Calcium in PDB 4i2y: Crystal Structure of the Genetically Encoded Calcium Indicator RGECO1

The structure of Crystal Structure of the Genetically Encoded Calcium Indicator RGECO1, PDB code: 4i2y was solved by J.Akerboom, 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)	68.28 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.160, 91.730, 68.570, 90.00, 95.29, 90.00
R / Rfree (%)	19.3 / 25.7

The binding sites of Calcium atom in the Crystal Structure of the Genetically Encoded Calcium Indicator RGECO1 (pdb code 4i2y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of the Genetically Encoded Calcium Indicator RGECO1, PDB code: 4i2y:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structure of the Genetically Encoded Calcium Indicator RGECO1


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 the Genetically Encoded Calcium Indicator RGECO1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca500 b:27.9 occ:1.00 OD1 A:ASP323 2.2 23.3 1.0 O A:HOH617 2.2 37.1 1.0 OD1 A:ASP327 2.3 31.9 1.0 O A:THR329 2.3 21.6 1.0 OE1 A:GLU334 2.3 25.1 1.0 OE2 A:GLU334 2.5 25.9 1.0 OD1 A:ASP325 2.7 40.9 1.0 CD A:GLU334 2.7 25.1 1.0 CG A:ASP327 3.2 37.2 1.0 CG A:ASP323 3.4 22.7 1.0 CG A:ASP325 3.4 39.8 1.0 C A:THR329 3.5 20.8 1.0 OD2 A:ASP325 3.6 42.4 1.0 OD2 A:ASP327 3.7 32.8 1.0 CG2 A:THR329 3.8 22.5 1.0 CA A:ASP323 4.0 26.3 1.0 CB A:ASP323 4.1 23.0 1.0 N A:ASP327 4.2 36.5 1.0 N A:THR329 4.2 22.0 1.0 CG A:GLU334 4.2 23.0 1.0 OD2 A:ASP323 4.3 21.7 1.0 CB A:ASP327 4.3 32.2 1.0 CA A:THR329 4.3 21.2 1.0 N A:ILE330 4.4 19.6 1.0 C A:ASP323 4.4 29.4 1.0 CB A:THR329 4.5 23.6 1.0 CA A:ILE330 4.5 19.3 1.0 CB A:ASP325 4.6 38.9 1.0 N A:ASP325 4.6 38.9 1.0 N A:LYS324 4.6 31.8 1.0 CA A:ASP327 4.7 33.3 1.0 CG2 A:THR331 4.7 27.7 1.0 N A:GLY326 4.7 33.2 1.0 N A:THR331 4.8 22.1 1.0 CA A:ASP325 4.9 38.9 1.0 C A:ASP325 4.9 35.3 1.0 O A:ASP323 5.0 30.2 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of the Genetically Encoded Calcium Indicator RGECO1


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 the Genetically Encoded Calcium Indicator RGECO1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:26.8 occ:1.00 O A:HOH611 2.1 22.9 1.0 O A:THR365 2.2 31.4 1.0 OD2 A:ASP359 2.4 20.1 1.0 OD1 A:ASP361 2.4 43.2 1.0 OE2 A:GLU370 2.4 28.9 1.0 OE1 A:GLU370 2.5 22.7 1.0 OD1 A:ASP363 2.6 35.4 1.0 CD A:GLU370 2.8 23.1 1.0 CG A:ASP363 3.3 42.3 1.0 C A:THR365 3.4 29.0 1.0 CG A:ASP361 3.4 36.9 1.0 CG A:ASP359 3.4 20.9 1.0 OG1 A:THR365 3.5 33.5 1.0 OD2 A:ASP363 3.7 47.8 1.0 OD2 A:ASP361 3.8 43.0 1.0 N A:THR365 4.0 32.5 1.0 OD1 A:ASP359 4.1 18.9 1.0 CA A:THR365 4.2 32.8 1.0 N A:ASP363 4.2 37.8 1.0 CA A:ASP359 4.2 21.7 1.0 N A:PHE366 4.3 25.7 1.0 CB A:ASP359 4.3 21.6 1.0 CG A:GLU370 4.3 21.3 1.0 N A:ASP361 4.4 31.1 1.0 CB A:ASP363 4.5 41.0 1.0 CB A:THR365 4.5 30.8 1.0 C A:ASP359 4.5 24.4 1.0 CA A:PHE366 4.5 25.2 1.0 N A:GLY362 4.6 36.0 1.0 CB A:ASP361 4.7 36.1 1.0 N A:ASP367 4.7 27.2 1.0 OD2 A:ASP367 4.7 35.0 1.0 CA A:ASP363 4.7 38.5 1.0 N A:GLY364 4.7 33.1 1.0 N A:ALA360 4.8 25.4 1.0 O A:HOH645 4.8 34.3 1.0 CG A:ASP367 4.8 31.8 1.0 CA A:ASP361 4.9 36.2 1.0 C A:ASP363 4.9 36.8 1.0 O A:ASP359 4.9 24.4 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of the Genetically Encoded Calcium Indicator RGECO1


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 the Genetically Encoded Calcium Indicator RGECO1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:24.3 occ:1.00 O A:HOH614 1.9 20.5 1.0 OD1 A:ASP432 2.1 20.9 1.0 O A:GLN438 2.3 22.1 1.0 OD2 A:ASP434 2.3 36.8 1.0 OD1 A:ASP436 2.4 26.4 1.0 OE2 A:GLU443 2.5 27.2 1.0 OE1 A:GLU443 2.5 27.3 1.0 CD A:GLU443 2.9 25.2 1.0 CG A:ASP436 3.2 29.0 1.0 CG A:ASP434 3.3 37.7 1.0 CG A:ASP432 3.3 25.7 1.0 OD2 A:ASP436 3.5 29.4 1.0 C A:GLN438 3.5 20.0 1.0 OD1 A:ASP434 3.6 42.1 1.0 OD2 A:ASP432 4.1 27.2 1.0 CA A:ASP432 4.1 28.9 1.0 N A:GLN438 4.2 21.3 1.0 N A:ASP436 4.2 30.3 1.0 CB A:ASP432 4.2 26.5 1.0 N A:VAL439 4.4 19.9 1.0 CA A:GLN438 4.4 21.8 1.0 CA A:VAL439 4.4 18.3 1.0 CB A:ASP436 4.4 28.0 1.0 N A:ASP434 4.4 38.3 1.0 CG A:GLU443 4.5 22.8 1.0 N A:ASN440 4.5 19.4 1.0 N A:GLY435 4.5 32.3 1.0 CB A:ASP434 4.6 36.7 1.0 C A:ASP432 4.6 31.9 1.0 ND2 A:ASN440 4.6 24.8 1.0 N A:ILE433 4.7 38.5 1.0 CA A:ASP436 4.8 29.0 1.0 CA A:ASP434 4.8 35.5 1.0 C A:ASP434 4.8 33.4 1.0 CB A:GLN438 4.9 22.0 1.0 N A:GLY437 4.9 28.2 1.0 C A:VAL439 4.9 17.9 1.0 C A:ASP436 5.0 29.2 1.0 CG A:ASN440 5.0 27.2 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of the Genetically Encoded Calcium Indicator RGECO1


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 the Genetically Encoded Calcium Indicator RGECO1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:17.8 occ:1.00 O A:TYR402 2.2 18.9 1.0 OE2 A:GLU407 2.3 22.4 1.0 OD2 A:ASP396 2.4 20.8 1.0 OD2 A:ASP398 2.4 24.4 1.0 OD1 A:ASN400 2.4 26.2 1.0 O A:HOH610 2.5 20.6 1.0 OE1 A:GLU407 2.5 22.0 1.0 CD A:GLU407 2.8 21.4 1.0 CG A:ASN400 3.2 25.3 1.0 CG A:ASP398 3.2 23.4 1.0 C A:TYR402 3.3 18.3 1.0 OD1 A:ASP398 3.5 25.4 1.0 ND2 A:ASN400 3.6 26.5 1.0 CG A:ASP396 3.6 20.0 1.0 N A:TYR402 4.0 19.5 1.0 CA A:TYR402 4.2 19.1 1.0 N A:ASN400 4.2 22.2 1.0 N A:ILE403 4.3 17.3 1.0 CG A:GLU407 4.3 21.0 1.0 CB A:ASN400 4.3 22.6 1.0 OD1 A:ASP396 4.4 18.9 1.0 N A:ASP398 4.4 27.1 1.0 CA A:ILE403 4.4 15.1 1.0 CA A:ASP396 4.4 21.8 1.0 C A:ASP396 4.5 21.6 1.0 N A:GLY399 4.5 25.2 1.0 CB A:ASP396 4.5 20.4 1.0 CB A:ASP398 4.5 23.3 1.0 N A:LYS397 4.7 26.8 1.0 N A:GLY404 4.7 19.0 1.0 N A:GLY401 4.7 24.5 1.0 CB A:TYR402 4.7 21.3 1.0 CA A:ASN400 4.7 23.1 1.0 CA A:ASP398 4.8 25.9 1.0 O A:ASP396 4.9 20.5 1.0 C A:ASN400 4.9 23.8 1.0 C A:ASP398 4.9 24.5 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of the Genetically Encoded Calcium Indicator RGECO1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Genetically Encoded Calcium Indicator RGECO1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:22.6 occ:1.00 O B:HOH617 2.1 21.1 1.0 OD1 B:ASP323 2.2 20.9 1.0 OD1 B:ASP325 2.4 33.7 1.0 OE1 B:GLU334 2.5 16.8 1.0 O B:THR329 2.5 24.6 1.0 OD1 B:ASP327 2.6 31.4 1.0 OE2 B:GLU334 2.9 20.2 1.0 CD B:GLU334 3.0 20.2 1.0 CG B:ASP325 3.2 33.1 1.0 CG B:ASP327 3.3 28.4 1.0 CG B:ASP323 3.3 21.4 1.0 OD2 B:ASP325 3.4 35.6 1.0 C B:THR329 3.6 23.6 1.0 OD2 B:ASP327 3.6 31.8 1.0 CG2 B:THR329 4.0 26.9 1.0 N B:ASP327 4.1 26.4 1.0 CA B:ASP323 4.1 23.3 1.0 OD2 B:ASP323 4.2 24.4 1.0 N B:THR329 4.2 24.2 1.0 CB B:ASP323 4.2 22.0 1.0 CB B:ASP327 4.3 26.3 1.0 CA B:THR329 4.3 25.5 1.0 CB B:THR329 4.4 27.4 1.0 C B:ASP323 4.4 26.1 1.0 N B:ILE330 4.5 20.3 1.0 CG B:GLU334 4.5 17.6 1.0 N B:ASP325 4.5 32.9 1.0 N B:GLY326 4.6 27.9 1.0 CB B:ASP325 4.6 31.8 1.0 CA B:ILE330 4.6 18.1 1.0 CA B:ASP327 4.6 26.5 1.0 N B:GLY328 4.7 27.2 1.0 N B:LYS324 4.8 27.8 1.0 C B:ASP327 4.8 26.1 1.0 O B:ASP323 4.9 25.6 1.0 C B:ASP325 4.9 29.2 1.0 CA B:ASP325 4.9 30.6 1.0 N B:THR331 5.0 16.5 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of the Genetically Encoded Calcium Indicator RGECO1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Genetically Encoded Calcium Indicator RGECO1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:21.4 occ:1.00 O B:THR365 2.2 15.9 1.0 O B:HOH605 2.2 17.5 1.0 OD2 B:ASP359 2.3 14.6 1.0 OD1 B:ASP363 2.3 18.4 1.0 OE2 B:GLU370 2.4 18.6 1.0 OD1 B:ASP361 2.5 34.5 1.0 OE1 B:GLU370 2.6 17.9 1.0 CD B:GLU370 2.8 20.3 1.0 CG B:ASP363 3.1 22.1 1.0 C B:THR365 3.4 18.0 1.0 CG B:ASP359 3.4 16.9 1.0 OG1 B:THR365 3.4 24.8 1.0 CG B:ASP361 3.4 31.5 1.0 OD2 B:ASP363 3.6 22.2 1.0 OD2 B:ASP361 3.7 34.5 1.0 N B:THR365 4.0 19.7 1.0 N B:ASP363 4.1 22.8 1.0 OD1 B:ASP359 4.1 15.9 1.0 CA B:THR365 4.1 20.0 1.0 CB B:ASP363 4.3 21.5 1.0 CA B:ASP359 4.4 17.1 1.0 N B:PHE366 4.4 17.4 1.0 CB B:ASP359 4.4 17.4 1.0 CG B:GLU370 4.4 19.0 1.0 CB B:THR365 4.4 22.4 1.0 N B:ASP361 4.4 24.2 1.0 OD2 B:ASP367 4.5 33.4 1.0 C B:ASP359 4.6 18.1 1.0 CA B:PHE366 4.6 16.5 1.0 CA B:ASP363 4.6 20.2 1.0 N B:GLY362 4.7 22.8 1.0 N B:ASP367 4.7 18.0 1.0 N B:GLY364 4.7 19.6 1.0 CB B:ASP361 4.7 28.0 1.0 CG B:ASP367 4.7 24.7 1.0 N B:ALA360 4.8 18.7 1.0 O B:HOH625 4.8 31.6 1.0 C B:ASP363 4.8 20.6 1.0 OD1 B:ASP367 4.9 26.2 1.0 O B:ASP359 5.0 16.8 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of the Genetically Encoded Calcium Indicator RGECO1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of the Genetically Encoded Calcium Indicator RGECO1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:37.4 occ:1.00 O B:TYR402 2.1 31.4 1.0 OD2 B:ASP396 2.4 53.7 1.0 OE1 B:GLU407 2.4 35.2 1.0 OD1 B:ASP398 2.4 45.4 1.0 OD1 B:ASN400 2.5 42.6 1.0 O B:HOH623 2.5 37.2 1.0 OE2 B:GLU407 2.6 39.1 1.0 CD B:GLU407 2.8 37.3 1.0 CG B:ASP398 3.2 46.7 1.0 OD2 B:ASP398 3.3 44.5 1.0 C B:TYR402 3.3 36.0 1.0 CG B:ASN400 3.3 40.0 1.0 CG B:ASP396 3.5 45.7 1.0 ND2 B:ASN400 3.8 33.9 1.0 CA B:ASP396 4.1 41.0 1.0 N B:TYR402 4.2 35.9 1.0 N B:ILE403 4.2 38.3 1.0 CB B:ASP396 4.2 43.1 1.0 CG B:GLU407 4.3 36.7 1.0 CA B:TYR402 4.3 38.5 1.0 CA B:ILE403 4.3 38.9 1.0 OD1 B:ASP396 4.3 43.0 1.0 N B:ASN400 4.4 42.7 1.0 C B:ASP396 4.4 40.5 1.0 N B:ASP398 4.4 56.2 1.0 CB B:ASN400 4.5 39.0 1.0 N B:GLY404 4.6 36.4 1.0 CB B:ASP398 4.6 44.9 1.0 N B:LYS397 4.7 42.3 1.0 N B:GLY399 4.7 47.9 1.0 CB B:TYR402 4.8 46.0 1.0 CA B:ASN400 4.9 40.7 1.0 CA B:ASP398 4.9 49.8 1.0 O B:ASP396 4.9 36.6 1.0 C B:ILE403 5.0 36.1 1.0 N B:GLY401 5.0 37.4 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of the Genetically Encoded Calcium Indicator RGECO1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of the Genetically Encoded Calcium Indicator RGECO1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:43.7 occ:1.00 OD1 B:ASP432 2.3 56.1 1.0 O B:GLN438 2.3 46.2 1.0 OE2 B:GLU443 2.5 39.6 1.0 OD1 B:ASP436 2.5 53.7 1.0 OE1 B:GLU443 2.6 49.6 1.0 O B:HOH615 2.7 33.5 1.0 OD2 B:ASP434 2.7 58.4 1.0 CD B:GLU443 2.9 42.8 1.0 CG B:ASP432 3.2 48.0 1.0 CG B:ASP436 3.2 51.0 1.0 C B:GLN438 3.5 49.3 1.0 CG B:ASP434 3.6 57.0 1.0 OD2 B:ASP436 3.7 42.6 1.0 OD2 B:ASP432 3.9 37.8 1.0 N B:ASP436 3.9 50.6 1.0 OD1 B:ASP434 3.9 57.5 1.0 CA B:ASP432 4.0 48.9 1.0 CB B:ASP432 4.0 47.5 1.0 N B:GLN438 4.1 48.4 1.0 CB B:ASP436 4.2 52.9 1.0 N B:GLY435 4.3 53.4 1.0 N B:ASP434 4.3 56.1 1.0 N B:ILE433 4.4 53.4 1.0 CA B:ASP436 4.4 52.7 1.0 CA B:VAL439 4.4 45.5 1.0 C B:ASP432 4.4 51.7 1.0 N B:VAL439 4.4 43.9 1.0 CA B:GLN438 4.5 51.3 1.0 CG B:GLU443 4.5 40.2 1.0 N B:ASN440 4.5 41.0 1.0 N B:GLY437 4.6 51.2 1.0 C B:ASP434 4.6 55.4 1.0 C B:ASP436 4.6 49.7 1.0 CB B:ASP434 4.7 55.5 1.0 CA B:ASP434 4.7 56.0 1.0 ND2 B:ASN440 4.8 39.7 1.0 C B:GLY435 4.9 51.4 1.0 CB B:GLN438 4.9 53.7 1.0 C B:ILE433 5.0 57.4 1.0 C B:VAL439 5.0 42.3 1.0 CG B:ASN440 5.0 42.5 1.0

J.Akerboom, N.Carreras Calderon, L.Tian, S.Wabnig, M.Prigge, J.Tolo, A.Gordus, M.B.Orger, K.E.Severi, J.J.Macklin, R.Patel, S.R.Pulver, T.J.Wardill, E.Fischer, C.Schuler, T.W.Chen, K.S.Sarkisyan, J.S.Marvin, C.I.Bargmann, D.S.Kim, S.Kugler, L.Lagnado, P.Hegemann, A.Gottschalk, E.R.Schreiter, L.L.Looger. Genetically Encoded Calcium Indicators For Multi-Color Neural Activity Imaging and Combination with Optogenetics. Front Mol Neurosci V. 6 2 2013.
ISSN: ESSN 1662-5099
PubMed: 23459413
DOI: 10.3389/FNMOL.2013.00002