Calcium in PDB 4ik5: High Resolution Structure of Delta-Rest-GCAMP3

The structure of High Resolution Structure of Delta-Rest-GCAMP3, PDB code: 4ik5 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)	46.95 / 2.50
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	120.021, 120.021, 96.876, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 22.8

The binding sites of Calcium atom in the High Resolution Structure of Delta-Rest-GCAMP3 (pdb code 4ik5). 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 Delta-Rest-GCAMP3, PDB code: 4ik5:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the High Resolution Structure of Delta-Rest-GCAMP3


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 Delta-Rest-GCAMP3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:30.4 occ:1.00 OD1 A:ASP322 2.2 34.9 1.0 OD1 A:ASP326 2.4 30.6 1.0 OE2 A:GLU333 2.4 40.3 1.0 O A:THR328 2.4 27.4 1.0 OD1 A:ASP324 2.4 36.7 1.0 O A:HOH629 2.5 28.0 1.0 OE1 A:GLU333 2.6 39.7 1.0 CD A:GLU333 2.8 38.0 1.0 CG A:ASP324 3.3 35.4 1.0 CG A:ASP322 3.4 34.5 1.0 CG A:ASP326 3.4 30.9 1.0 C A:THR328 3.5 28.6 1.0 OD2 A:ASP324 3.6 34.0 1.0 OD2 A:ASP326 3.9 32.9 1.0 CB A:ASP322 4.0 33.1 1.0 CA A:ASP322 4.0 34.1 1.0 N A:THR328 4.2 27.0 1.0 N A:ASP326 4.2 29.1 1.0 O A:HOH870 4.3 34.0 1.0 CG A:GLU333 4.3 31.1 1.0 OD2 A:ASP322 4.3 36.3 1.0 CA A:THR328 4.4 29.6 1.0 C A:ASP322 4.4 34.4 1.0 OG1 A:THR328 4.4 35.2 1.0 CB A:ASP326 4.4 29.4 1.0 N A:ILE329 4.5 29.3 1.0 N A:ASP324 4.6 33.0 1.0 CA A:ILE329 4.6 29.9 1.0 CA A:ASP326 4.6 28.9 1.0 CB A:ASP324 4.7 31.5 1.0 N A:GLY325 4.7 29.1 1.0 O A:HOH716 4.7 34.8 1.0 N A:GLY327 4.8 29.2 1.0 N A:LYS323 4.8 34.7 1.0 O A:ASP322 4.9 34.5 1.0 O A:HOH697 4.9 39.2 1.0 C A:ASP326 4.9 29.3 1.0 CA A:ASP324 4.9 31.9 1.0 N A:THR330 5.0 29.9 1.0

Calcium binding site 2 out of 4 in the High Resolution Structure of Delta-Rest-GCAMP3


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 Delta-Rest-GCAMP3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:29.1 occ:1.00 OD1 A:ASP358 2.3 28.8 1.0 OD1 A:ASP362 2.3 31.6 1.0 O A:THR364 2.3 30.8 1.0 OD1 A:ASP360 2.4 37.6 1.0 O A:HOH609 2.4 34.5 1.0 OE2 A:GLU369 2.5 30.2 1.0 OE1 A:GLU369 2.6 29.3 1.0 CD A:GLU369 2.9 30.2 1.0 CG A:ASP362 3.1 30.1 1.0 CG A:ASP360 3.2 35.7 1.0 OD2 A:ASP360 3.4 36.9 1.0 CG A:ASP358 3.5 31.9 1.0 C A:THR364 3.5 28.8 1.0 OD2 A:ASP362 3.5 35.6 1.0 OG1 A:THR364 4.0 29.3 1.0 N A:THR364 4.0 26.7 1.0 N A:ASP362 4.1 31.0 1.0 OD2 A:ASP358 4.2 32.4 1.0 CB A:ASP362 4.3 30.4 1.0 N A:ASP360 4.3 32.5 1.0 CA A:THR364 4.3 27.9 1.0 N A:ASP366 4.3 29.7 1.0 CA A:ASP358 4.4 30.4 1.0 CB A:ASP358 4.4 31.2 1.0 CB A:ASP360 4.5 32.1 1.0 CG A:GLU369 4.5 27.7 1.0 N A:ILE365 4.5 28.2 1.0 N A:GLY361 4.5 32.5 1.0 CA A:ILE365 4.6 28.4 1.0 C A:ASP358 4.6 31.4 1.0 CA A:ASP362 4.6 30.3 1.0 N A:GLY363 4.7 29.2 1.0 N A:ALA359 4.7 30.3 1.0 CG A:ASP366 4.7 34.9 1.0 CA A:ASP360 4.7 32.5 1.0 OD2 A:ASP366 4.8 37.1 1.0 CB A:THR364 4.8 28.4 1.0 C A:ILE365 4.9 29.7 1.0 C A:ASP362 4.9 30.6 1.0 CB A:ASP366 4.9 30.1 1.0 C A:ASP360 4.9 32.7 1.0 O A:HOH701 4.9 46.0 1.0

Calcium binding site 3 out of 4 in the High Resolution Structure of Delta-Rest-GCAMP3


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 Delta-Rest-GCAMP3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:50.0 occ:1.00 O A:TYR401 2.3 45.6 1.0 OD1 A:ASN399 2.4 48.6 1.0 OE1 A:GLU406 2.4 45.8 1.0 OD1 A:ASP395 2.4 51.0 1.0 OE2 A:GLU406 2.5 47.8 1.0 OD1 A:ASP397 2.6 53.7 1.0 O A:HOH727 2.6 41.6 1.0 CD A:GLU406 2.8 49.1 1.0 CG A:ASN399 3.3 51.2 1.0 CG A:ASP397 3.3 57.7 1.0 C A:TYR401 3.4 45.1 1.0 OD2 A:ASP397 3.5 60.1 1.0 CG A:ASP395 3.6 50.4 1.0 ND2 A:ASN399 3.9 50.6 1.0 N A:TYR401 4.1 43.9 1.0 CA A:TYR401 4.2 44.5 1.0 CA A:ASP395 4.2 49.6 1.0 N A:ASN399 4.3 51.0 1.0 CG A:GLU406 4.3 50.5 1.0 O A:HOH827 4.3 46.6 1.0 N A:ASP397 4.4 55.5 1.0 CB A:ASN399 4.4 50.0 1.0 C A:ASP395 4.4 50.3 1.0 N A:ILE402 4.4 46.0 1.0 OD2 A:ASP395 4.4 51.1 1.0 CB A:ASP395 4.5 49.4 1.0 N A:GLY398 4.6 53.5 1.0 CA A:ILE402 4.6 47.0 1.0 O A:HOH788 4.6 48.0 1.0 CB A:ASP397 4.6 55.4 1.0 N A:LYS396 4.7 51.8 1.0 CB A:TYR401 4.7 43.7 1.0 N A:SER403 4.7 49.6 1.0 O A:ASP395 4.8 49.6 1.0 CA A:ASN399 4.8 50.1 1.0 CA A:ASP397 4.8 55.2 1.0 C A:ASP397 4.9 54.7 1.0 N A:GLY400 5.0 47.6 1.0

Calcium binding site 4 out of 4 in the High Resolution Structure of Delta-Rest-GCAMP3


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 Delta-Rest-GCAMP3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:50.4 occ:1.00 OD1 A:ASP435 2.3 46.5 1.0 OD1 A:ASP431 2.3 57.6 1.0 O A:HOH616 2.3 38.6 1.0 O A:GLN437 2.4 52.0 1.0 OD1 A:ASP433 2.4 59.5 1.0 OE2 A:GLU442 2.6 47.5 1.0 OE1 A:GLU442 2.6 54.3 1.0 CD A:GLU442 2.9 51.9 1.0 CG A:ASP435 3.0 50.6 1.0 CG A:ASP431 3.3 61.3 1.0 CG A:ASP433 3.3 59.9 1.0 C A:GLN437 3.5 50.1 1.0 OD2 A:ASP435 3.5 47.2 1.0 OD2 A:ASP433 3.6 60.0 1.0 OD2 A:ASP431 3.9 62.9 1.0 N A:ASP435 4.0 54.5 1.0 N A:GLN437 4.0 51.6 1.0 CB A:ASP435 4.2 51.8 1.0 CB A:ASP431 4.3 61.4 1.0 CA A:GLN437 4.3 50.7 1.0 CA A:ASP431 4.3 61.9 1.0 N A:GLY434 4.3 60.0 1.0 N A:VAL438 4.4 49.3 1.0 CA A:VAL438 4.4 47.5 1.0 N A:ASP433 4.4 61.6 1.0 N A:ASN439 4.5 44.9 1.0 CG A:GLU442 4.5 52.2 1.0 CA A:ASP435 4.5 52.5 1.0 CB A:ASP433 4.6 59.9 1.0 C A:ASP431 4.6 61.8 1.0 CB A:GLN437 4.7 50.7 1.0 N A:GLY436 4.7 53.0 1.0 N A:ILE432 4.8 61.5 1.0 CA A:ASP433 4.8 60.6 1.0 C A:ASP433 4.8 60.2 1.0 C A:ASP435 4.8 52.9 1.0 C A:GLY434 4.9 56.6 1.0 C A:VAL438 4.9 46.3 1.0 CG A:ASN439 5.0 46.3 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