.0 OD2 A:ASP359 4.4 6.0 1.0 OD1 A:ASP303 4.4 3.5 1.0 O A:HOH604 4.4 5.0 1.0 CA A:TYR358 4.5 3.1 1.0 O A:ASP357 4.5 2.7 1.0 CA A:ASP303 4.5 1.7 1.0 O A:HOH647 4.6 17.1 1.0 CB A:ASP357 4.6 2.4 1.0 HB3 A:ASP297 4.6 3.2 1.0 HB3 A:ASP303 4.7 2.8 1.0 C A:SER302 4.7 1.9 1.0 H A:TYR358 4.7 2.7 1.0 HB2 A:ASP297 4.7 3.2 1.0 HB3 A:ASP359 4.8 4.8 1.0 HB3 A:TYR358 4.9 4.3 1.0 CA A:SER302 4.9 2.1 1.0 H A:ASP359 4.9 3.4 1.0 CA A:ASP357 5.0 2.5 1.0 HA A:ASP297 5.0 4.1 1.0 HA A:ASP357 5.0 3.0 1.0

M.Giladi, L.Michaeli, L.Almagor, D.Bar-On, T.Buki, U.Ashery, D.Khananshvili, J.A.Hirsch. The C2B Domain Is the Primary Ca(2+) Sensor in DOC2B: A Structural and Functional Analysis. J.Mol.Biol. V. 425 4629 2013.
ISSN: ISSN 0022-2836
PubMed: 23994332
DOI: 10.1016/J.JMB.2013.08.017