Calcium in PDB 4ik3: High Resolution Structure of GCAMP3 at pH 8.5

The structure of High Resolution Structure of GCAMP3 at pH 8.5, PDB code: 4ik3 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)	31.01 / 2.01
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	125.993, 46.614, 68.585, 90.00, 100.09, 90.00
R / Rfree (%)	18.5 / 21.4

The binding sites of Calcium atom in the High Resolution Structure of GCAMP3 at pH 8.5 (pdb code 4ik3). 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 at pH 8.5, PDB code: 4ik3:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the High Resolution Structure of GCAMP3 at pH 8.5


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 at pH 8.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:28.0 occ:1.00 O A:THR328 2.3 24.7 1.0 OD1 A:ASP322 2.3 27.4 1.0 OE1 A:GLU333 2.4 20.3 1.0 OD1 A:ASP326 2.4 25.4 1.0 OD1 A:ASP324 2.5 29.6 1.0 OE2 A:GLU333 2.5 25.0 1.0 O A:HOH614 2.6 35.4 1.0 CD A:GLU333 2.8 21.6 1.0 CG A:ASP326 3.4 27.4 1.0 CG A:ASP324 3.4 28.6 1.0 CG A:ASP322 3.5 24.7 1.0 C A:THR328 3.5 23.9 1.0 OD2 A:ASP324 3.8 31.1 1.0 OD2 A:ASP326 4.0 30.5 1.0 CA A:ASP322 4.1 27.7 1.0 N A:THR328 4.2 29.7 1.0 CB A:ASP322 4.2 25.1 1.0 N A:ASP326 4.2 24.6 1.0 CG A:GLU333 4.3 28.7 1.0 OD2 A:ASP322 4.4 23.9 1.0 CA A:THR328 4.4 23.6 1.0 CB A:ASP326 4.4 27.8 1.0 C A:ASP322 4.4 25.7 1.0 N A:ILE329 4.4 22.9 1.0 CA A:ILE329 4.5 23.5 1.0 N A:ASP324 4.5 24.1 1.0 CG2 A:THR328 4.6 25.7 1.0 O A:HOH777 4.6 30.6 1.0 O A:HOH694 4.7 28.7 1.0 CA A:ASP326 4.7 26.6 1.0 N A:LYS323 4.7 26.3 1.0 CB A:ASP324 4.7 28.3 1.0 N A:GLY325 4.8 25.0 1.0 N A:THR330 4.8 25.2 1.0 N A:GLY327 4.8 22.9 1.0 CG2 A:THR330 4.8 29.9 1.0 C A:ASP326 4.9 23.0 1.0 O A:ASP322 4.9 24.6 1.0 CA A:ASP324 5.0 26.6 1.0

Calcium binding site 2 out of 4 in the High Resolution Structure of GCAMP3 at pH 8.5


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 at pH 8.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:30.4 occ:1.00 OD1 A:ASP358 2.2 33.4 1.0 OD1 A:ASP360 2.3 41.0 1.0 OD1 A:ASP362 2.3 31.9 1.0 O A:THR364 2.4 29.6 1.0 OE2 A:GLU369 2.4 31.9 1.0 OE1 A:GLU369 2.4 34.5 1.0 O A:HOH603 2.5 29.2 1.0 CD A:GLU369 2.7 33.4 1.0 CG A:ASP360 3.3 44.9 1.0 CG A:ASP362 3.3 38.3 1.0 CG A:ASP358 3.4 38.9 1.0 C A:THR364 3.5 27.7 1.0 OD2 A:ASP360 3.8 44.7 1.0 OD2 A:ASP358 3.9 35.6 1.0 OD2 A:ASP362 4.0 38.7 1.0 N A:ASP360 4.1 45.1 1.0 N A:THR364 4.1 25.9 1.0 N A:ASP362 4.2 33.4 1.0 CG A:GLU369 4.2 33.9 1.0 OG1 A:THR364 4.3 26.0 1.0 CB A:ASP362 4.3 35.3 1.0 N A:ALA359 4.3 46.7 1.0 CA A:THR364 4.4 29.0 1.0 N A:ILE365 4.4 23.5 1.0 CB A:ASP358 4.5 38.7 1.0 CA A:ILE365 4.5 24.3 1.0 CB A:ASP360 4.5 44.2 1.0 CA A:ASP358 4.6 39.3 1.0 N A:ASP366 4.6 28.3 1.0 N A:GLY363 4.6 38.8 1.0 OD2 A:ASP366 4.7 28.3 1.0 CA A:ASP362 4.7 33.7 1.0 N A:GLY361 4.7 43.3 1.0 CA A:ASP360 4.7 43.8 1.0 C A:ASP360 4.8 41.2 1.0 C A:ASP358 4.8 47.4 1.0 O A:HOH619 4.8 33.6 1.0 C A:ASP362 4.9 37.4 1.0

Calcium binding site 3 out of 4 in the High Resolution Structure of GCAMP3 at pH 8.5


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 at pH 8.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:26.5 occ:1.00 O A:TYR401 2.3 29.0 1.0 OD1 A:ASP395 2.3 27.7 1.0 OD1 A:ASP397 2.4 35.7 1.0 OE2 A:GLU406 2.4 24.0 1.0 OD1 A:ASN399 2.4 29.4 1.0 OE1 A:GLU406 2.4 22.1 1.0 CD A:GLU406 2.7 23.6 1.0 CG A:ASP397 3.3 32.4 1.0 CG A:ASN399 3.3 31.2 1.0 CG A:ASP395 3.4 32.0 1.0 C A:TYR401 3.5 29.5 1.0 OD2 A:ASP397 3.7 36.0 1.0 ND2 A:ASN399 3.9 29.4 1.0 N A:TYR401 4.2 31.7 1.0 CA A:ASP395 4.2 30.1 1.0 N A:ASN399 4.2 26.7 1.0 OD2 A:ASP395 4.2 29.4 1.0 CG A:GLU406 4.3 23.6 1.0 CB A:ASP395 4.3 28.3 1.0 N A:ASP397 4.3 33.3 1.0 CA A:TYR401 4.3 27.3 1.0 N A:ILE402 4.4 27.4 1.0 C A:ASP395 4.4 32.5 1.0 CB A:ASN399 4.4 32.5 1.0 CA A:ILE402 4.5 25.7 1.0 CB A:ASP397 4.5 31.0 1.0 N A:GLY398 4.5 35.9 1.0 N A:SER403 4.6 27.9 1.0 N A:LYS396 4.6 31.8 1.0 CA A:ASN399 4.7 26.7 1.0 CA A:ASP397 4.7 33.0 1.0 CB A:TYR401 4.8 25.6 1.0 N A:GLY400 4.8 31.4 1.0 C A:ASP397 4.8 34.9 1.0 O A:HOH639 4.8 38.0 1.0 O A:ASP395 4.9 32.7 1.0 OE1 A:GLN437 5.0 38.9 1.0 C A:ILE402 5.0 29.3 1.0

Calcium binding site 4 out of 4 in the High Resolution Structure of GCAMP3 at pH 8.5


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 at pH 8.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:25.4 occ:1.00 OD1 A:ASP431 2.2 26.4 1.0 OD1 A:ASP433 2.3 20.6 1.0 O A:GLN437 2.4 24.1 1.0 OD1 A:ASP435 2.4 28.9 1.0 OE1 A:GLU442 2.4 29.3 1.0 OE2 A:GLU442 2.5 28.1 1.0 O A:HOH609 2.6 31.2 1.0 CD A:GLU442 2.8 28.9 1.0 CG A:ASP435 3.3 25.6 1.0 CG A:ASP433 3.4 27.7 1.0 CG A:ASP431 3.4 27.8 1.0 C A:GLN437 3.5 25.5 1.0 OD2 A:ASP435 3.8 25.5 1.0 OD2 A:ASP433 3.8 30.0 1.0 CA A:ASP431 4.1 27.8 1.0 N A:ASP435 4.1 23.2 1.0 OD2 A:ASP431 4.2 26.3 1.0 N A:ASP433 4.2 27.3 1.0 N A:GLN437 4.2 22.1 1.0 CB A:ASP431 4.2 26.0 1.0 CG A:GLU442 4.3 29.4 1.0 N A:ASN439 4.4 29.5 1.0 N A:GLY434 4.4 24.9 1.0 N A:VAL438 4.4 26.6 1.0 CA A:VAL438 4.4 27.1 1.0 C A:ASP431 4.4 29.4 1.0 CA A:GLN437 4.5 23.1 1.0 CB A:ASP435 4.5 25.6 1.0 N A:ILE432 4.5 30.2 1.0 CB A:ASP433 4.6 25.1 1.0 CA A:ASP433 4.7 28.4 1.0 C A:ASP433 4.7 28.2 1.0 CA A:ASP435 4.7 24.9 1.0 N A:GLY436 4.8 25.1 1.0 C A:VAL438 4.9 26.6 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