Calcium in PDB 1edm: Epidermal Growth Factor-Like Domain From Human Factor IX

The structure of Epidermal Growth Factor-Like Domain From Human Factor IX, PDB code: 1edm was solved by Z.Rao, P.Handford, M.Mayhew, V.Knott, G.G.Brownlee, D.Stuart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.50
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	40.300, 40.300, 98.300, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / n/a

The binding sites of Calcium atom in the Epidermal Growth Factor-Like Domain From Human Factor IX (pdb code 1edm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Epidermal Growth Factor-Like Domain From Human Factor IX, PDB code: 1edm:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Epidermal Growth Factor-Like Domain From Human Factor IX


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Epidermal Growth Factor-Like Domain From Human Factor IX within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca3 b:23.1 occ:1.00 O B:HOH234 2.3 28.5 1.0 O B:SER53 2.4 13.2 1.0 O B:HOH209 2.4 38.3 1.0 O B:HOH254 2.5 44.5 1.0 O B:HOH210 2.5 27.8 1.0 O B:HOH208 2.6 26.3 1.0 OG B:SER53 2.6 30.6 1.0 C B:SER53 3.4 14.9 1.0 CB B:SER53 3.6 23.3 1.0 CA B:SER53 3.8 11.2 1.0 O B:HOH281 4.3 41.3 1.0 O B:ASN54 4.5 14.2 1.0 N B:ASN54 4.6 11.6 1.0 C B:ASN54 4.8 11.5 1.0 CB B:ASN54 5.0 11.7 1.0

Calcium binding site 2 out of 3 in the Epidermal Growth Factor-Like Domain From Human Factor IX


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Epidermal Growth Factor-Like Domain From Human Factor IX within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2 b:13.4 occ:1.00 O B:GLY48 2.3 17.8 1.0 O B:ASP65 2.3 15.3 1.0 OD2 B:ASP47 2.3 17.4 1.0 OD1 C:ASN58 2.4 16.1 1.0 OD2 B:ASP64 2.4 17.2 1.0 OE1 B:GLN50 2.4 18.1 1.0 OD1 B:ASP64 2.6 13.2 1.0 CG B:ASP64 2.8 18.6 1.0 CG B:ASP47 3.4 28.6 1.0 CD B:GLN50 3.4 22.4 1.0 C B:GLY48 3.5 17.3 1.0 C B:ASP65 3.5 20.4 1.0 CG C:ASN58 3.5 14.7 1.0 NE2 B:GLN50 3.9 18.5 1.0 N B:ASN67 3.9 16.2 1.0 N B:GLN50 4.1 13.2 1.0 CB B:ASP47 4.2 17.0 1.0 OD1 B:ASP47 4.2 36.2 1.0 N B:ASP65 4.2 16.8 1.0 CA B:ILE66 4.2 22.7 1.0 CA C:ASN58 4.2 16.9 1.0 CB B:ASP64 4.3 11.6 1.0 CA B:ASP49 4.3 14.0 1.0 N B:ASP49 4.3 12.9 1.0 N C:ASN58 4.4 16.6 1.0 N B:ILE66 4.4 18.8 1.0 ND2 C:ASN58 4.4 18.0 1.0 N B:GLY48 4.4 22.1 1.0 C B:ASP47 4.4 24.1 1.0 CB C:ASN58 4.5 16.6 1.0 O B:SER68 4.5 16.6 1.0 CA B:ASP65 4.5 13.0 1.0 CA B:GLY48 4.6 21.8 1.0 C B:ILE66 4.6 13.0 1.0 O B:ASP47 4.6 39.3 1.0 C B:ASP64 4.7 16.1 1.0 CG B:GLN50 4.7 17.2 1.0 C B:ASP49 4.7 13.5 1.0 CA B:ASN67 4.8 20.1 1.0 N B:SER68 4.9 16.9 1.0 CB B:GLN50 4.9 15.9 1.0 CA B:ASP64 4.9 10.5 1.0 CA B:ASP47 5.0 22.9 1.0

Calcium binding site 3 out of 3 in the Epidermal Growth Factor-Like Domain From Human Factor IX


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Epidermal Growth Factor-Like Domain From Human Factor IX within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1 b:11.3 occ:1.00 O C:ASP65 2.2 12.6 1.0 OD2 C:ASP47 2.3 14.1 1.0 OE1 C:GLN50 2.4 13.4 1.0 O C:GLY48 2.4 14.1 1.0 OD1 C:ASP64 2.6 12.5 1.0 OD2 C:ASP64 2.6 14.0 1.0 CG C:ASP64 2.9 16.0 1.0 CG C:ASP47 3.4 15.9 1.0 C C:ASP65 3.4 13.8 1.0 CD C:GLN50 3.4 19.6 1.0 C C:GLY48 3.6 11.9 1.0 NE2 C:GLN50 3.9 21.9 1.0 N C:ASN67 3.9 18.3 1.0 CB C:ASP47 4.1 12.1 1.0 N C:GLN50 4.1 11.1 1.0 CA C:ILE66 4.1 15.9 1.0 N C:ASP65 4.2 14.6 1.0 N C:ILE66 4.3 19.7 1.0 OD1 C:ASP47 4.3 36.3 1.0 CA C:ASP49 4.3 12.6 1.0 CB C:ASP64 4.3 9.6 1.0 N C:ASP49 4.4 11.6 1.0 C C:ASP47 4.4 14.8 1.0 CA C:ASP65 4.4 12.5 1.0 N C:GLY48 4.5 14.7 1.0 O C:SER68 4.5 17.6 1.0 C C:ILE66 4.5 21.4 1.0 O C:ASP47 4.6 13.4 1.0 CA C:GLY48 4.6 14.7 1.0 C C:ASP64 4.7 13.9 1.0 CG C:GLN50 4.7 13.3 1.0 C C:ASP49 4.8 14.2 1.0 CB C:GLN50 4.9 12.8 1.0 CA C:ASN67 4.9 16.4 1.0 CA C:ASP47 4.9 13.2 1.0 CA C:ASP64 4.9 10.3 1.0 N C:SER68 5.0 14.8 1.0

Z.Rao, P.Handford, M.Mayhew, V.Knott, G.G.Brownlee, D.Stuart. The Structure of A Ca(2+)-Binding Epidermal Growth Factor-Like Domain: Its Role in Protein-Protein Interactions. Cell(Cambridge,Mass.) V. 82 131 1995.
ISSN: ISSN 0092-8674
PubMed: 7606779
DOI: 10.1016/0092-8674(95)90059-4