Calcium in PDB 4ik8: High Resolution Structure of GCAMP3 Dimer Form 1 at pH 7.5

The structure of High Resolution Structure of GCAMP3 Dimer Form 1 at pH 7.5, PDB code: 4ik8 was solved by Y.Chen, X.Song, L.Miao, Y.Zhu, G.Ji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.60 / 1.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	126.340, 47.352, 66.740, 90.00, 100.27, 90.00
R / Rfree (%)	17.9 / 20.9

The binding sites of Calcium atom in the High Resolution Structure of GCAMP3 Dimer Form 1 at pH 7.5 (pdb code 4ik8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the High Resolution Structure of GCAMP3 Dimer Form 1 at pH 7.5, PDB code: 4ik8:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the High Resolution Structure of GCAMP3 Dimer Form 1 at pH 7.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of High Resolution Structure of GCAMP3 Dimer Form 1 at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:22.7 occ:1.00 OD1 A:ASP322 2.3 24.2 1.0 OD1 A:ASP324 2.3 26.1 1.0 O A:THR328 2.3 21.4 1.0 OD1 A:ASP326 2.4 25.3 1.0 O A:HOH638 2.4 28.8 1.0 OE1 A:GLU333 2.5 25.0 1.0 OE2 A:GLU333 2.5 23.4 1.0 CD A:GLU333 2.9 25.1 1.0 CG A:ASP324 3.3 29.2 1.0 CG A:ASP326 3.3 31.4 1.0 CG A:ASP322 3.4 21.5 1.0 C A:THR328 3.5 20.0 1.0 OD2 A:ASP324 3.7 28.4 1.0 OG1 A:THR328 3.8 25.6 1.0 OD2 A:ASP326 3.9 34.3 1.0 CA A:ASP322 4.0 21.5 1.0 CB A:ASP322 4.1 21.2 1.0 N A:THR328 4.1 19.9 1.0 N A:ASP326 4.2 23.4 1.0 CA A:THR328 4.3 21.2 1.0 CG A:GLU333 4.3 24.2 1.0 OD2 A:ASP322 4.4 23.4 1.0 CB A:ASP326 4.4 29.8 1.0 C A:ASP322 4.4 24.0 1.0 N A:ILE329 4.5 19.3 1.0 N A:ASP324 4.6 29.0 1.0 O A:HOH935 4.6 37.6 1.0 CA A:ILE329 4.6 19.9 1.0 CB A:THR328 4.7 22.6 1.0 CB A:ASP324 4.7 28.0 1.0 CA A:ASP326 4.7 29.1 1.0 N A:LYS323 4.7 24.2 1.0 N A:GLY325 4.7 24.6 1.0 N A:GLY327 4.9 24.7 1.0 O A:ASP322 4.9 25.3 1.0 O A:HOH671 4.9 28.4 1.0 CA A:ASP324 5.0 26.7 1.0 N A:THR330 5.0 21.6 1.0 C A:ASP326 5.0 26.4 1.0

Calcium binding site 2 out of 4 in the High Resolution Structure of GCAMP3 Dimer Form 1 at pH 7.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of High Resolution Structure of GCAMP3 Dimer Form 1 at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:18.5 occ:1.00 OD1 A:ASP358 2.2 22.2 1.0 O A:THR364 2.3 17.9 1.0 OD1 A:ASP362 2.3 22.5 1.0 OD1 A:ASP360 2.4 22.9 1.0 OE2 A:GLU369 2.5 18.4 1.0 O A:HOH618 2.5 30.3 1.0 OE1 A:GLU369 2.5 22.0 1.0 CD A:GLU369 2.8 23.1 1.0 CG A:ASP362 3.3 23.9 1.0 CG A:ASP360 3.4 23.0 1.0 CG A:ASP358 3.4 21.7 1.0 C A:THR364 3.5 15.1 1.0 OD2 A:ASP360 3.7 25.9 1.0 OD2 A:ASP362 3.9 25.3 1.0 N A:THR364 4.1 19.4 1.0 OG1 A:THR364 4.1 22.6 1.0 OD2 A:ASP358 4.2 22.7 1.0 N A:ASP362 4.2 20.6 1.0 CA A:ASP358 4.2 18.2 1.0 N A:ASP366 4.3 16.3 1.0 CB A:ASP358 4.3 18.7 1.0 N A:ASP360 4.3 20.3 1.0 CA A:THR364 4.3 17.1 1.0 CB A:ASP362 4.4 27.4 1.0 CG A:GLU369 4.4 17.8 1.0 N A:ILE365 4.4 17.4 1.0 CA A:ILE365 4.4 14.4 1.0 C A:ASP358 4.5 21.6 1.0 N A:ALA359 4.5 18.4 1.0 N A:GLY361 4.6 22.7 1.0 O A:HOH684 4.6 27.9 1.0 CB A:ASP360 4.6 25.0 1.0 CA A:ASP362 4.7 21.2 1.0 N A:GLY363 4.7 20.4 1.0 C A:ILE365 4.8 18.1 1.0 CG A:ASP366 4.8 26.4 1.0 OD2 A:ASP366 4.8 27.7 1.0 CA A:ASP360 4.9 21.7 1.0 CB A:THR364 4.9 21.1 1.0 C A:ASP362 4.9 24.1 1.0 C A:ASP360 5.0 27.2 1.0

Calcium binding site 3 out of 4 in the High Resolution Structure of GCAMP3 Dimer Form 1 at pH 7.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of High Resolution Structure of GCAMP3 Dimer Form 1 at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:25.1 occ:1.00 OD1 A:ASP395 2.2 28.2 1.0 O A:TYR401 2.3 32.3 1.0 OD1 A:ASN399 2.4 30.4 1.0 OD1 A:ASP397 2.4 30.4 1.0 OE1 A:GLU406 2.4 25.6 1.0 OE2 A:GLU406 2.6 27.6 1.0 O A:HOH622 2.6 28.1 1.0 CD A:GLU406 2.8 25.7 1.0 CG A:ASN399 3.3 35.9 1.0 CG A:ASP395 3.4 27.0 1.0 CG A:ASP397 3.4 37.3 1.0 C A:TYR401 3.4 27.1 1.0 ND2 A:ASN399 3.9 41.2 1.0 OD2 A:ASP397 3.9 44.0 1.0 N A:ASN399 4.0 33.4 1.0 N A:TYR401 4.2 30.6 1.0 OD2 A:ASP395 4.2 31.7 1.0 O A:HOH979 4.2 49.3 1.0 N A:ASP397 4.2 31.0 1.0 CA A:ASP395 4.3 26.3 1.0 CB A:ASN399 4.3 35.8 1.0 CA A:TYR401 4.3 30.0 1.0 C A:ASP395 4.3 26.6 1.0 CB A:ASP395 4.4 25.6 1.0 CG A:GLU406 4.4 24.8 1.0 N A:ILE402 4.4 25.9 1.0 N A:GLY398 4.4 33.1 1.0 CA A:ILE402 4.5 24.7 1.0 N A:LYS396 4.5 29.1 1.0 O A:HOH668 4.5 30.3 1.0 N A:SER403 4.5 25.1 1.0 CB A:ASP397 4.5 32.4 1.0 CA A:ASN399 4.6 33.1 1.0 CA A:ASP397 4.7 32.0 1.0 CB A:TYR401 4.7 38.5 1.0 N A:GLY400 4.8 33.1 1.0 C A:ASP397 4.8 40.0 1.0 O A:ASP395 4.8 29.6 1.0 C A:ASN399 4.9 37.6 1.0 C A:ILE402 5.0 25.9 1.0

Calcium binding site 4 out of 4 in the High Resolution Structure of GCAMP3 Dimer Form 1 at pH 7.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of High Resolution Structure of GCAMP3 Dimer Form 1 at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:26.3 occ:1.00 OD1 A:ASP431 2.2 28.9 1.0 OD1 A:ASP433 2.2 32.0 1.0 O A:GLN437 2.3 27.4 1.0 OE1 A:GLU442 2.4 28.9 1.0 O A:HOH675 2.4 27.9 1.0 OD1 A:ASP435 2.5 30.1 1.0 OE2 A:GLU442 2.5 33.1 1.0 CD A:GLU442 2.8 29.4 1.0 CG A:ASP431 3.3 29.1 1.0 CG A:ASP433 3.4 38.2 1.0 CG A:ASP435 3.4 31.2 1.0 C A:GLN437 3.5 29.5 1.0 OD2 A:ASP435 3.8 32.5 1.0 OD2 A:ASP433 3.9 43.0 1.0 N A:ASP433 4.1 32.3 1.0 OD2 A:ASP431 4.2 31.8 1.0 CA A:ASP431 4.2 27.3 1.0 N A:GLN437 4.2 30.9 1.0 CB A:ASP431 4.2 27.0 1.0 N A:ILE432 4.3 29.7 1.0 N A:ASP435 4.3 31.2 1.0 CG A:GLU442 4.3 32.0 1.0 N A:VAL438 4.4 26.0 1.0 CA A:VAL438 4.4 27.1 1.0 N A:ASN439 4.4 27.9 1.0 CA A:GLN437 4.4 27.6 1.0 N A:GLY434 4.5 36.5 1.0 CB A:ASP433 4.5 35.1 1.0 CB A:ASP435 4.6 35.6 1.0 CA A:ASP433 4.7 34.0 1.0 C A:ASP431 4.7 30.5 1.0 ND2 A:ASN439 4.8 37.8 1.0 C A:ASP433 4.8 33.2 1.0 O A:HOH937 4.8 33.8 1.0 N A:GLY436 4.8 28.7 1.0 CA A:ASP435 4.9 35.9 1.0 C A:VAL438 4.9 27.1 1.0 CG A:ASN439 4.9 41.6 1.0

Y.Chen, X.Song, S.Ye, L.Miao, Y.Zhu, R.G.Zhang, G.Ji. Structural Insight Into Enhanced Calcium Indicator GCAMP3 and Gcampj to Promote Further Improvement. Protein Cell V. 4 299 2013.
ISSN: ISSN 1674-800X
PubMed: 23549615
DOI: 10.1007/S13238-013-2103-4