Calcium in PDB 9k8w: Crystal Structure of the Calcium Indicator GCAMP6S-Brus in Calcium- Bound State

The structure of Crystal Structure of the Calcium Indicator GCAMP6S-Brus in Calcium- Bound State, PDB code: 9k8w was solved by L.A.Varfolomeeva, T.R.Simonyan, A.V.Mamontova, A.M.Bogdanov, V.O.Popov, K.M.Boyko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.52 / 2.65
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	121.54, 121.54, 97.902, 90, 90, 90
R / Rfree (%)	18.1 / 23.6

The binding sites of Calcium atom in the Crystal Structure of the Calcium Indicator GCAMP6S-Brus in Calcium- Bound State (pdb code 9k8w). 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 the Calcium Indicator GCAMP6S-Brus in Calcium- Bound State, PDB code: 9k8w:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the Calcium Indicator GCAMP6S-Brus in Calcium- Bound State


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 Calcium Indicator GCAMP6S-Brus in Calcium- Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:38.5 occ:1.00 OD1 A:ASP337 2.3 39.7 1.0 O A:HOH624 2.3 39.6 1.0 OD1 A:ASP339 2.3 40.0 1.0 OD1 A:ASP335 2.3 39.9 1.0 O A:THR341 2.3 41.2 1.0 OE2 A:GLU346 2.3 54.1 1.0 OE1 A:GLU346 2.5 55.9 1.0 CD A:GLU346 2.7 48.0 1.0 CG A:ASP339 3.1 40.1 1.0 CG A:ASP337 3.4 40.0 1.0 CG A:ASP335 3.4 39.4 1.0 C A:THR341 3.6 39.0 1.0 OD2 A:ASP339 3.6 48.5 1.0 OD2 A:ASP337 3.9 35.0 1.0 CB A:ASP335 4.1 33.8 1.0 CA A:ASP335 4.1 38.3 1.0 CG A:GLU346 4.2 38.9 1.0 CB A:ASP339 4.3 36.7 1.0 N A:ASP339 4.3 33.9 1.0 N A:THR341 4.3 36.8 1.0 N A:ASP337 4.4 40.5 1.0 OD2 A:ASP335 4.4 44.3 1.0 C A:ASP335 4.5 43.9 1.0 CA A:THR341 4.5 37.0 1.0 N A:ILE342 4.5 32.9 1.0 CB A:ASP337 4.5 37.1 1.0 CG2 A:THR341 4.6 32.4 1.0 CA A:ILE342 4.6 34.5 1.0 N A:GLY338 4.6 38.0 1.0 CA A:ASP339 4.6 36.3 1.0 N A:LYS336 4.7 45.7 1.0 CA A:ASP337 4.8 39.4 1.0 N A:GLY340 4.9 36.5 1.0 C A:ASP337 4.9 40.0 1.0 O A:ASP335 4.9 39.0 1.0 N A:THR343 4.9 36.4 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the Calcium Indicator GCAMP6S-Brus in Calcium- Bound State


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 Calcium Indicator GCAMP6S-Brus in Calcium- Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:37.0 occ:1.00 OD1 A:ASP375 2.3 50.3 1.0 OD1 A:ASP371 2.3 37.7 1.0 OE1 A:GLU382 2.4 45.7 1.0 O A:THR377 2.4 38.4 1.0 OD1 A:ASP373 2.5 47.7 1.0 OE2 A:GLU382 2.6 40.6 1.0 CD A:GLU382 2.8 40.2 1.0 CG A:ASP375 3.1 50.3 1.0 CG A:ASP373 3.2 51.5 1.0 OD2 A:ASP379 3.3 66.5 1.0 OD2 A:ASP373 3.4 65.5 1.0 CG A:ASP371 3.5 43.2 1.0 OD2 A:ASP375 3.5 59.9 1.0 C A:THR377 3.6 33.5 1.0 OG1 A:THR377 4.1 34.5 1.0 CG A:ASP379 4.2 50.5 1.0 N A:ASP379 4.2 33.7 1.0 CB A:ASP375 4.2 41.6 1.0 N A:THR377 4.3 33.8 1.0 OD2 A:ASP371 4.3 50.1 1.0 CG A:GLU382 4.3 33.2 1.0 N A:ASP375 4.3 42.2 1.0 N A:ASP373 4.4 41.6 1.0 CB A:ASP371 4.4 39.1 1.0 CA A:ASP371 4.4 40.7 1.0 CB A:ASP373 4.5 38.1 1.0 CA A:THR377 4.5 35.4 1.0 N A:ILE378 4.5 34.2 1.0 CA A:ILE378 4.6 37.5 1.0 N A:GLY374 4.7 34.8 1.0 C A:ASP371 4.7 40.0 1.0 CA A:ASP375 4.7 39.2 1.0 CA A:ASP373 4.8 38.5 1.0 N A:ALA372 4.8 36.8 1.0 N A:GLY376 4.8 34.9 1.0 C A:ILE378 4.8 37.2 1.0 OD1 A:ASP379 4.9 49.2 1.0 CB A:ASP379 4.9 38.5 1.0 C A:ASP373 4.9 40.8 1.0 CB A:THR377 5.0 39.5 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the Calcium Indicator GCAMP6S-Brus in Calcium- Bound State


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 Calcium Indicator GCAMP6S-Brus in Calcium- Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:68.6 occ:0.70 OD1 A:ASP448 2.2 99.7 1.0 O A:GLN450 2.3 88.1 1.0 OD1 A:ASP444 2.3 94.9 1.0 OE1 A:GLU455 2.4 99.7 1.0 OD1 A:ASP446 2.5 91.3 1.0 OE2 A:GLU455 2.5 97.8 1.0 CD A:GLU455 2.8 95.6 1.0 CG A:ASP448 3.0 105.8 1.0 CG A:ASP446 3.3 100.3 1.0 CG A:ASP444 3.4 104.7 1.0 C A:GLN450 3.5 79.9 1.0 OD2 A:ASP446 3.7 98.0 1.0 OD2 A:ASP448 3.8 103.9 1.0 CB A:ASP448 3.8 103.2 1.0 N A:ASP448 3.8 88.2 1.0 OD2 A:ASP444 4.1 99.0 1.0 CA A:ASP448 4.2 90.0 1.0 N A:ASP446 4.2 104.8 1.0 N A:GLN450 4.3 83.4 1.0 CG A:GLU455 4.3 83.8 1.0 N A:VAL451 4.4 74.2 1.0 C A:ASP446 4.4 106.8 1.0 CB A:ASP444 4.4 100.3 1.0 CB A:ASP446 4.4 96.8 1.0 CA A:ASP446 4.5 104.5 1.0 CA A:ASP444 4.5 104.3 1.0 CA A:GLN450 4.5 76.8 1.0 CA A:VAL451 4.5 68.8 1.0 N A:GLY447 4.5 94.9 1.0 N A:GLY449 4.7 106.0 1.0 N A:ASN452 4.7 64.8 1.0 C A:ASP444 4.7 90.8 1.0 C A:ASP448 4.8 91.2 1.0 ND2 A:ASN452 4.8 80.6 1.0 O A:ASP446 4.8 123.1 1.0 C A:GLY447 4.9 79.4 1.0 C A:VAL451 4.9 67.6 1.0 N A:ILE445 5.0 89.7 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the Calcium Indicator GCAMP6S-Brus in Calcium- Bound State


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 Calcium Indicator GCAMP6S-Brus in Calcium- Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:61.6 occ:0.70 O A:TYR414 2.2 60.4 1.0 OE2 A:GLU419 2.3 67.4 1.0 OE1 A:GLU419 2.3 75.8 1.0 OD1 A:ASP410 2.3 88.2 1.0 OD1 A:ASN412 2.3 83.8 1.0 OD1 A:ASP408 2.5 96.4 1.0 CD A:GLU419 2.5 72.6 1.0 CG A:ASN412 3.0 98.3 1.0 CG A:ASP410 3.1 91.9 1.0 ND2 A:ASN412 3.1 100.0 1.0 OD2 A:ASP410 3.3 95.4 1.0 C A:TYR414 3.4 68.8 1.0 CG A:ASP408 3.7 86.0 1.0 CG A:GLU419 4.0 69.4 1.0 CA A:ASP408 4.1 63.8 1.0 N A:SER416 4.2 80.3 1.0 CB A:ASP408 4.3 68.7 1.0 CB A:ASN412 4.3 85.5 1.0 N A:ILE415 4.3 68.4 1.0 CA A:TYR414 4.4 70.8 1.0 N A:TYR414 4.4 69.2 1.0 CA A:ILE415 4.5 73.1 1.0 OG A:SER416 4.5 78.4 1.0 CB A:ASP410 4.5 84.0 1.0 N A:ASN412 4.6 78.8 1.0 C A:ASP408 4.6 66.6 1.0 N A:ASP410 4.6 84.8 1.0 N A:LYS409 4.7 71.8 1.0 OD2 A:ASP408 4.7 91.3 1.0 CB A:SER416 4.7 86.8 1.0 CB A:TYR414 4.9 70.1 1.0 C A:ILE415 4.9 72.6 1.0 CA A:ASN412 4.9 82.6 1.0 CB A:GLU419 4.9 87.2 1.0 N A:GLY411 5.0 74.3 1.0

T.R.Simonyan, L.A.Varfolomeeva, A.V.Mamontova, A.A.Kotlobay, A.Y.Gorokhovatsky, A.M.Bogdanov, K.M.Boyko. Calcium Indicators with Fluorescence Lifetime-Based Signal Readout: A Structure-Function Study Int J Mol Sci V. 25 2024.
ISSN: ESSN 1422-0067
DOI: 10.3390/IJMS252312493