Calcium in PDB 2pmy: Ef-Hand Domain of Human Rasef

The structure of Ef-Hand Domain of Human Rasef, PDB code: 2pmy was solved by H.Zhu, Y.Shen, J.Wang, W.Tempel, R.Landry, C.H.Arrowsmith, A.M.Edwards, M.Sundstrom, J.Weigelt, A.Bochkarev, H.Park, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.30
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.259, 61.259, 101.598, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 26.3

The binding sites of Calcium atom in the Ef-Hand Domain of Human Rasef (pdb code 2pmy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Ef-Hand Domain of Human Rasef, PDB code: 2pmy:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Ef-Hand Domain of Human Rasef


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ef-Hand Domain of Human Rasef within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:18.8 occ:1.00 OD1 A:ASP21 1.9 24.5 1.0 OE1 A:GLU32 2.1 32.0 1.0 OD1 A:ASN23 2.1 26.2 1.0 OE1 A:GLU29 2.2 26.5 1.0 O A:ARG27 2.2 23.0 1.0 OG A:SER25 2.5 30.7 1.0 CD A:GLU32 3.0 33.4 1.0 CG A:ASN23 3.1 29.2 1.0 CG A:ASP21 3.2 27.8 1.0 CD A:GLU29 3.2 27.4 1.0 OE2 A:GLU32 3.3 34.1 1.0 C A:ARG27 3.4 24.4 1.0 ND2 A:ASN23 3.5 26.7 1.0 CB A:SER25 3.5 27.9 1.0 OE2 A:GLU29 3.5 27.8 1.0 N A:SER25 3.8 31.5 1.0 OD2 A:ASP21 4.0 22.8 1.0 CB A:ASP21 4.1 24.4 1.0 N A:ARG27 4.1 28.5 1.0 N A:GLU29 4.2 24.3 1.0 CA A:SER25 4.2 27.8 1.0 CA A:LEU28 4.2 24.7 1.0 CA A:ASP21 4.2 27.7 1.0 N A:LEU28 4.2 26.3 1.0 CG A:GLU32 4.3 34.8 1.0 CA A:ARG27 4.4 26.8 1.0 CB A:ASN23 4.4 29.5 1.0 N A:ARG24 4.5 32.5 1.0 CG A:GLU29 4.5 27.7 1.0 N A:ASN23 4.5 27.3 1.0 C A:ASP21 4.6 28.5 1.0 N A:GLY26 4.6 27.8 1.0 C A:SER25 4.7 25.9 1.0 C A:ASN23 4.7 31.7 1.0 C A:LEU28 4.7 24.8 1.0 CA A:ASN23 4.7 29.0 1.0 CB A:GLU29 4.9 27.8 1.0 O A:ASP21 4.9 25.9 1.0 C A:ARG24 5.0 35.5 1.0 N A:ALA22 5.0 28.4 1.0 CB A:ARG27 5.0 26.2 1.0

Calcium binding site 2 out of 4 in the Ef-Hand Domain of Human Rasef


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ef-Hand Domain of Human Rasef within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca103 b:33.5 occ:1.00 OD1 A:ASP59 2.1 40.1 1.0 OD1 A:ASP55 2.3 32.9 1.0 OD1 A:ASP57 2.3 39.8 1.0 O A:ALA61 2.3 29.7 1.0 OE2 A:GLU66 2.5 29.7 1.0 OE1 A:GLU66 2.5 30.6 1.0 CD A:GLU66 2.9 29.2 1.0 CG A:ASP59 3.3 42.2 1.0 CG A:ASP57 3.4 42.9 1.0 CG A:ASP55 3.4 32.2 1.0 C A:ALA61 3.5 24.3 1.0 OD2 A:ASP57 3.9 40.8 1.0 OD2 A:ASP59 3.9 43.6 1.0 OD2 A:ASP55 4.1 29.6 1.0 N A:ASP59 4.2 41.4 1.0 N A:ALA61 4.3 28.7 1.0 CA A:ILE62 4.3 24.9 1.0 N A:ILE62 4.3 27.6 1.0 CB A:ASP59 4.3 40.5 1.0 CA A:ASP55 4.4 34.4 1.0 N A:ASP57 4.4 39.5 1.0 CG A:GLU66 4.4 27.7 1.0 CB A:ASP55 4.4 30.9 1.0 CA A:ALA61 4.5 28.0 1.0 N A:THR63 4.6 24.9 1.0 CB A:ASP57 4.6 41.8 1.0 C A:ASP55 4.6 37.1 1.0 N A:ARG58 4.6 43.2 1.0 CA A:ASP59 4.7 39.7 1.0 N A:GLY60 4.8 33.1 1.0 CG2 A:THR63 4.8 17.4 1.0 CA A:ASP57 4.8 41.2 1.0 C A:ASP57 4.8 42.8 1.0 N A:ALA56 4.9 37.7 1.0 C A:ILE62 4.9 23.8 1.0 C A:ASP59 5.0 36.5 1.0

Calcium binding site 3 out of 4 in the Ef-Hand Domain of Human Rasef


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ef-Hand Domain of Human Rasef within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca101 b:26.6 occ:1.00 OE2 B:GLU32 1.9 25.8 1.0 OD1 B:ASP21 2.0 32.7 1.0 OG B:SER25 2.1 35.9 1.0 OE2 B:GLU29 2.1 27.1 1.0 O B:ARG27 2.2 32.9 1.0 OD1 B:ASN23 2.2 40.6 1.0 CD B:GLU32 3.0 31.6 1.0 CD B:GLU29 3.0 29.4 1.0 CG B:ASN23 3.2 38.8 1.0 CG B:ASP21 3.2 31.4 1.0 OE1 B:GLU29 3.2 30.0 1.0 CB B:SER25 3.3 38.9 1.0 C B:ARG27 3.4 33.9 1.0 OE1 B:GLU32 3.5 33.9 1.0 ND2 B:ASN23 3.5 32.8 1.0 N B:SER25 3.7 41.0 1.0 OD2 B:ASP21 4.0 29.6 1.0 CA B:SER25 4.1 38.7 1.0 N B:ARG27 4.1 36.9 1.0 CB B:ASP21 4.1 31.6 1.0 N B:GLU29 4.1 32.2 1.0 CA B:ASP21 4.2 34.6 1.0 CG B:GLU32 4.2 30.6 1.0 N B:LEU28 4.3 33.0 1.0 CA B:LEU28 4.3 29.4 1.0 CA B:ARG27 4.3 36.6 1.0 CG B:GLU29 4.4 27.6 1.0 N B:ARG24 4.5 41.7 1.0 CB B:ASN23 4.5 36.9 1.0 C B:ASP21 4.6 36.1 1.0 N B:ASN23 4.6 36.0 1.0 N B:GLY26 4.6 39.9 1.0 C B:SER25 4.7 39.1 1.0 C B:ASN23 4.7 40.5 1.0 C B:LEU28 4.7 30.3 1.0 CB B:GLU29 4.7 29.3 1.0 CA B:ASN23 4.8 37.3 1.0 C B:ARG24 4.9 42.9 1.0 CB B:ARG27 4.9 37.1 1.0 O B:ASP21 5.0 34.8 1.0 N B:ALA22 5.0 36.4 1.0

Calcium binding site 4 out of 4 in the Ef-Hand Domain of Human Rasef


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Ef-Hand Domain of Human Rasef within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca104 b:32.6 occ:1.00 OD1 B:ASP55 2.2 31.6 1.0 O B:ALA61 2.3 31.4 1.0 OD1 B:ASP59 2.3 34.7 1.0 O B:HOH209 2.4 31.9 1.0 OD2 B:ASP57 2.4 40.4 1.0 OE1 B:GLU66 2.5 27.4 1.0 OE2 B:GLU66 2.7 29.2 1.0 CD B:GLU66 2.9 30.5 1.0 CG B:ASP59 3.2 33.8 1.0 CG B:ASP57 3.3 39.5 1.0 CG B:ASP55 3.4 29.7 1.0 C B:ALA61 3.5 28.3 1.0 OD1 B:ASP57 3.6 41.8 1.0 OD2 B:ASP59 3.7 34.5 1.0 N B:ASP59 4.2 35.5 1.0 N B:ALA61 4.2 27.8 1.0 OD2 B:ASP55 4.2 30.4 1.0 CA B:ILE62 4.3 24.1 1.0 N B:ILE62 4.3 26.7 1.0 CA B:ASP55 4.3 28.2 1.0 CB B:ASP59 4.3 32.0 1.0 N B:ASP57 4.4 33.8 1.0 CB B:ASP55 4.4 28.9 1.0 CA B:ALA61 4.4 28.5 1.0 CG B:GLU66 4.4 32.0 1.0 N B:ARG58 4.5 38.3 1.0 CB B:ASP57 4.5 37.5 1.0 C B:ASP55 4.6 30.9 1.0 N B:THR63 4.6 25.8 1.0 CA B:ASP59 4.7 34.8 1.0 C B:ASP57 4.7 36.4 1.0 CA B:ASP57 4.7 34.7 1.0 N B:ALA56 4.8 31.8 1.0 N B:GLY60 4.8 34.3 1.0 CG2 B:THR63 4.9 27.6 1.0 C B:ILE62 4.9 24.3 1.0 C B:ASP59 5.0 34.9 1.0

H.Zhu, Y.Shen, J.Wang, W.Tempel, R.Landry, C.H.Arrowsmith, A.M.Edwards, M.Sundstrom, J.Weigelt, A.Bochkarev, H.Park. Ef-Hand Domain of Human Rasef To Be Published.