Calcium in PDB 9k8x: Crystal Structure of the Calcium Indicator GCAMP6S-Brus-145 in Calcium-Bounded State

The structure of Crystal Structure of the Calcium Indicator GCAMP6S-Brus-145 in Calcium-Bounded State, PDB code: 9k8x was solved by L.A.Varfolomeeva, T.R.Simonyan, A.V.Mamontova, V.O.Popov, A.M.Bogdanov, K.M.Boyko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.01 / 2.05
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	118.293, 118.293, 98.703, 90, 90, 90
R / Rfree (%)	21.1 / 25.1

The structure of Crystal Structure of the Calcium Indicator GCAMP6S-Brus-145 in Calcium-Bounded State also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Crystal Structure of the Calcium Indicator GCAMP6S-Brus-145 in Calcium-Bounded State (pdb code 9k8x). 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-145 in Calcium-Bounded State, PDB code: 9k8x:
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-145 in Calcium-Bounded 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-145 in Calcium-Bounded State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca507 b:22.5 occ:1.00 O A:HOH710 2.2 24.8 1.0 OD1 A:ASP334 2.3 22.4 1.0 OD1 A:ASP338 2.3 23.4 1.0 OD1 A:ASP336 2.3 22.8 1.0 O A:THR340 2.4 19.5 1.0 OE2 A:GLU345 2.5 25.3 1.0 OE1 A:GLU345 2.6 22.4 1.0 CD A:GLU345 2.9 27.5 1.0 CG A:ASP338 3.3 28.0 1.0 CG A:ASP336 3.3 23.1 1.0 CG A:ASP334 3.4 20.7 1.0 C A:THR340 3.6 20.1 1.0 OD2 A:ASP336 3.7 23.9 1.0 OD2 A:ASP338 3.9 27.4 1.0 N A:ASP338 4.1 21.6 1.0 N A:THR340 4.1 19.4 1.0 CA A:ASP334 4.1 22.6 1.0 CB A:ASP334 4.2 19.5 1.0 CB A:ASP338 4.3 24.8 1.0 N A:ASP336 4.3 23.7 1.0 OD2 A:ASP334 4.3 21.0 1.0 CG A:GLU345 4.4 23.7 1.0 CA A:THR340 4.5 20.7 1.0 C A:ASP334 4.5 25.5 1.0 CG2 A:THR340 4.5 22.1 1.0 N A:ILE341 4.6 17.8 1.0 CA A:ILE341 4.6 21.1 1.0 CA A:ASP338 4.6 21.3 1.0 CB A:ASP336 4.6 24.9 1.0 N A:GLY339 4.7 20.0 1.0 N A:GLY337 4.7 22.1 1.0 N A:LYS335 4.7 26.0 1.0 CA A:ASP336 4.8 24.2 1.0 O A:HOH726 4.9 32.6 1.0 C A:ASP338 4.9 21.9 1.0 O A:HOH630 4.9 34.8 1.0 CG2 A:THR342 4.9 24.1 1.0 N A:THR342 4.9 20.1 1.0 C A:ASP336 4.9 23.0 1.0 O A:ASP334 5.0 25.4 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the Calcium Indicator GCAMP6S-Brus-145 in Calcium-Bounded 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-145 in Calcium-Bounded State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca508 b:23.8 occ:1.00 OD1 A:ASP370 2.2 22.2 1.0 OD1 A:ASP372 2.3 25.8 1.0 OD1 A:ASP374 2.3 22.8 1.0 OD2 A:ASP378 2.3 18.0 0.7 O A:THR376 2.4 20.0 1.0 OE1 A:GLU381 2.4 20.4 1.0 OE2 A:GLU381 2.7 21.3 1.0 CD A:GLU381 2.9 20.4 1.0 CG A:ASP374 3.2 26.3 1.0 CG A:ASP372 3.3 29.1 1.0 CG A:ASP370 3.4 22.9 1.0 C A:THR376 3.5 18.7 1.0 CG A:ASP378 3.6 21.3 0.7 OD2 A:ASP374 3.7 30.1 1.0 OD2 A:ASP372 3.8 31.4 1.0 N A:THR376 4.0 20.7 1.0 OG1 A:THR376 4.1 19.0 1.0 N A:ASP378 4.1 18.5 1.0 OD2 A:ASP370 4.1 26.5 1.0 N A:ASP374 4.2 22.1 1.0 CB A:ASP370 4.3 23.2 1.0 CA A:ASP370 4.3 22.2 1.0 CB A:ASP374 4.3 25.4 1.0 CB A:ASP378 4.3 18.6 0.7 CA A:THR376 4.3 18.7 1.0 CG A:ASP378 4.4 18.1 0.3 CG A:GLU381 4.4 21.7 1.0 N A:ASP372 4.4 28.2 1.0 CB A:ASP378 4.4 17.8 0.3 OD2 A:ASP378 4.5 17.9 0.3 N A:ILE377 4.5 17.6 1.0 CA A:ILE377 4.6 20.4 1.0 OD1 A:ASP378 4.6 24.0 0.7 CB A:ASP372 4.6 27.7 1.0 C A:ASP370 4.6 22.2 1.0 N A:GLY373 4.6 24.4 1.0 CA A:ASP374 4.7 20.9 1.0 N A:ALA371 4.7 26.7 1.0 N A:GLY375 4.7 21.8 1.0 OD1 A:ASP378 4.8 18.6 0.3 C A:ILE377 4.8 21.1 1.0 CA A:ASP372 4.9 27.0 1.0 O A:HOH697 4.9 12.3 0.5 CB A:THR376 4.9 18.9 1.0 CA A:ASP378 4.9 20.2 1.0 C A:ASP372 4.9 26.0 1.0 C A:ASP374 4.9 23.4 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the Calcium Indicator GCAMP6S-Brus-145 in Calcium-Bounded 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-145 in Calcium-Bounded State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca509 b:35.8 occ:0.80 O A:TYR413 2.2 47.2 1.0 OE2 A:GLU418 2.3 40.4 1.0 OD1 A:ASP409 2.3 50.3 1.0 OE1 A:GLU418 2.3 43.1 1.0 OD1 A:ASN411 2.4 45.8 1.0 OD1 A:ASP407 2.4 48.6 1.0 O A:HOH616 2.6 30.9 0.8 CD A:GLU418 2.6 38.0 1.0 CG A:ASP409 3.1 58.0 1.0 OD2 A:ASP409 3.4 56.8 1.0 C A:TYR413 3.4 43.6 1.0 CG A:ASN411 3.4 51.9 1.0 CG A:ASP407 3.5 49.9 1.0 ND2 A:ASN411 4.1 46.8 1.0 N A:TYR413 4.2 39.8 1.0 CA A:ASP407 4.2 41.4 1.0 CG A:GLU418 4.2 36.0 1.0 N A:ASN411 4.2 42.4 1.0 N A:ASP409 4.2 47.1 1.0 CA A:TYR413 4.3 41.1 1.0 CB A:ASP407 4.3 39.9 1.0 OD2 A:ASP407 4.3 42.9 1.0 CB A:ASP409 4.3 55.7 1.0 N A:ILE414 4.4 40.8 1.0 C A:ASP407 4.4 40.6 1.0 N A:GLY410 4.4 46.0 1.0 CB A:ASN411 4.5 46.2 1.0 CA A:ILE414 4.6 37.6 1.0 CA A:ASP409 4.6 51.3 1.0 N A:LYS408 4.6 43.0 1.0 CB A:TYR413 4.7 40.1 1.0 O A:ASP407 4.8 41.9 1.0 CA A:ASN411 4.8 47.5 1.0 N A:SER415 4.8 41.1 1.0 C A:ASP409 4.8 47.6 1.0 N A:GLY412 4.9 41.8 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the Calcium Indicator GCAMP6S-Brus-145 in Calcium-Bounded 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-145 in Calcium-Bounded State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca510 b:41.5 occ:0.80 OD1 A:ASP443 2.2 46.8 1.0 O A:HOH663 2.2 40.4 0.8 O A:GLN449 2.3 51.3 1.0 OD1 A:ASP447 2.4 54.8 1.0 OD1 A:ASP445 2.5 57.0 1.0 OE1 A:GLU454 2.5 47.6 1.0 OE2 A:GLU454 2.5 62.1 1.0 CD A:GLU454 2.8 58.2 1.0 CG A:ASP447 3.2 50.1 1.0 CG A:ASP443 3.3 52.1 1.0 C A:GLN449 3.4 49.6 1.0 CG A:ASP445 3.4 58.5 1.0 OD2 A:ASP447 3.6 45.4 1.0 OD2 A:ASP445 3.9 56.1 1.0 OD2 A:ASP443 4.0 54.6 1.0 ND2 A:ASN451 4.1 79.8 1.0 N A:ASP447 4.2 55.1 1.0 N A:VAL450 4.2 47.1 1.0 N A:GLN449 4.3 44.0 1.0 CB A:ASP443 4.3 60.9 1.0 CG A:GLU454 4.3 57.0 1.0 CA A:ASP443 4.3 58.7 1.0 CA A:GLN449 4.3 50.4 1.0 CB A:ASP447 4.3 50.3 1.0 CA A:VAL450 4.3 41.8 1.0 N A:ASP445 4.3 62.4 1.0 N A:ASN451 4.4 41.3 1.0 N A:ILE444 4.5 60.7 1.0 N A:GLY446 4.6 59.6 1.0 CB A:ASP445 4.6 62.4 1.0 CA A:ASP447 4.7 53.8 1.0 C A:ASP443 4.7 61.6 1.0 CA A:ASP445 4.8 62.1 1.0 CB A:GLN449 4.8 51.7 1.0 C A:VAL450 4.8 42.5 1.0 CG A:ASN451 4.9 64.8 1.0 C A:ASP445 4.9 64.1 1.0 N A:GLY448 4.9 51.0 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