Calcium in PDB 3vpp: Crystal Structure of the Human CLEC9A C-Type Lectin-Like Domain

The structure of Crystal Structure of the Human CLEC9A C-Type Lectin-Like Domain, PDB code: 3vpp was solved by P.E.Czabotar, J.G.Zhang, A.N.Policheni, K.Shortman, M.H.Lahoud, P.M.Colman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.89 / 1.64
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.170, 53.824, 57.446, 90.00, 109.35, 90.00
R / Rfree (%)	18.9 / 22.7

The binding sites of Calcium atom in the Crystal Structure of the Human CLEC9A C-Type Lectin-Like Domain (pdb code 3vpp). 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 the Human CLEC9A C-Type Lectin-Like Domain, PDB code: 3vpp:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of the Human CLEC9A C-Type Lectin-Like 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 the Human CLEC9A C-Type Lectin-Like Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:11.9 occ:1.00 O A:GLN150 2.5 12.6 1.0 OE1 A:GLU233 2.7 17.1 1.0 OE1 A:GLU152 2.7 19.2 1.0 O A:HOH403 2.7 17.3 1.0 OE2 A:GLU156 2.7 16.6 1.0 O A:HOH428 2.7 25.8 1.0 OE2 A:GLU233 2.7 13.5 1.0 OE1 A:GLU156 2.7 18.5 1.0 CD A:GLU233 3.0 20.5 1.0 CD A:GLU156 3.1 20.6 1.0 C A:GLN150 3.5 16.9 1.0 CD A:GLU152 3.8 29.1 1.0 OE2 A:GLU152 4.1 26.3 1.0 CA A:GLN150 4.3 12.6 1.0 O A:HOH476 4.3 35.1 1.0 N A:GLN150 4.4 9.0 1.0 CB A:GLN150 4.4 15.4 1.0 N A:ILE151 4.5 10.8 1.0 OG A:SER123 4.5 30.1 1.0 N A:GLU152 4.5 14.2 1.0 CG A:GLU156 4.5 14.1 1.0 CG A:GLU233 4.5 14.5 1.0 CA A:ILE151 4.5 9.6 1.0 OH A:TYR125 4.6 18.2 1.0 O A:HOH407 4.6 19.1 1.0 O A:HOH530 4.8 38.8 1.0 CD1 A:LEU149 4.9 15.5 1.0 CE2 A:TYR125 5.0 14.0 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of the Human CLEC9A C-Type Lectin-Like 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 the Human CLEC9A C-Type Lectin-Like Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:11.9 occ:1.00 O B:GLN150 2.5 12.1 1.0 OE1 B:GLU233 2.7 17.4 1.0 OE2 B:GLU152 2.7 23.1 1.0 OE2 B:GLU156 2.7 16.0 1.0 O B:HOH412 2.7 21.9 1.0 O B:HOH407 2.7 19.4 1.0 OE1 B:GLU156 2.7 15.2 1.0 OE2 B:GLU233 2.7 14.2 1.0 CD B:GLU233 3.0 17.4 1.0 CD B:GLU156 3.1 18.6 1.0 C B:GLN150 3.5 17.4 1.0 CD B:GLU152 3.7 32.8 1.0 OE1 B:GLU152 4.0 29.3 1.0 CA B:GLN150 4.3 12.5 1.0 CB B:GLN150 4.3 15.8 1.0 O B:HOH440 4.3 33.3 1.0 N B:GLN150 4.3 8.0 1.0 O B:HOH501 4.4 41.6 1.0 N B:ILE151 4.5 11.7 1.0 CG B:GLU156 4.5 15.2 1.0 CG B:GLU233 4.5 17.0 1.0 N B:GLU152 4.5 14.8 1.0 CA B:ILE151 4.6 11.3 1.0 OH B:TYR125 4.6 13.8 1.0 OG B:SER123 4.6 31.8 1.0 O B:HOH545 4.6 44.7 1.0 O B:HOH414 4.7 17.4 1.0 O B:HOH533 4.7 40.8 1.0 CD1 B:LEU149 4.8 12.1 1.0 CG B:GLU152 5.0 33.6 1.0 CE2 B:TYR125 5.0 12.0 1.0

J.G.Zhang, P.E.Czabotar, A.N.Policheni, I.Caminschi, S.S.Wan, S.Kitsoulis, K.M.Tullett, A.Y.Robin, R.Brammananth, M.F.Van Delft, J.Lu, L.A.O'reilly, E.C.Josefsson, B.T.Kile, W.J.Chin, J.D.Mintern, M.A.Olshina, W.Wong, J.Baum, M.D.Wright, D.C.Huang, N.Mohandas, R.L.Coppel, P.M.Colman, N.A.Nicola, K.Shortman, M.H.Lahoud. The Dendritic Cell Receptor CLEC9A Binds Damaged Cells Via Exposed Actin Filaments. Immunity V. 36 646 2012.
ISSN: ISSN 1074-7613
PubMed: 22483802
DOI: 10.1016/J.IMMUNI.2012.03.009