Calcium in PDB 2dpk: The Crystal Structure of the Primary CA2+ Sensor of the Na+/CA2+ Exchanger

The structure of The Crystal Structure of the Primary CA2+ Sensor of the Na+/CA2+ Exchanger, PDB code: 2dpk was solved by J.Abramson, M.Sawaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.26 / 2.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	59.624, 45.524, 57.269, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 28.4

The binding sites of Calcium atom in the The Crystal Structure of the Primary CA2+ Sensor of the Na+/CA2+ Exchanger (pdb code 2dpk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the The Crystal Structure of the Primary CA2+ Sensor of the Na+/CA2+ Exchanger, PDB code: 2dpk:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the The Crystal Structure of the Primary CA2+ Sensor of the Na+/CA2+ Exchanger


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of the Primary CA2+ Sensor of the Na+/CA2+ Exchanger within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:62.2 occ:1.00 OE2 A:GLU451 2.5 45.6 1.0 OE2 A:GLU454 2.6 49.2 1.0 OD2 A:ASP421 2.7 43.0 1.0 OD1 A:ASP421 2.8 40.1 1.0 OE1 A:GLU454 2.9 50.6 1.0 CD A:GLU454 3.1 48.7 1.0 CG A:ASP421 3.1 42.1 1.0 CD A:GLU451 3.5 47.7 1.0 O A:HOH5 4.0 29.5 1.0 CA A:CA2001 4.3 59.3 1.0 OE1 A:GLU451 4.3 52.6 1.0 CG A:GLU451 4.4 44.9 1.0 CG A:GLU454 4.6 45.5 1.0 CB A:ASP421 4.6 41.2 1.0 OG A:SER420 4.7 51.3 1.0 O A:HOH15 4.7 46.1 1.0 O A:THR415 4.8 34.7 1.0 CB A:GLU451 4.9 45.0 1.0 ND2 A:ASN417 4.9 37.1 1.0

Calcium binding site 2 out of 4 in the The Crystal Structure of the Primary CA2+ Sensor of the Na+/CA2+ Exchanger


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Crystal Structure of the Primary CA2+ Sensor of the Na+/CA2+ Exchanger within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2001 b:59.3 occ:1.00 O A:HOH16 2.3 47.0 1.0 O A:HOH1 2.3 63.1 1.0 O A:HOH15 2.5 46.1 1.0 OD2 A:ASP421 2.5 43.0 1.0 OE1 A:GLU451 2.7 52.6 1.0 OE2 A:GLU451 2.9 45.6 1.0 CD A:GLU451 3.1 47.7 1.0 CD A:GLU385 3.4 47.5 1.0 OE2 A:GLU385 3.4 46.0 1.0 OE1 A:GLU385 3.5 55.3 1.0 CG A:ASP421 3.6 42.1 1.0 CB A:ASP421 4.1 41.2 1.0 CG A:GLU385 4.2 48.6 1.0 CA A:ASP421 4.2 41.7 1.0 O A:ILE445 4.2 41.8 1.0 OE1 A:GLU454 4.2 50.6 1.0 CA A:CA1001 4.3 62.2 1.0 CA A:CA3001 4.3 55.5 1.0 OD1 A:ASP447 4.4 42.4 1.0 O A:HOH14 4.4 35.2 1.0 CG A:GLU451 4.6 44.9 1.0 O A:SER420 4.6 45.4 1.0 OD1 A:ASP421 4.6 40.1 1.0 CG2 A:ILE496 4.7 35.5 1.0 OD2 A:ASP447 4.8 41.7 1.0 O A:ASP421 4.8 40.8 1.0 CG A:ASP447 4.9 44.6 1.0 OD1 A:ASP498 4.9 55.7 1.0

Calcium binding site 3 out of 4 in the The Crystal Structure of the Primary CA2+ Sensor of the Na+/CA2+ Exchanger


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Crystal Structure of the Primary CA2+ Sensor of the Na+/CA2+ Exchanger within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3001 b:55.5 occ:1.00 O A:ILE449 2.4 42.2 1.0 OD2 A:ASP500 2.4 60.5 1.0 OD2 A:ASP447 2.4 41.7 1.0 OD1 A:ASP498 2.4 55.7 1.0 OE1 A:GLU451 2.6 52.6 1.0 OE1 A:GLU385 2.7 55.3 1.0 OE2 A:GLU385 2.7 46.0 1.0 CD A:GLU385 3.0 47.5 1.0 CD A:GLU451 3.5 47.7 1.0 CG A:ASP447 3.5 44.6 1.0 C A:ILE449 3.5 48.8 1.0 CG A:ASP500 3.5 57.6 1.0 CG A:ASP498 3.6 62.5 1.0 CG A:GLU451 3.7 44.9 1.0 CD1 A:ILE449 3.9 62.9 1.0 CA A:CA4001 3.9 57.7 1.0 N A:ILE449 3.9 51.4 1.0 OD1 A:ASP447 4.0 42.4 1.0 O A:ASP447 4.2 41.8 1.0 OD2 A:ASP498 4.2 65.9 1.0 O A:HOH1 4.2 63.1 1.0 CA A:ILE449 4.3 51.6 1.0 CA A:CA2001 4.3 59.3 1.0 CB A:ASP500 4.3 62.5 1.0 OD1 A:ASP500 4.4 53.8 1.0 C A:ASP447 4.4 49.4 1.0 CB A:GLU451 4.5 45.0 1.0 CG A:GLU385 4.5 48.6 1.0 OE2 A:GLU451 4.6 45.6 1.0 N A:PHE450 4.6 48.4 1.0 CG1 A:ILE449 4.6 58.3 1.0 OD1 A:ASP499 4.7 73.8 1.0 N A:GLU451 4.7 42.1 1.0 N A:ASP447 4.8 43.0 1.0 CB A:ASP447 4.8 46.2 1.0 O A:HOH15 4.8 46.1 1.0 CB A:ASP498 4.8 63.6 1.0 C A:PHE450 4.8 46.9 1.0 CA A:PHE450 4.8 45.9 1.0 C A:ASP448 4.9 56.7 1.0 CA A:ASP447 4.9 47.5 1.0 N A:ASP448 4.9 54.1 1.0

Calcium binding site 4 out of 4 in the The Crystal Structure of the Primary CA2+ Sensor of the Na+/CA2+ Exchanger


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Crystal Structure of the Primary CA2+ Sensor of the Na+/CA2+ Exchanger within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4001 b:57.7 occ:1.00 OD1 A:ASP499 2.3 73.8 1.0 O A:ASP447 2.3 41.8 1.0 OD2 A:ASP446 2.3 50.8 1.0 OD1 A:ASP500 2.5 53.8 1.0 OD2 A:ASP500 2.8 60.5 1.0 CG A:ASP500 3.0 57.6 1.0 CG A:ASP499 3.2 73.3 1.0 OE2 A:GLU385 3.4 46.0 1.0 C A:ASP447 3.5 49.4 1.0 O A:HOH8 3.5 38.9 1.0 CG A:ASP446 3.5 49.0 1.0 CD A:GLU385 3.5 47.5 1.0 OD2 A:ASP499 3.6 77.2 1.0 N A:ASP447 3.7 43.0 1.0 OE1 A:GLU385 3.9 55.3 1.0 CA A:CA3001 3.9 55.5 1.0 CG A:GLU385 4.0 48.6 1.0 OD1 A:ASP446 4.1 43.7 1.0 OD2 A:ASP447 4.1 41.7 1.0 CA A:ASP447 4.3 47.5 1.0 CB A:GLU385 4.3 45.1 1.0 N A:ASP448 4.4 54.1 1.0 O A:ASP499 4.5 74.0 1.0 C A:ASP499 4.5 69.8 1.0 C A:ASP446 4.5 44.1 1.0 CB A:ASP500 4.5 62.5 1.0 CB A:ASP499 4.6 71.3 1.0 CA A:ASP448 4.6 57.9 1.0 CA A:ASP446 4.6 42.9 1.0 CB A:ASP446 4.7 45.1 1.0 N A:ASP499 4.7 66.8 1.0 N A:ASP500 4.8 69.1 1.0 CA A:ASP499 4.9 69.3 1.0 OD1 A:ASP498 4.9 55.7 1.0

D.A.Nicoll, M.Sawaya, S.Kwon, D.Cascio, K.D.Philipson, J.Abramson. The Crystal Structure of the Primary CA2+ Sensor of the Na+/CA2+ Exchanger Reveals A Novel CA2+ Binding Motif. J.Biol.Chem. V. 281 21577 2006.
ISSN: ISSN 0021-9258
PubMed: 16774926
DOI: 10.1074/JBC.C600117200