Calcium in PDB 3us9: Crystal Structure of the NCX1 Intracellular Tandem Calcium Binding Domains(CBD12)

The structure of Crystal Structure of the NCX1 Intracellular Tandem Calcium Binding Domains(CBD12), PDB code: 3us9 was solved by M.Giladi, Y.Sasson, J.A.Hirsch, D.Khananshvili, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.02 / 2.68
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	80.670, 152.550, 79.700, 90.00, 90.00, 90.00
R / Rfree (%)	23.4 / 27.4

The binding sites of Calcium atom in the Crystal Structure of the NCX1 Intracellular Tandem Calcium Binding Domains(CBD12) (pdb code 3us9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of the NCX1 Intracellular Tandem Calcium Binding Domains(CBD12), PDB code: 3us9:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of the NCX1 Intracellular Tandem Calcium Binding Domains(CBD12)


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 NCX1 Intracellular Tandem Calcium Binding Domains(CBD12) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1 b:69.6 occ:1.00 OE2 A:GLU451 2.5 73.2 1.0 OE2 A:GLU385 2.8 71.0 1.0 OE1 A:GLU451 2.9 82.8 1.0 O A:HOH660 3.0 50.1 1.0 CD A:GLU451 3.1 28.6 1.0 CD A:GLU385 3.2 58.7 1.0 OD1 A:ASP421 3.4 72.7 1.0 CG A:GLU385 3.7 41.6 1.0 OE1 A:GLU385 3.8 88.4 1.0 O A:HOH8 3.9 49.2 1.0 O A:ILE445 4.2 61.4 1.0 CA A:ASP421 4.2 54.9 1.0 CG A:ASP421 4.3 49.2 1.0 CB A:ASP421 4.4 37.4 1.0 OD1 A:ASP498 4.4 70.1 1.0 CA A:CA3 4.4 45.5 1.0 CG A:GLU451 4.5 37.8 1.0 O A:ASP421 4.6 60.0 1.0 CB A:GLU385 4.7 36.3 1.0 OD1 A:ASP447 4.7 33.6 1.0 CG2 A:ILE496 4.7 30.8 1.0 O A:SER420 4.9 68.6 1.0 CB A:GLU451 4.9 42.2 1.0 C A:ASP421 4.9 65.4 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of the NCX1 Intracellular Tandem Calcium Binding Domains(CBD12)


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 NCX1 Intracellular Tandem Calcium Binding Domains(CBD12) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2 b:61.5 occ:1.00 OD2 A:ASP500 2.2 72.7 1.0 OD2 A:ASP499 2.3 0.4 1.0 OD1 A:ASP446 2.4 0.7 1.0 O A:ASP447 2.5 49.7 1.0 OD1 A:ASP500 2.7 55.6 1.0 CG A:ASP500 2.8 49.9 1.0 OE1 A:GLU385 3.0 88.4 1.0 CD A:GLU385 3.4 58.7 1.0 CG A:ASP499 3.4 80.2 1.0 CG A:ASP446 3.5 89.3 1.0 CA A:CA3 3.6 45.5 1.0 C A:ASP447 3.7 36.6 1.0 OE2 A:GLU385 3.8 71.0 1.0 OD1 A:ASP499 3.9 81.6 1.0 OD2 A:ASP446 4.0 95.1 1.0 N A:ASP447 4.2 39.3 1.0 CG A:GLU385 4.2 41.6 1.0 CB A:GLU385 4.3 36.3 1.0 CB A:ASP500 4.3 58.0 1.0 C A:ASP499 4.4 68.0 1.0 OD1 A:ASP498 4.4 70.1 1.0 O A:ASP499 4.4 49.2 1.0 N A:ASP499 4.5 57.9 1.0 CA A:ASP448 4.5 57.9 1.0 N A:ASP448 4.6 69.0 1.0 OD1 A:ASP448 4.6 99.1 1.0 N A:ASP500 4.6 60.4 1.0 OD1 A:ASP447 4.6 33.6 1.0 CA A:ASP447 4.6 30.3 1.0 NH1 A:ARG532 4.6 59.8 1.0 CB A:ASP499 4.7 55.6 1.0 CA A:ASP499 4.7 54.8 1.0 CB A:ASP446 4.8 44.4 1.0 CA A:ASP500 4.9 36.0 1.0 CA A:ASP446 4.9 41.4 1.0 C A:ASP446 4.9 52.9 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of the NCX1 Intracellular Tandem Calcium Binding Domains(CBD12)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the NCX1 Intracellular Tandem Calcium Binding Domains(CBD12) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3 b:45.5 occ:1.00 OD1 A:ASP500 1.9 55.6 1.0 OE2 A:GLU451 2.5 73.2 1.0 OD1 A:ASP498 2.6 70.1 1.0 O A:ILE449 2.7 56.6 1.0 OE2 A:GLU385 2.7 71.0 1.0 OD1 A:ASP447 2.8 33.6 1.0 OE1 A:GLU385 3.1 88.4 1.0 CG A:ASP500 3.1 49.9 1.0 CD A:GLU385 3.3 58.7 1.0 C A:ILE449 3.3 50.5 1.0 CD A:GLU451 3.5 28.6 1.0 CG A:ASP498 3.6 23.3 1.0 N A:ILE449 3.6 54.2 1.0 CA A:CA2 3.6 61.5 1.0 O A:ASP447 3.7 49.7 1.0 OD2 A:ASP498 3.8 62.5 1.0 CG A:GLU451 3.9 37.8 1.0 OD2 A:ASP500 3.9 72.7 1.0 CA A:ILE449 4.0 40.3 1.0 CG A:ASP447 4.0 50.0 1.0 CB A:ASP500 4.1 58.0 1.0 C A:ASP447 4.1 36.6 1.0 N A:PHE450 4.2 36.8 1.0 C A:ASP448 4.3 56.1 1.0 CA A:CA1 4.4 69.6 1.0 CA A:PHE450 4.4 30.4 1.0 N A:GLU451 4.5 69.5 1.0 N A:ASP448 4.6 69.0 1.0 OE1 A:GLU451 4.6 82.8 1.0 C A:PHE450 4.6 50.6 1.0 CA A:ASP448 4.7 57.9 1.0 CB A:ILE449 4.7 29.4 1.0 N A:ASP447 4.7 39.3 1.0 CB A:GLU451 4.7 42.2 1.0 OD2 A:ASP447 4.7 98.5 1.0 O A:HOH660 4.7 50.1 1.0 CG A:GLU385 4.7 41.6 1.0 CA A:ASP447 4.8 30.3 1.0 CB A:ASP498 4.9 26.6 1.0 OD1 A:ASP446 4.9 0.7 1.0 CB A:ASP447 5.0 31.8 1.0 O A:ASP448 5.0 54.3 1.0

M.Giladi, Y.Sasson, X.Fang, R.Hiller, T.Buki, Y.X.Wang, J.A.Hirsch, D.Khananshvili. A Common CA2+-Driven Interdomain Module Governs Eukaryotic Ncx Regulation. Plos One V. 7 39985 2012.
ISSN: ESSN 1932-6203
PubMed: 22768191
DOI: 10.1371/JOURNAL.PONE.0039985