Calcium in PDB 3ek7: Calcium-Saturated GCAMP2 Dimer

The structure of Calcium-Saturated GCAMP2 Dimer, PDB code: 3ek7 was solved by J.Akerboom, J.D.Velez Rivera, L.L.Looger, E.R.Schreiter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.67 / 1.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	126.131, 47.310, 68.940, 90.00, 100.48, 90.00
R / Rfree (%)	18.9 / 24.1

The binding sites of Calcium atom in the Calcium-Saturated GCAMP2 Dimer (pdb code 3ek7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Calcium-Saturated GCAMP2 Dimer, PDB code: 3ek7:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Calcium-Saturated GCAMP2 Dimer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Calcium-Saturated GCAMP2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca452 b:19.4 occ:1.00 O A:THR329 2.1 18.8 1.0 OD1 A:ASP323 2.3 22.2 1.0 O A:HOH507 2.4 27.6 1.0 OD1 A:ASP327 2.5 25.5 1.0 OD1 A:ASP325 2.5 27.9 1.0 OE2 A:GLU334 2.5 19.3 1.0 OE1 A:GLU334 2.5 21.6 1.0 CD A:GLU334 2.8 20.9 1.0 C A:THR329 3.4 18.2 1.0 CG A:ASP325 3.4 26.8 1.0 CG A:ASP323 3.5 19.8 1.0 CG A:ASP327 3.5 25.7 1.0 OD2 A:ASP325 3.8 30.2 1.0 CA A:ASP323 4.1 20.9 1.0 N A:THR329 4.1 18.7 1.0 OD2 A:ASP327 4.1 26.5 1.0 CB A:ASP323 4.2 19.6 1.0 N A:ASP327 4.3 24.8 1.0 CG A:GLU334 4.3 21.1 1.0 CA A:THR329 4.3 19.3 1.0 N A:ILE330 4.3 18.7 1.0 OD2 A:ASP323 4.4 21.7 1.0 N A:ASP325 4.4 25.4 1.0 CA A:ILE330 4.4 17.4 1.0 C A:ASP323 4.4 22.6 1.0 CB A:ASP327 4.5 23.2 1.0 CG2 A:THR329 4.5 21.6 1.0 N A:LYS324 4.6 24.3 1.0 CB A:ASP325 4.7 26.6 1.0 N A:GLY326 4.7 24.2 1.0 O A:HOH571 4.7 25.7 1.0 CA A:ASP327 4.7 23.6 1.0 N A:GLY328 4.8 21.5 1.0 CG2 A:THR331 4.8 20.2 1.0 N A:THR331 4.8 17.7 1.0 CA A:ASP325 4.9 25.5 1.0 C A:ASP327 4.9 23.0 1.0 C A:ASP325 5.0 25.5 1.0 O A:HOH528 5.0 44.2 1.0

Calcium binding site 2 out of 4 in the Calcium-Saturated GCAMP2 Dimer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Calcium-Saturated GCAMP2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca453 b:23.2 occ:1.00 OD2 A:ASP359 2.2 29.7 1.0 OD1 A:ASN363 2.3 26.0 1.0 OD1 A:ASP361 2.4 22.6 1.0 O A:THR365 2.4 22.3 1.0 O A:HOH518 2.5 31.2 1.0 OE1 A:GLU370 2.5 25.5 1.0 OE2 A:GLU370 2.6 30.9 1.0 CD A:GLU370 2.9 27.1 1.0 CG A:ASP361 3.3 31.8 1.0 CG A:ASN363 3.4 24.8 1.0 CG A:ASP359 3.4 30.6 1.0 C A:THR365 3.6 23.7 1.0 OD2 A:ASP361 3.7 26.3 1.0 ND2 A:ASN363 4.0 23.4 1.0 OD1 A:ASP359 4.2 30.2 1.0 N A:THR365 4.3 23.7 1.0 N A:ASN363 4.3 28.6 1.0 CB A:ASP359 4.4 29.2 1.0 CA A:ASP359 4.4 29.6 1.0 CG A:GLU370 4.4 25.1 1.0 OG1 A:THR365 4.4 22.6 1.0 N A:ASP361 4.4 33.7 1.0 N A:ASP367 4.5 23.9 1.0 CB A:ASN363 4.5 27.1 1.0 CA A:ILE366 4.5 23.0 1.0 N A:ILE366 4.5 22.4 1.0 CB A:ASP361 4.5 32.9 1.0 O A:HOH517 4.5 32.5 1.0 CA A:THR365 4.5 23.1 1.0 OD2 A:ASP367 4.6 35.9 1.0 N A:GLY362 4.6 32.1 1.0 C A:ASP359 4.7 30.8 1.0 N A:GLY364 4.7 26.4 1.0 O A:HOH614 4.7 37.9 1.0 CA A:ASN363 4.8 27.5 1.0 CA A:ASP361 4.8 33.2 1.0 N A:ALA360 4.8 31.8 1.0 C A:ASP361 4.9 33.0 1.0 C A:ILE366 4.9 23.4 1.0 CG A:ASP367 5.0 30.4 1.0 C A:ASN363 5.0 27.1 1.0

Calcium binding site 3 out of 4 in the Calcium-Saturated GCAMP2 Dimer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Calcium-Saturated GCAMP2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca454 b:17.3 occ:1.00 O A:TYR402 2.1 17.3 1.0 OD2 A:ASP396 2.3 18.7 1.0 OE2 A:GLU407 2.4 17.0 1.0 OD1 A:ASN400 2.4 20.9 1.0 OD2 A:ASP398 2.4 25.0 1.0 O A:HOH550 2.5 24.9 1.0 OE1 A:GLU407 2.6 24.2 1.0 CD A:GLU407 2.9 19.1 1.0 C A:TYR402 3.4 15.9 1.0 CG A:ASP398 3.4 21.7 1.0 CG A:ASN400 3.4 22.7 1.0 CG A:ASP396 3.4 19.4 1.0 OD1 A:ASP398 3.8 25.9 1.0 ND2 A:ASN400 4.0 23.1 1.0 N A:TYR402 4.2 16.6 1.0 OD1 A:ASP396 4.2 19.0 1.0 N A:ASN400 4.2 20.2 1.0 CA A:TYR402 4.3 16.6 1.0 CA A:ASP396 4.3 19.6 1.0 CB A:ASP396 4.3 18.8 1.0 N A:ILE403 4.3 15.7 1.0 N A:ASP398 4.3 23.8 1.0 CG A:GLU407 4.3 20.8 1.0 CA A:ILE403 4.4 15.3 1.0 CB A:ASN400 4.5 21.4 1.0 C A:ASP396 4.5 21.1 1.0 N A:SER404 4.5 16.0 1.0 CB A:ASP398 4.6 24.7 1.0 CB A:TYR402 4.6 17.1 1.0 N A:GLY399 4.6 22.9 1.0 N A:LYS397 4.7 22.8 1.0 CA A:ASN400 4.8 20.5 1.0 OE1 A:GLN438 4.8 30.3 1.0 CA A:ASP398 4.8 23.3 1.0 C A:ILE403 4.9 14.8 1.0 C A:ASP398 4.9 23.9 1.0 N A:GLY401 4.9 17.2 1.0 O A:ASP396 5.0 22.2 1.0

Calcium binding site 4 out of 4 in the Calcium-Saturated GCAMP2 Dimer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Calcium-Saturated GCAMP2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca455 b:17.7 occ:1.00 OD1 A:ASP432 2.3 19.3 1.0 O A:GLN438 2.3 17.3 1.0 OD1 A:ASP436 2.3 18.2 1.0 O A:HOH525 2.4 20.0 1.0 OD2 A:ASP434 2.4 21.3 1.0 OE1 A:GLU443 2.5 16.8 1.0 OE2 A:GLU443 2.7 22.0 1.0 CD A:GLU443 2.9 22.7 1.0 CG A:ASP436 3.3 18.0 1.0 CG A:ASP432 3.4 21.1 1.0 CG A:ASP434 3.4 20.7 1.0 C A:GLN438 3.5 17.1 1.0 OD2 A:ASP436 3.7 22.2 1.0 OD1 A:ASP434 3.8 26.1 1.0 CA A:ASP432 4.1 24.1 1.0 CB A:ASP432 4.2 22.8 1.0 N A:GLN438 4.2 16.6 1.0 N A:ASP436 4.2 18.5 1.0 N A:ASP434 4.3 21.7 1.0 OD2 A:ASP432 4.3 18.5 1.0 N A:VAL439 4.4 16.5 1.0 CA A:VAL439 4.4 16.1 1.0 CA A:GLN438 4.5 17.4 1.0 N A:ASN440 4.5 17.5 1.0 CG A:GLU443 4.5 20.9 1.0 N A:GLY435 4.5 19.3 1.0 N A:ILE433 4.5 24.1 1.0 CB A:ASP436 4.6 19.4 1.0 C A:ASP432 4.6 24.6 1.0 CB A:ASP434 4.6 21.6 1.0 CA A:ASP434 4.8 21.1 1.0 CA A:ASP436 4.8 18.4 1.0 C A:ASP434 4.8 21.2 1.0 N A:GLY437 4.9 17.3 1.0 C A:VAL439 4.9 16.5 1.0 ND2 A:ASN440 5.0 25.1 1.0 CG A:ASN440 5.0 22.0 1.0

J.Akerboom, J.D.Rivera, M.M.Guilbe, E.C.Malave, H.H.Hernandez, L.Tian, S.A.Hires, J.S.Marvin, L.L.Looger, E.R.Schreiter. Crystal Structures of the Gcamp Calcium Sensor Reveal the Mechanism of Fluorescence Signal Change and Aid Rational Design J.Biol.Chem. V. 284 6455 2009.
ISSN: ISSN 0021-9258
PubMed: 19098007
DOI: 10.1074/JBC.M807657200