Calcium in PDB 5ukg: Crystal Structure of the Genetically Encoded Calcium Indicator K-Geco

The structure of Crystal Structure of the Genetically Encoded Calcium Indicator K-Geco, PDB code: 5ukg was solved by E.R.Schreiter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	75.56 / 2.36
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.284, 129.249, 78.715, 90.00, 106.27, 90.00
R / Rfree (%)	20.6 / 27.5

The binding sites of Calcium atom in the Crystal Structure of the Genetically Encoded Calcium Indicator K-Geco (pdb code 5ukg). 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 K-Geco, PDB code: 5ukg:
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 K-Geco


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 K-Geco within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:38.1 occ:1.00 O A:THR291 2.2 32.5 1.0 O A:HOH615 2.3 38.0 1.0 OD1 A:ASP287 2.4 36.2 1.0 OD1 A:ASP285 2.4 36.4 1.0 OD1 A:ASP289 2.5 41.9 1.0 OE1 A:GLU296 2.5 30.9 1.0 OE2 A:GLU296 2.6 35.3 1.0 CD A:GLU296 3.0 32.4 1.0 CG A:ASP287 3.4 35.4 1.0 C A:THR291 3.4 31.0 1.0 CG A:ASP289 3.5 40.4 1.0 CG A:ASP285 3.7 36.4 1.0 OD2 A:ASP287 3.8 34.0 1.0 N A:THR291 3.9 34.3 1.0 OD2 A:ASP289 4.0 44.0 1.0 CA A:THR291 4.2 32.6 1.0 N A:ASP289 4.3 37.0 1.0 CA A:ASP285 4.3 33.2 1.0 N A:ILE292 4.4 28.0 1.0 CA A:ILE292 4.5 28.9 1.0 N A:ASP287 4.5 33.3 1.0 CG A:GLU296 4.5 30.6 1.0 OD2 A:ASP285 4.5 39.5 1.0 C A:ASP285 4.5 32.9 1.0 CB A:ASP289 4.6 38.0 1.0 CB A:ASP285 4.6 33.5 1.0 N A:GLY290 4.6 38.4 1.0 CB A:THR291 4.6 32.2 1.0 N A:LYS286 4.7 32.7 1.0 CB A:ASP287 4.7 33.3 1.0 CA A:ASP289 4.7 37.7 1.0 N A:GLY288 4.8 38.7 1.0 C A:ASP289 4.8 37.6 1.0 CG1 A:ILE292 4.9 31.1 1.0 CA A:ASP287 5.0 34.0 1.0 O A:ASP285 5.0 37.2 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of the Genetically Encoded Calcium Indicator K-Geco


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 K-Geco within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:60.2 occ:1.00 OD1 A:ASP321 2.4 57.0 1.0 OD1 A:ASP323 2.5 63.4 1.0 O A:HOH609 2.8 33.8 1.0 O A:THR327 2.8 33.9 1.0 OE1 A:GLU332 2.8 31.0 1.0 OD1 A:ASP325 3.0 55.7 1.0 OE2 A:GLU332 3.1 38.0 1.0 CD A:GLU332 3.4 34.6 1.0 CG A:ASP321 3.6 53.8 1.0 CG A:ASP323 3.6 64.0 1.0 C A:THR327 3.7 36.0 1.0 CG A:ASP325 3.8 52.1 1.0 CA A:PHE328 3.8 33.4 1.0 OD2 A:ASP325 3.9 56.6 1.0 OD2 A:ASP323 4.1 66.2 1.0 N A:PHE328 4.2 35.0 1.0 OG1 A:THR327 4.3 37.5 1.0 CB A:ASP321 4.3 49.2 1.0 CA A:ASP321 4.4 47.6 1.0 OD2 A:ASP321 4.6 56.7 1.0 N A:ASP329 4.6 34.2 1.0 CB A:PHE328 4.6 31.9 1.0 C A:PHE328 4.6 32.8 1.0 N A:ASP323 4.7 59.5 1.0 N A:THR327 4.8 40.6 1.0 CA A:THR327 4.8 37.5 1.0 C A:ASP321 4.8 48.4 1.0 N A:ASP325 4.8 45.1 1.0 CG A:GLU332 4.9 32.6 1.0 CB A:ASP323 4.9 56.8 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of the Genetically Encoded Calcium Indicator K-Geco


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 K-Geco within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:40.2 occ:1.00 O A:TYR364 2.2 35.5 1.0 OD1 A:ASP358 2.3 36.1 1.0 OD1 A:ASN362 2.4 35.2 1.0 OD1 A:ASP360 2.4 40.3 1.0 O A:HOH616 2.4 41.1 1.0 OE1 A:GLU369 2.5 36.3 1.0 OE2 A:GLU369 2.7 34.1 1.0 CD A:GLU369 2.9 34.0 1.0 CG A:ASP360 3.2 38.4 1.0 CG A:ASN362 3.2 32.6 1.0 OD2 A:ASP360 3.3 43.2 1.0 C A:TYR364 3.4 32.4 1.0 CG A:ASP358 3.5 37.3 1.0 ND2 A:ASN362 3.7 34.0 1.0 N A:TYR364 4.1 31.8 1.0 CA A:TYR364 4.2 32.5 1.0 OD2 A:ASP358 4.3 37.5 1.0 CG A:GLU369 4.4 34.7 1.0 N A:ILE365 4.4 30.6 1.0 CB A:ASN362 4.4 32.9 1.0 CB A:TYR364 4.4 33.3 1.0 N A:ASN362 4.5 35.9 1.0 N A:ASP360 4.5 34.0 1.0 CB A:ASP360 4.5 36.9 1.0 CA A:ASP358 4.6 34.3 1.0 CA A:ILE365 4.6 30.9 1.0 CB A:ASP358 4.6 36.5 1.0 N A:GLY366 4.6 33.3 1.0 C A:ASP358 4.7 33.8 1.0 CA A:ASP360 4.9 36.2 1.0 CA A:ASN362 4.9 35.3 1.0 N A:GLY361 4.9 36.8 1.0 C A:ASP360 4.9 36.7 1.0 O A:ASP358 5.0 34.1 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of the Genetically Encoded Calcium Indicator K-Geco


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 K-Geco within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:37.9 occ:1.00 OD1 A:ASP394 2.2 33.9 1.0 OD1 A:ASP396 2.2 34.2 1.0 O A:GLN400 2.2 36.5 1.0 OE1 A:GLU405 2.3 38.8 1.0 O A:HOH606 2.4 51.8 1.0 OD1 A:ASP398 2.6 38.1 1.0 OE2 A:GLU405 2.6 37.8 1.0 CD A:GLU405 2.9 37.7 1.0 CG A:ASP396 3.2 36.6 1.0 CG A:ASP394 3.3 35.9 1.0 C A:GLN400 3.4 36.7 1.0 CG A:ASP398 3.5 40.1 1.0 OD2 A:ASP396 3.5 36.2 1.0 OD2 A:ASP398 3.9 40.8 1.0 OD2 A:ASP394 4.0 38.5 1.0 N A:GLN400 4.1 37.2 1.0 CB A:ASP394 4.3 37.3 1.0 N A:VAL401 4.3 33.5 1.0 CA A:ASP394 4.3 40.4 1.0 N A:ASP398 4.3 41.9 1.0 CA A:GLN400 4.3 36.7 1.0 CG A:GLU405 4.4 37.6 1.0 CA A:VAL401 4.4 31.2 1.0 N A:ASP396 4.4 38.3 1.0 N A:GLY397 4.5 41.6 1.0 CB A:ASP396 4.5 36.6 1.0 ND2 A:ASN402 4.5 32.6 1.0 N A:ASN402 4.6 30.5 1.0 CB A:ASP398 4.6 40.4 1.0 N A:GLY399 4.7 35.7 1.0 N A:ILE395 4.7 42.9 1.0 C A:ASP394 4.7 43.5 1.0 CA A:ASP396 4.8 38.1 1.0 CB A:GLN400 4.8 39.1 1.0 CA A:ASP398 4.8 41.7 1.0 C A:ASP396 4.8 37.8 1.0 C A:VAL401 5.0 30.1 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of the Genetically Encoded Calcium Indicator K-Geco


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 K-Geco within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:44.6 occ:1.00 OD1 B:ASP287 2.3 52.1 1.0 OD1 B:ASP289 2.3 43.3 1.0 O B:HOH627 2.3 43.8 1.0 O B:THR291 2.4 39.6 1.0 OD1 B:ASP285 2.4 37.3 1.0 OE1 B:GLU296 2.5 39.5 1.0 OE2 B:GLU296 2.8 40.6 1.0 CD B:GLU296 3.0 37.7 1.0 CG B:ASP289 3.3 43.5 1.0 CG B:ASP287 3.3 49.2 1.0 C B:THR291 3.6 34.8 1.0 CG B:ASP285 3.7 37.2 1.0 OD2 B:ASP289 3.7 46.6 1.0 OD2 B:ASP287 3.7 50.3 1.0 N B:THR291 4.1 32.3 1.0 CA B:ASP285 4.1 38.5 1.0 N B:ASP287 4.3 42.5 1.0 N B:ASP289 4.3 38.6 1.0 N B:LYS286 4.3 41.3 1.0 C B:ASP285 4.3 40.7 1.0 CA B:THR291 4.4 33.5 1.0 CB B:ASP285 4.5 36.6 1.0 CB B:ASP289 4.5 41.1 1.0 N B:ILE292 4.5 33.2 1.0 CG B:GLU296 4.6 34.9 1.0 CA B:ILE292 4.6 33.8 1.0 OD2 B:ASP285 4.6 38.0 1.0 N B:GLY290 4.6 34.3 1.0 N B:GLY288 4.6 46.0 1.0 CB B:ASP287 4.6 45.7 1.0 CA B:ASP289 4.8 39.7 1.0 CB B:THR291 4.8 35.0 1.0 CA B:ASP287 4.9 44.8 1.0 CG1 B:ILE292 4.9 35.2 1.0 O B:ASP285 4.9 42.9 1.0 O B:PHE284 5.0 35.7 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of the Genetically Encoded Calcium Indicator K-Geco


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 K-Geco within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:48.3 occ:1.00 OD1 B:ASP321 2.6 47.7 1.0 O B:HOH615 2.7 36.9 1.0 OD1 B:ASP323 2.7 49.6 1.0 O B:THR327 2.8 37.5 1.0 OE2 B:GLU332 2.9 44.8 1.0 OE1 B:GLU332 2.9 38.7 1.0 OD2 B:ASP325 3.1 53.7 1.0 OD1 B:ASP325 3.1 50.2 1.0 CD B:GLU332 3.3 38.5 1.0 CG B:ASP325 3.3 50.6 1.0 CG B:ASP321 3.6 44.1 1.0 CG B:ASP323 3.7 52.0 1.0 C B:THR327 3.8 36.4 1.0 OD2 B:ASP323 4.1 56.0 1.0 CA B:PHE328 4.3 35.5 1.0 OG1 B:THR327 4.3 35.0 1.0 N B:ASP323 4.3 58.9 1.0 OD2 B:ASP321 4.3 43.9 1.0 N B:ALA322 4.3 50.4 1.0 CA B:ASP321 4.3 44.0 1.0 CB B:ASP321 4.4 44.0 1.0 N B:PHE328 4.5 36.4 1.0 CB B:ASP325 4.6 46.5 1.0 N B:ASP325 4.6 42.7 1.0 N B:THR327 4.7 36.0 1.0 C B:ASP323 4.8 50.0 1.0 CG B:GLU332 4.8 38.2 1.0 CA B:THR327 4.8 36.4 1.0 O B:ASP323 4.8 53.0 1.0 C B:ASP321 4.8 46.1 1.0 OD1 B:ASP329 4.8 51.9 1.0 CA B:ASP323 4.9 53.7 1.0 CB B:ASP323 4.9 52.3 1.0 CB B:PHE328 5.0 31.9 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of the Genetically Encoded Calcium Indicator K-Geco


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 K-Geco within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:34.0 occ:1.00 O B:TYR364 2.2 27.8 1.0 OD1 B:ASP360 2.3 34.9 1.0 OD1 B:ASP358 2.3 29.8 1.0 OD1 B:ASN362 2.3 35.3 1.0 OE1 B:GLU369 2.4 31.8 1.0 OE2 B:GLU369 2.4 30.6 1.0 O B:HOH617 2.7 40.0 1.0 CD B:GLU369 2.8 29.3 1.0 CG B:ASP360 3.2 35.6 1.0 CG B:ASN362 3.2 34.6 1.0 C B:TYR364 3.4 27.2 1.0 CG B:ASP358 3.5 30.0 1.0 OD2 B:ASP360 3.5 39.2 1.0 ND2 B:ASN362 3.7 35.8 1.0 N B:TYR364 4.0 28.3 1.0 N B:ASN362 4.2 33.9 1.0 OD2 B:ASP358 4.2 32.8 1.0 CG B:GLU369 4.2 29.6 1.0 CA B:TYR364 4.2 29.3 1.0 N B:ASP360 4.3 29.0 1.0 CB B:ASN362 4.3 33.9 1.0 N B:ILE365 4.4 26.1 1.0 CA B:ASP358 4.4 27.7 1.0 C B:ASP358 4.4 27.7 1.0 CB B:ASP358 4.4 27.9 1.0 CB B:ASP360 4.5 32.6 1.0 CA B:ILE365 4.6 26.6 1.0 CB B:TYR364 4.6 30.9 1.0 N B:GLY361 4.6 32.0 1.0 N B:LYS359 4.7 28.8 1.0 O B:ASP358 4.7 28.2 1.0 CA B:ASN362 4.7 33.4 1.0 N B:GLY363 4.7 31.0 1.0 CA B:ASP360 4.8 30.4 1.0 N B:GLY366 4.8 28.7 1.0 C B:ASP360 5.0 30.6 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of the Genetically Encoded Calcium Indicator K-Geco


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 K-Geco within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:31.0 occ:1.00 OD1 B:ASP394 2.2 29.2 1.0 O B:GLN400 2.2 29.6 1.0 OD1 B:ASP396 2.3 33.8 1.0 OE1 B:GLU405 2.4 27.5 1.0 OE2 B:GLU405 2.5 27.0 1.0 O B:HOH605 2.5 26.9 1.0 OD1 B:ASP398 2.6 28.9 1.0 CD B:GLU405 2.8 29.3 1.0 CG B:ASP396 3.3 34.0 1.0 CG B:ASP394 3.4 28.4 1.0 C B:GLN400 3.4 31.6 1.0 CG B:ASP398 3.4 30.8 1.0 OD2 B:ASP398 3.7 34.4 1.0 OD2 B:ASP396 3.8 34.9 1.0 CA B:ASP394 4.0 31.2 1.0 CB B:ASP394 4.2 30.2 1.0 OD2 B:ASP394 4.2 29.5 1.0 ND2 B:ASN402 4.2 34.2 1.0 N B:VAL401 4.2 32.1 1.0 N B:ASP396 4.3 33.4 1.0 N B:ASN402 4.3 31.9 1.0 CG B:GLU405 4.3 28.3 1.0 CA B:VAL401 4.3 32.3 1.0 N B:GLN400 4.3 33.3 1.0 N B:ASP398 4.3 31.2 1.0 CA B:GLN400 4.4 33.3 1.0 C B:ASP394 4.5 33.3 1.0 N B:ILE395 4.5 34.0 1.0 CB B:ASP396 4.5 33.7 1.0 N B:GLY397 4.6 35.1 1.0 CB B:ASP398 4.6 31.4 1.0 CA B:ASP396 4.7 34.8 1.0 C B:VAL401 4.8 31.2 1.0 C B:ASP396 4.8 36.1 1.0 CB B:GLN400 4.8 36.6 1.0 CG B:ASN402 4.9 32.0 1.0 CA B:ASP398 4.9 31.3 1.0

Y.Shen, H.Dana, A.S.Abdelfattah, R.Patel, J.Shea, R.S.Molina, B.Rawal, V.Rancic, Y.F.Chang, L.Wu, Y.Chen, Y.Qian, M.D.Wiens, N.Hambleton, K.Ballanyi, T.E.Hughes, M.Drobizhev, D.S.Kim, M.Koyama, E.R.Schreiter, R.E.Campbell. A Genetically Encoded CA2+Indicator Based on Circularly Permutated Sea Anemone Red Fluorescent Protein EQFP578. Bmc Biol. V. 16 9 2018.
ISSN: ESSN 1741-7007
PubMed: 29338710
DOI: 10.1186/S12915-018-0480-0