Calcium in PDB 3rb5: Crystal Structure of Calcium Binding Domain CBD12 of CALX1.1

The structure of Crystal Structure of Calcium Binding Domain CBD12 of CALX1.1, PDB code: 3rb5 was solved by M.Wu, L.Zheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.46 / 2.35
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	63.091, 63.091, 227.499, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 25.8

The binding sites of Calcium atom in the Crystal Structure of Calcium Binding Domain CBD12 of CALX1.1 (pdb code 3rb5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Calcium Binding Domain CBD12 of CALX1.1, PDB code: 3rb5:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structure of Calcium Binding Domain CBD12 of CALX1.1


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 Calcium Binding Domain CBD12 of CALX1.1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1 b:51.5 occ:1.00 OE1 A:GLU523 2.6 42.3 1.0 OE2 A:GLU520 2.6 48.2 1.0 OD1 A:ASP490 2.7 47.8 1.0 OE2 A:GLU523 2.7 44.3 1.0 OD2 A:ASP490 2.9 55.0 1.0 CD A:GLU523 3.0 46.5 1.0 CG A:ASP490 3.1 53.3 1.0 CD A:GLU520 3.8 48.5 1.0 OG1 A:THR489 3.9 53.1 1.0 CB A:THR489 4.3 51.4 1.0 OG A:SER486 4.3 50.2 1.0 OE1 A:GLU520 4.5 48.0 1.0 CG A:GLU523 4.5 44.9 1.0 CB A:ASP490 4.6 53.4 1.0 CG A:GLU520 4.6 48.0 1.0 N A:SER486 4.7 58.4 1.0 O A:THR484 4.8 52.2 1.0 CA A:CA4 4.8 36.8 1.0 CB A:SER486 4.9 46.3 1.0 CB A:GLU520 5.0 48.3 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of Calcium Binding Domain CBD12 of CALX1.1


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 Calcium Binding Domain CBD12 of CALX1.1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2 b:41.3 occ:1.00 OD1 A:ASP551 2.6 39.3 1.0 OD2 A:ASP515 2.7 49.5 1.0 O A:ASP516 2.7 49.1 1.0 OD1 A:ASP552 2.8 46.8 1.0 OD2 A:ASP552 2.9 44.6 1.0 OE2 A:GLU455 2.9 51.3 1.0 CG A:ASP552 3.1 47.6 1.0 CD A:GLU455 3.6 51.0 1.0 CG A:ASP551 3.6 42.8 1.0 CG A:ASP515 3.7 51.5 1.0 CA A:CA3 3.8 39.8 1.0 C A:ASP516 3.9 48.6 1.0 N A:ASP551 3.9 44.0 1.0 N A:ASP516 4.0 45.5 1.0 CG A:GLU455 4.0 46.3 1.0 CB A:GLU455 4.2 44.0 1.0 OD2 A:ASP551 4.2 37.6 1.0 OD1 A:ASP515 4.2 49.5 1.0 C A:ASP551 4.3 45.0 1.0 N A:ASP552 4.5 46.8 1.0 OE1 A:GLU455 4.5 49.2 1.0 CB A:ASP552 4.5 49.5 1.0 CA A:ASP551 4.5 44.5 1.0 O A:ASP551 4.5 48.9 1.0 CA A:ASP516 4.6 47.1 1.0 OD2 A:ASP550 4.7 50.0 1.0 CB A:ASP551 4.7 42.3 1.0 CA A:ASP515 4.9 47.3 1.0 CA A:ASP552 4.9 46.4 1.0 CB A:ASP515 4.9 47.1 1.0 N A:ASP517 4.9 48.7 1.0 C A:ASP515 4.9 45.1 1.0 C A:ASP550 4.9 45.1 1.0 CG A:ASP550 4.9 46.0 1.0 NH2 A:ARG584 5.0 35.5 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of Calcium Binding Domain CBD12 of CALX1.1


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 Calcium Binding Domain CBD12 of CALX1.1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3 b:39.8 occ:1.00 OD2 A:ASP552 2.4 44.6 1.0 OE1 A:GLU520 2.6 48.0 1.0 O A:VAL518 2.6 41.3 1.0 OD2 A:ASP516 2.7 46.9 1.0 OE2 A:GLU455 2.7 51.3 1.0 OD1 A:ASP550 2.9 48.3 1.0 OE1 A:GLU455 3.0 49.2 1.0 CD A:GLU455 3.2 51.0 1.0 OD2 A:ASP550 3.2 50.0 1.0 CG A:ASP516 3.2 45.9 1.0 OD1 A:ASP516 3.3 49.2 1.0 CG A:ASP550 3.3 46.0 1.0 CD A:GLU520 3.5 48.5 1.0 CG A:GLU520 3.6 48.0 1.0 CG A:ASP552 3.7 47.6 1.0 O A:ASP516 3.8 49.1 1.0 C A:VAL518 3.8 46.9 1.0 CA A:CA2 3.8 41.3 1.0 N A:VAL518 4.1 49.4 1.0 C A:ASP516 4.2 48.6 1.0 CA A:VAL518 4.5 50.0 1.0 CB A:ASP516 4.5 40.9 1.0 CB A:ASP552 4.5 49.5 1.0 OD1 A:ASP552 4.5 46.8 1.0 CA A:CA4 4.6 36.8 1.0 N A:ASP516 4.6 45.5 1.0 N A:GLU520 4.6 48.0 1.0 CG A:GLU455 4.6 46.3 1.0 OE2 A:GLU520 4.6 48.2 1.0 CA A:ASP516 4.6 47.1 1.0 CB A:ASP550 4.7 42.7 1.0 N A:ASP517 4.8 48.7 1.0 N A:PHE519 4.8 46.6 1.0 CB A:GLU520 4.8 48.3 1.0 CB A:VAL518 4.9 45.1 1.0 C A:ASP517 4.9 50.8 1.0 CA A:PHE519 4.9 46.0 1.0 C A:PHE519 5.0 49.8 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of Calcium Binding Domain CBD12 of CALX1.1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Calcium Binding Domain CBD12 of CALX1.1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4 b:36.8 occ:1.00 OE1 A:GLU520 2.5 48.0 1.0 OE1 A:GLU455 2.7 49.2 1.0 OD2 A:ASP490 2.8 55.0 1.0 O A:HOH18 2.9 39.5 1.0 OE2 A:GLU520 2.9 48.2 1.0 CD A:GLU520 3.0 48.5 1.0 CG2 A:ILE548 3.2 43.7 1.0 OE1 A:GLU523 3.3 42.3 1.0 CG A:ASP490 3.3 53.3 1.0 CD A:GLU455 3.5 51.0 1.0 OD1 A:ASP550 3.8 48.3 1.0 CB A:ASP490 3.9 53.4 1.0 CB A:ILE548 4.0 47.0 1.0 OE2 A:GLU455 4.0 51.3 1.0 OD1 A:ASP490 4.1 47.8 1.0 CD1 A:ILE548 4.2 44.7 1.0 CG A:GLU455 4.3 46.3 1.0 CG A:GLU520 4.3 48.0 1.0 CD A:GLU523 4.4 46.5 1.0 CA A:ASP490 4.5 51.1 1.0 CA A:CA3 4.6 39.8 1.0 CB A:GLU523 4.6 46.5 1.0 CG1 A:ILE548 4.7 43.7 1.0 O A:ILE548 4.8 41.9 1.0 CB A:GLU520 4.8 48.3 1.0 CA A:CA1 4.8 51.5 1.0 CG A:GLU523 4.8 44.9 1.0 CG A:ASP550 5.0 46.0 1.0 OD1 A:ASP516 5.0 49.2 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of Calcium Binding Domain CBD12 of CALX1.1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Calcium Binding Domain CBD12 of CALX1.1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1 b:43.8 occ:1.00 OD2 B:ASP490 2.6 41.6 1.0 OE2 B:GLU523 2.7 31.4 1.0 OD1 B:ASP490 2.9 40.0 1.0 CG B:ASP490 3.1 44.9 1.0 OE2 B:GLU520 3.1 38.2 1.0 CD B:GLU520 3.4 38.4 1.0 CD B:GLU523 3.5 41.2 1.0 OE1 B:GLU523 3.5 41.1 1.0 CG B:GLU520 3.9 35.7 1.0 OE1 B:GLU520 3.9 40.3 1.0 CA B:CA4 4.3 28.8 1.0 CB B:GLU520 4.6 39.0 1.0 CB B:ASP490 4.6 38.4 1.0 CG B:GLU523 4.9 39.8 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of Calcium Binding Domain CBD12 of CALX1.1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Calcium Binding Domain CBD12 of CALX1.1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2 b:27.5 occ:1.00 OD2 B:ASP515 2.4 37.5 1.0 O B:ASP516 2.5 45.1 1.0 OD1 B:ASP552 2.6 38.4 1.0 OD2 B:ASP552 2.8 40.9 1.0 OE2 B:GLU455 2.9 32.6 1.0 OD1 B:ASP551 3.0 33.6 1.0 CG B:ASP552 3.0 39.6 1.0 CG B:ASP515 3.2 41.5 1.0 OD2 B:ASP551 3.2 36.6 1.0 OD1 B:ASP515 3.3 39.5 1.0 CG B:ASP551 3.4 37.2 1.0 NH2 B:ARG584 3.6 41.2 1.0 C B:ASP516 3.7 46.9 1.0 CD B:GLU455 4.0 37.2 1.0 N B:ASP516 4.1 41.7 1.0 CG B:GLU455 4.4 36.2 1.0 CB B:ASP552 4.5 38.2 1.0 CA B:ASP517 4.6 45.2 1.0 CB B:ASP515 4.6 34.6 1.0 CA B:ASP516 4.6 42.6 1.0 N B:ASP517 4.6 48.9 1.0 CZ B:ARG584 4.7 38.8 1.0 OD2 B:ASP517 4.7 53.6 1.0 CA B:CA3 4.8 44.5 1.0 OD2 B:ASP516 4.8 37.8 1.0 NE B:ARG584 4.8 41.1 1.0 CB B:GLU455 4.8 35.6 1.0 CB B:ASP551 4.9 40.7 1.0 OD1 B:ASP550 5.0 41.3 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of Calcium Binding Domain CBD12 of CALX1.1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Calcium Binding Domain CBD12 of CALX1.1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca3 b:44.5 occ:1.00 OD1 B:ASP550 2.5 41.3 1.0 O B:VAL518 2.6 39.3 1.0 OD2 B:ASP516 2.6 37.8 1.0 OE1 B:GLU455 2.6 40.6 1.0 OE2 B:GLU455 2.6 32.6 1.0 OD2 B:ASP552 2.8 40.9 1.0 OE1 B:GLU520 2.9 40.3 1.0 CD B:GLU455 3.0 37.2 1.0 CG B:ASP550 3.2 39.4 1.0 C B:VAL518 3.3 41.0 1.0 OD2 B:ASP550 3.4 36.1 1.0 CD B:GLU520 3.4 38.4 1.0 CG B:ASP552 3.6 39.6 1.0 CG B:ASP516 3.7 43.3 1.0 CB B:ASP552 3.9 38.2 1.0 N B:VAL518 3.9 41.2 1.0 CG B:GLU520 3.9 35.7 1.0 N B:PHE519 3.9 45.6 1.0 CA B:PHE519 4.1 43.7 1.0 N B:GLU520 4.1 44.1 1.0 OE2 B:GLU520 4.1 38.2 1.0 CA B:VAL518 4.1 44.2 1.0 OD1 B:ASP516 4.1 47.8 1.0 C B:PHE519 4.2 44.3 1.0 O B:ASP516 4.3 45.1 1.0 CB B:ASP550 4.4 38.5 1.0 CB B:GLU520 4.4 39.0 1.0 CG B:GLU455 4.5 36.2 1.0 OD1 B:ASP552 4.5 38.4 1.0 OD1 B:ASP551 4.7 33.6 1.0 C B:ASP516 4.7 46.9 1.0 CA B:CA2 4.8 27.5 1.0 CA B:CA4 4.8 28.8 1.0 N B:ASP552 4.8 36.7 1.0 O B:PHE519 4.9 45.9 1.0 C B:ASP517 4.9 39.4 1.0 CA B:GLU520 4.9 41.6 1.0 CB B:VAL518 4.9 43.6 1.0 CB B:ASP516 4.9 41.4 1.0 CA B:ASP552 5.0 39.9 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of Calcium Binding Domain CBD12 of CALX1.1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Calcium Binding Domain CBD12 of CALX1.1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4 b:28.8 occ:1.00 OD2 B:ASP490 2.6 41.6 1.0 OE2 B:GLU520 2.9 38.2 1.0 OE1 B:GLU455 2.9 40.6 1.0 OE1 B:GLU520 3.2 40.3 1.0 OD1 B:ASP516 3.3 47.8 1.0 CD B:GLU520 3.4 38.4 1.0 CG B:ASP490 3.6 44.9 1.0 O B:ILE514 3.6 44.4 1.0 CA B:ASP490 3.6 43.4 1.0 CD B:GLU455 3.7 37.2 1.0 O B:THR489 3.8 47.6 1.0 CB B:ASP490 3.9 38.4 1.0 OE1 B:GLU523 4.1 41.1 1.0 CG B:GLU455 4.1 36.2 1.0 CG B:ASP516 4.2 43.3 1.0 CA B:CA1 4.3 43.8 1.0 O B:ASP490 4.3 36.1 1.0 OD2 B:ASP516 4.5 37.8 1.0 C B:ASP490 4.5 40.3 1.0 N B:ASP490 4.6 39.9 1.0 C B:THR489 4.6 43.2 1.0 OD1 B:ASP490 4.6 40.0 1.0 OE2 B:GLU455 4.6 32.6 1.0 O B:HOH15 4.8 38.0 1.0 CA B:CA3 4.8 44.5 1.0 C B:ILE514 4.8 39.2 1.0 CG B:GLU520 4.9 35.7 1.0

M.Wu, S.Tong, J.Gonzalez, V.Jayaraman, J.L.Spudich, L.Zheng. Structural Basis of the Ca(2+) Inhibitory Mechanism of Drosophila Na(+)/Ca(2+) Exchanger Calx and Its Modification By Alternative Splicing. Structure V. 19 1509 2011.
ISSN: ISSN 0969-2126
PubMed: 22000518
DOI: 10.1016/J.STR.2011.07.008