Calcium in PDB 4d90: Crystal Structure of Del-1 Egf Domains

The structure of Crystal Structure of Del-1 Egf Domains, PDB code: 4d90 was solved by Q.Chen, T.Schurpf, T.Springer, J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.32 / 2.60
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	82.680, 82.680, 56.422, 90.00, 90.00, 120.00
R / Rfree (%)	20.4 / 25.9

The binding sites of Calcium atom in the Crystal Structure of Del-1 Egf Domains (pdb code 4d90). 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 Del-1 Egf Domains, PDB code: 4d90:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Del-1 Egf Domains


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 Del-1 Egf Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca604 b:51.0 occ:1.00 O A:ILE120 2.6 45.9 1.0 O A:LEU137 2.7 44.3 1.0 OD1 A:ASN119 2.7 43.4 1.0 O A:HOH701 2.7 40.6 1.0 OD2 A:ASP136 2.8 48.0 1.0 OD1 A:ASP136 2.8 46.1 1.0 OE1 A:GLU122 2.8 51.9 1.0 CG A:ASP136 3.1 47.7 1.0 CG A:ASN119 3.4 41.4 1.0 C A:LEU137 3.5 42.8 1.0 CD A:GLU122 3.7 53.7 1.0 C A:ILE120 3.8 45.2 1.0 ND2 A:ASN119 3.8 43.6 1.0 OE2 A:GLU122 4.1 48.4 1.0 N A:LEU137 4.1 45.4 1.0 N A:ALA139 4.2 42.9 1.0 CA A:VAL138 4.2 46.9 1.0 N A:ILE120 4.2 39.8 1.0 N A:VAL138 4.2 46.4 1.0 O A:ASN140 4.3 39.1 1.0 N A:GLU122 4.3 41.5 1.0 O A:HOH723 4.4 52.3 1.0 C A:ASN119 4.4 42.8 1.0 CA A:LEU137 4.4 44.2 1.0 CB A:ASP136 4.5 44.7 1.0 CA A:ILE120 4.5 38.7 1.0 CB A:ASN119 4.5 40.2 1.0 C A:VAL138 4.6 45.0 1.0 O A:HOH715 4.6 47.4 1.0 O A:GLY110 4.6 39.3 1.0 C A:ASP136 4.7 42.1 1.0 CB A:GLU122 4.7 43.1 1.0 CA A:ASN121 4.7 40.2 1.0 N A:ASN121 4.8 47.5 1.0 O A:ASN119 4.8 42.8 1.0 CG A:GLU122 4.8 44.2 1.0 N A:ASN140 4.9 46.1 1.0 CB A:ILE120 4.9 43.7 1.0 CA A:ASN119 4.9 41.8 1.0 CA A:ASP136 4.9 43.3 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Del-1 Egf Domains


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 Del-1 Egf Domains within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca604 b:47.8 occ:1.00 OD1 B:ASN119 2.6 39.1 1.0 O B:ILE120 2.6 45.0 1.0 O B:LEU137 2.7 44.2 1.0 OE1 B:GLU122 2.7 51.1 1.0 OD1 B:ASP136 2.8 45.9 1.0 O B:HOH701 2.8 44.1 1.0 OD2 B:ASP136 2.8 46.3 1.0 CG B:ASP136 3.1 45.9 1.0 C B:LEU137 3.5 43.7 1.0 CG B:ASN119 3.5 40.3 1.0 C B:ILE120 3.8 44.0 1.0 CD B:GLU122 3.9 53.9 1.0 ND2 B:ASN119 3.9 42.2 1.0 N B:LEU137 4.1 42.1 1.0 CA B:VAL138 4.1 45.0 1.0 N B:VAL138 4.1 45.5 1.0 N B:ALA139 4.1 41.1 1.0 N B:GLU122 4.2 41.5 1.0 O B:ASN140 4.3 40.4 1.0 N B:ILE120 4.3 39.6 1.0 CA B:LEU137 4.4 44.4 1.0 CB B:ASP136 4.5 42.9 1.0 C B:ASN119 4.5 43.3 1.0 C B:VAL138 4.5 43.0 1.0 CB B:GLU122 4.6 45.2 1.0 CA B:ILE120 4.6 40.2 1.0 CA B:ASN121 4.6 41.2 1.0 C B:ASP136 4.7 40.6 1.0 OE2 B:GLU122 4.7 53.3 1.0 CB B:ASN119 4.7 40.5 1.0 N B:ASN121 4.7 50.3 1.0 O B:ASN119 4.7 42.9 1.0 O B:GLY110 4.7 40.1 1.0 CG B:GLU122 4.9 46.0 1.0 O B:HOH704 4.9 52.4 1.0 N B:ASN140 4.9 44.3 1.0 CA B:ASP136 4.9 42.6 1.0 C B:ASN121 5.0 41.2 1.0

T.Schurpf, Q.Chen, J.H.Liu, R.Wang, T.A.Springer, J.H.Wang. The Rgd Finger of Del-1 Is A Unique Structural Feature Critical For Integrin Binding. Faseb J. V. 26 3412 2012.
ISSN: ISSN 0892-6638
PubMed: 22601780
DOI: 10.1096/FJ.11-202036