Calcium in PDB 4ik9: High Resolution Structure of GCAMP3 Dimer Form 2 at pH 7.5

The structure of High Resolution Structure of GCAMP3 Dimer Form 2 at pH 7.5, PDB code: 4ik9 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)	26.00 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	125.617, 46.749, 68.753, 90.00, 100.06, 90.00
R / Rfree (%)	15.9 / 19.5

The binding sites of Calcium atom in the High Resolution Structure of GCAMP3 Dimer Form 2 at pH 7.5 (pdb code 4ik9). 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 2 at pH 7.5, PDB code: 4ik9:
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 2 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 2 at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:13.7 occ:1.00 OD1 A:ASP322 2.2 14.7 1.0 O A:THR328 2.3 13.5 1.0 OD1 A:ASP326 2.3 15.9 1.0 OD1 A:ASP324 2.4 19.9 1.0 OE1 A:GLU333 2.4 13.6 1.0 OE2 A:GLU333 2.6 16.1 1.0 O A:HOH747 2.6 21.9 1.0 CD A:GLU333 2.8 15.7 1.0 CG A:ASP326 3.4 19.6 1.0 CG A:ASP324 3.4 19.8 1.0 CG A:ASP322 3.4 15.7 1.0 C A:THR328 3.5 12.9 1.0 OD2 A:ASP324 3.8 26.1 1.0 CA A:ASP322 4.1 14.4 1.0 OD2 A:ASP326 4.1 21.4 1.0 N A:THR328 4.1 13.8 1.0 CB A:ASP322 4.2 15.9 1.0 N A:ASP326 4.2 15.2 1.0 CB A:ASP326 4.4 16.6 1.0 OD2 A:ASP322 4.4 15.2 1.0 CG A:GLU333 4.4 15.2 1.0 CA A:THR328 4.4 15.0 1.0 N A:ASP324 4.4 18.5 1.0 C A:ASP322 4.4 15.6 1.0 N A:ILE329 4.4 12.7 1.0 CA A:ILE329 4.5 12.5 1.0 O A:HOH706 4.6 24.0 1.0 CG2 A:THR328 4.6 15.9 1.0 CA A:ASP326 4.6 16.9 1.0 CB A:ASP324 4.7 19.4 1.0 N A:LYS323 4.7 17.6 1.0 O A:HOH699 4.7 20.6 1.0 N A:GLY327 4.7 14.7 1.0 N A:GLY325 4.7 16.8 1.0 N A:THR330 4.8 13.9 1.0 C A:ASP326 4.8 16.5 1.0 CA A:ASP324 4.8 17.8 1.0 CG2 A:THR330 4.9 17.8 1.0 O A:HOH784 4.9 33.1 1.0 O A:ASP322 5.0 15.1 1.0

Calcium binding site 2 out of 4 in the High Resolution Structure of GCAMP3 Dimer Form 2 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 2 at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:18.8 occ:1.00 OD1 A:ASP358 2.2 28.6 1.0 OD1 A:ASP360 2.3 22.4 1.0 OE2 A:GLU369 2.3 23.5 1.0 OE1 A:GLU369 2.4 17.2 1.0 O A:THR364 2.4 14.1 1.0 OD1 A:ASP362 2.4 25.2 1.0 O A:HOH659 2.5 29.2 1.0 CD A:GLU369 2.7 22.0 1.0 CG A:ASP360 3.3 31.9 1.0 CG A:ASP362 3.4 30.6 1.0 CG A:ASP358 3.4 22.9 1.0 C A:THR364 3.6 18.2 1.0 OD2 A:ASP360 3.8 31.7 1.0 OD2 A:ASP362 4.0 33.7 1.0 OD2 A:ASP358 4.1 22.4 1.0 N A:THR364 4.2 17.3 1.0 CG A:GLU369 4.2 18.2 1.0 N A:ASP360 4.2 29.4 1.0 OG1 A:THR364 4.2 24.4 1.0 CA A:ASP358 4.3 23.3 1.0 N A:ASP362 4.3 23.8 1.0 CB A:ASP358 4.3 22.7 1.0 CA A:ILE365 4.4 14.2 1.0 CB A:ASP362 4.4 28.0 1.0 N A:ILE365 4.5 16.8 1.0 CA A:THR364 4.5 16.8 1.0 CB A:ASP360 4.5 28.8 1.0 N A:ASP366 4.5 14.7 1.0 C A:ASP358 4.5 30.3 1.0 N A:ALA359 4.6 25.8 1.0 CA A:ASP360 4.7 26.9 1.0 N A:GLY363 4.7 23.5 1.0 N A:GLY361 4.7 30.4 1.0 CA A:ASP362 4.8 25.2 1.0 OD2 A:ASP366 4.8 29.1 1.0 C A:ASP360 4.9 28.2 1.0 O A:HOH757 4.9 25.5 1.0 C A:ILE365 5.0 15.4 1.0 CG A:ASP366 5.0 25.5 1.0 C A:ASP362 5.0 23.6 1.0 CD1 A:ILE365 5.0 26.4 1.0 O A:HOH780 5.0 29.2 1.0 O A:HOH843 5.0 44.3 1.0

Calcium binding site 3 out of 4 in the High Resolution Structure of GCAMP3 Dimer Form 2 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 2 at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:12.4 occ:1.00 OD1 A:ASP395 2.2 13.4 1.0 O A:TYR401 2.2 15.6 1.0 OD1 A:ASP397 2.3 19.5 1.0 OE1 A:GLU406 2.4 11.8 1.0 OD1 A:ASN399 2.5 14.4 1.0 OE2 A:GLU406 2.5 17.9 1.0 O A:HOH697 2.6 25.1 1.0 CD A:GLU406 2.8 14.0 1.0 CG A:ASP397 3.3 16.5 1.0 CG A:ASP395 3.4 13.6 1.0 CG A:ASN399 3.4 20.4 1.0 C A:TYR401 3.5 12.1 1.0 OD2 A:ASP397 3.7 20.7 1.0 ND2 A:ASN399 4.0 20.1 1.0 N A:ASN399 4.2 15.5 1.0 N A:TYR401 4.2 12.1 1.0 OD2 A:ASP395 4.2 14.6 1.0 CA A:ASP395 4.2 13.1 1.0 N A:ASP397 4.3 17.6 1.0 CB A:ASP395 4.3 13.1 1.0 CG A:GLU406 4.3 12.6 1.0 CA A:TYR401 4.4 12.1 1.0 O A:HOH1009 4.4 29.8 1.0 N A:ILE402 4.4 11.4 1.0 C A:ASP395 4.4 14.3 1.0 CB A:ASN399 4.5 18.1 1.0 CA A:ILE402 4.5 10.7 1.0 CB A:ASP397 4.5 16.2 1.0 N A:GLY398 4.6 17.6 1.0 N A:SER403 4.7 12.2 1.0 N A:LYS396 4.7 15.9 1.0 CA A:ASN399 4.7 15.4 1.0 CA A:ASP397 4.7 17.2 1.0 CB A:TYR401 4.8 13.3 1.0 N A:GLY400 4.8 13.3 1.0 C A:ASP397 4.8 18.9 1.0 O A:ASP395 4.9 17.1 1.0 O A:HOH693 4.9 32.1 1.0 OE1 A:GLN437 4.9 25.8 1.0

Calcium binding site 4 out of 4 in the High Resolution Structure of GCAMP3 Dimer Form 2 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 2 at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:13.2 occ:1.00 OD1 A:ASP431 2.2 13.2 1.0 OD1 A:ASP435 2.3 12.7 1.0 O A:GLN437 2.3 14.8 1.0 OD1 A:ASP433 2.4 14.9 1.0 OE1 A:GLU442 2.5 14.1 1.0 O A:HOH637 2.5 15.5 1.0 OE2 A:GLU442 2.7 14.4 1.0 CD A:GLU442 2.9 16.6 1.0 CG A:ASP435 3.2 14.9 1.0 CG A:ASP433 3.3 20.4 1.0 CG A:ASP431 3.4 14.9 1.0 C A:GLN437 3.5 12.3 1.0 OD2 A:ASP435 3.7 17.4 1.0 OD2 A:ASP433 3.8 23.1 1.0 CA A:ASP431 4.2 13.4 1.0 N A:ASP435 4.2 12.3 1.0 CB A:ASP431 4.2 13.0 1.0 OD2 A:ASP431 4.2 13.3 1.0 N A:GLN437 4.2 11.6 1.0 N A:ASP433 4.3 15.8 1.0 CA A:VAL438 4.4 10.8 1.0 N A:VAL438 4.4 11.6 1.0 N A:ASN439 4.4 13.1 1.0 CB A:ASP435 4.4 13.5 1.0 CA A:GLN437 4.5 12.2 1.0 CG A:GLU442 4.5 17.1 1.0 N A:GLY434 4.5 13.1 1.0 C A:ASP431 4.5 18.6 1.0 CB A:ASP433 4.5 18.3 1.0 N A:ILE432 4.6 16.8 1.0 CA A:ASP433 4.7 16.0 1.0 CA A:ASP435 4.7 12.9 1.0 C A:ASP433 4.7 14.4 1.0 N A:GLY436 4.8 12.0 1.0 C A:VAL438 4.9 11.6 1.0 ND2 A:ASN439 4.9 22.5 1.0 CG A:ASN439 4.9 19.1 1.0 C A:ASP435 5.0 14.8 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