Calcium in PDB 3sg3: Crystal Structure of GCAMP3-D380Y

The structure of Crystal Structure of GCAMP3-D380Y, PDB code: 3sg3 was solved by E.R.Schreiter, J.Akerboom, L.L.Looger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.80 / 2.10
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	120.444, 120.444, 98.000, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 19.9

The binding sites of Calcium atom in the Crystal Structure of GCAMP3-D380Y (pdb code 3sg3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of GCAMP3-D380Y, PDB code: 3sg3:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of GCAMP3-D380Y


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 GCAMP3-D380Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca451 b:17.9 occ:1.00 OD1 A:ASP322 2.2 19.1 1.0 O A:HOH494 2.3 25.5 1.0 O A:THR328 2.3 19.7 1.0 OD1 A:ASP326 2.4 17.0 1.0 OD1 A:ASP324 2.4 21.5 1.0 OE1 A:GLU333 2.5 22.4 1.0 OE2 A:GLU333 2.5 22.5 1.0 CD A:GLU333 2.9 27.1 1.0 CG A:ASP326 3.3 18.4 1.0 CG A:ASP324 3.3 21.4 1.0 CG A:ASP322 3.4 18.0 1.0 C A:THR328 3.5 19.8 1.0 OD2 A:ASP324 3.7 19.0 1.0 OD2 A:ASP326 3.9 19.1 1.0 CA A:ASP322 4.1 20.9 1.0 N A:ASP326 4.2 19.1 1.0 N A:THR328 4.2 17.2 1.0 CB A:ASP322 4.2 19.3 1.0 OD2 A:ASP322 4.3 17.6 1.0 O A:HOH543 4.3 29.0 1.0 N A:ASP324 4.3 20.3 1.0 C A:ASP322 4.4 22.2 1.0 CB A:ASP326 4.4 18.3 1.0 CG A:GLU333 4.4 23.6 1.0 CA A:THR328 4.4 20.2 1.0 N A:ILE329 4.4 17.2 1.0 CA A:ILE329 4.5 18.1 1.0 N A:LYS323 4.6 24.1 1.0 CB A:ASP324 4.6 21.8 1.0 CA A:ASP326 4.6 17.4 1.0 CG2 A:THR328 4.6 19.6 1.0 N A:GLY325 4.7 21.2 1.0 O A:HOH528 4.8 24.9 1.0 CA A:ASP324 4.8 20.6 1.0 N A:GLY327 4.8 16.5 1.0 C A:ASP324 4.9 19.1 1.0 C A:ASP326 4.9 17.3 1.0 O A:ASP322 4.9 22.1 1.0 N A:THR330 4.9 18.5 1.0 O A:HOH554 4.9 31.5 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of GCAMP3-D380Y


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 GCAMP3-D380Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca452 b:20.3 occ:1.00 OD2 A:ASP358 2.2 18.7 1.0 O A:HOH714 2.3 26.2 1.0 OD1 A:ASP362 2.3 23.4 1.0 O A:THR364 2.4 18.4 1.0 OE1 A:GLU369 2.4 18.8 1.0 OD1 A:ASP360 2.4 23.6 1.0 OE2 A:GLU369 2.6 19.6 1.0 CD A:GLU369 2.9 18.3 1.0 CG A:ASP362 3.3 27.6 1.0 CG A:ASP360 3.3 24.3 1.0 CG A:ASP358 3.4 21.7 1.0 C A:THR364 3.5 18.7 1.0 OD2 A:ASP360 3.7 28.0 1.0 OD2 A:ASP362 3.8 26.7 1.0 OG1 A:THR364 4.1 19.3 1.0 N A:THR364 4.1 19.4 1.0 OD1 A:ASP358 4.2 17.7 1.0 N A:ASP362 4.2 24.8 1.0 N A:ASP360 4.3 25.3 1.0 CA A:ASP358 4.3 19.9 1.0 N A:ASP366 4.3 18.5 1.0 CA A:THR364 4.3 19.2 1.0 CB A:ASP358 4.4 19.1 1.0 CG A:GLU369 4.4 18.6 1.0 CB A:ASP362 4.4 27.1 1.0 N A:ILE365 4.5 19.0 1.0 CA A:ILE365 4.5 17.1 1.0 N A:GLY361 4.5 25.4 1.0 C A:ASP358 4.5 20.6 1.0 CB A:ASP360 4.6 26.0 1.0 OD2 A:ASP366 4.6 30.8 1.0 N A:GLY363 4.7 24.6 1.0 N A:ALA359 4.7 20.8 1.0 CG A:ASP366 4.7 27.8 1.0 CA A:ASP362 4.7 26.9 1.0 CA A:ASP360 4.8 25.7 1.0 O A:HOH578 4.8 31.8 1.0 CB A:THR364 4.9 21.0 1.0 C A:ILE365 4.9 19.5 1.0 C A:ASP362 4.9 28.7 1.0 C A:ASP360 4.9 28.1 1.0 CB A:ASP366 5.0 22.4 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of GCAMP3-D380Y


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 GCAMP3-D380Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca453 b:41.0 occ:1.00 OD1 A:ASN399 2.2 45.4 1.0 O A:TYR401 2.2 40.0 1.0 OE1 A:GLU406 2.3 34.3 1.0 OE2 A:GLU406 2.4 36.0 1.0 OD2 A:ASP395 2.5 38.2 1.0 O A:HOH655 2.5 38.7 1.0 OD2 A:ASP397 2.5 57.7 1.0 CD A:GLU406 2.7 34.5 1.0 CG A:ASP397 3.1 61.3 1.0 OD1 A:ASP397 3.2 62.3 1.0 CG A:ASN399 3.4 49.2 1.0 C A:TYR401 3.4 37.4 1.0 CG A:ASP395 3.6 43.1 1.0 N A:TYR401 4.1 37.2 1.0 CG A:GLU406 4.2 38.0 1.0 ND2 A:ASN399 4.2 55.7 1.0 CA A:TYR401 4.3 37.2 1.0 N A:ASP397 4.3 55.6 1.0 O A:HOH674 4.3 45.7 1.0 CA A:ASP395 4.3 38.6 1.0 N A:ASN399 4.3 38.9 1.0 CB A:ASN399 4.3 48.6 1.0 N A:ILE402 4.4 38.5 1.0 CB A:ASP397 4.4 56.2 1.0 C A:ASP395 4.5 39.7 1.0 OD1 A:ASP395 4.5 37.8 1.0 CB A:ASP395 4.5 40.0 1.0 CA A:ILE402 4.5 41.5 1.0 N A:SER403 4.6 45.6 1.0 N A:GLY398 4.6 45.4 1.0 CB A:TYR401 4.7 39.5 1.0 N A:LYS396 4.7 39.4 1.0 CA A:ASP397 4.7 55.4 1.0 N A:GLY400 4.7 42.0 1.0 CA A:ASN399 4.8 42.6 1.0 O A:ASP395 4.8 39.8 1.0 C A:ASP397 4.8 48.8 1.0 C A:ILE402 5.0 40.4 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of GCAMP3-D380Y


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 GCAMP3-D380Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca454 b:45.3 occ:1.00 O A:HOH576 2.2 43.3 1.0 OD1 A:ASP431 2.2 40.7 1.0 OD1 A:ASP435 2.4 46.6 1.0 O A:GLN437 2.4 40.3 1.0 OE2 A:GLU442 2.4 55.2 1.0 OE1 A:GLU442 2.6 53.5 1.0 OD2 A:ASP433 2.6 47.9 1.0 CD A:GLU442 2.8 56.8 1.0 CG A:ASP431 3.3 41.7 1.0 CG A:ASP433 3.3 46.6 1.0 CG A:ASP435 3.3 53.9 1.0 C A:GLN437 3.5 39.1 1.0 OD1 A:ASP433 3.5 42.3 1.0 OD2 A:ASP435 3.8 49.7 1.0 OD2 A:ASP431 4.0 47.3 1.0 N A:ASP435 4.0 43.2 1.0 CA A:ASP431 4.1 51.3 1.0 N A:GLN437 4.1 42.0 1.0 CB A:ASP431 4.2 47.4 1.0 N A:ASP433 4.3 56.0 1.0 CG A:GLU442 4.3 56.8 1.0 CA A:GLN437 4.4 40.7 1.0 CA A:VAL438 4.4 39.1 1.0 N A:VAL438 4.4 39.4 1.0 CB A:ASP435 4.4 49.4 1.0 N A:GLY434 4.5 56.5 1.0 N A:ASN439 4.5 38.0 1.0 N A:ILE432 4.5 54.0 1.0 CB A:ASP433 4.5 46.8 1.0 C A:ASP431 4.5 51.0 1.0 C A:ASP433 4.6 52.2 1.0 CA A:ASP435 4.6 42.3 1.0 CA A:ASP433 4.7 52.9 1.0 N A:GLY436 4.7 41.7 1.0 C A:VAL438 4.9 31.8 1.0 CB A:GLN437 4.9 41.6 1.0 C A:ASP435 4.9 45.9 1.0

J.Akerboom, T.W.Chen, T.J.Wardill, L.Tian, J.S.Marvin, S.Mutlu, N.C.Calderon, F.Esposti, B.G.Borghuis, X.R.Sun, A.Gordus, M.B.Orger, R.Portugues, F.Engert, J.J.Macklin, A.Filosa, A.Aggarwal, R.A.Kerr, R.Takagi, S.Kracun, E.Shigetomi, B.S.Khakh, H.Baier, L.Lagnado, S.S.Wang, C.I.Bargmann, B.E.Kimmel, V.Jayaraman, K.Svoboda, D.S.Kim, E.R.Schreiter, L.L.Looger. Optimization of A Gcamp Calcium Indicator For Neural Activity Imaging. J.Neurosci. V. 32 13819 2012.
ISSN: ISSN 0270-6474
PubMed: 23035093
DOI: 10.1523/JNEUROSCI.2601-12.2012