Calcium in PDB 3wld: Crystal Structure of Monomeric GCAMP6M

The structure of Crystal Structure of Monomeric GCAMP6M, PDB code: 3wld was solved by J.Ding, A.F.Luo, L.Y.Hu, D.C.Wang, F.Shao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.06 / 2.70
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	120.880, 120.880, 97.620, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 21.2

The binding sites of Calcium atom in the Crystal Structure of Monomeric GCAMP6M (pdb code 3wld). 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 Monomeric GCAMP6M, PDB code: 3wld:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Monomeric GCAMP6M


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 Monomeric GCAMP6M within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:36.0 occ:1.00 O A:TYR401 2.2 29.9 1.0 OD1 A:ASP397 2.2 48.9 1.0 OE1 A:GLU406 2.4 30.0 1.0 OE2 A:GLU406 2.5 29.8 1.0 OD1 A:ASP395 2.5 40.2 1.0 OD1 A:ASN399 2.5 43.1 1.0 CD A:GLU406 2.7 32.4 1.0 O A:HOH663 2.9 31.9 1.0 CG A:ASP397 3.0 49.8 1.0 CG A:ASN399 3.1 49.2 1.0 OD2 A:ASP397 3.3 44.0 1.0 C A:TYR401 3.5 34.5 1.0 ND2 A:ASN399 3.5 54.4 1.0 CG A:ASP395 3.7 34.3 1.0 CG A:GLU406 4.2 33.8 1.0 N A:TYR401 4.2 32.0 1.0 CB A:ASN399 4.2 47.0 1.0 CA A:ASP395 4.3 30.6 1.0 CA A:TYR401 4.3 39.1 1.0 CB A:ASP397 4.3 34.1 1.0 N A:ASP397 4.4 47.0 1.0 N A:ILE402 4.4 34.5 1.0 N A:ASN399 4.4 42.6 1.0 N A:SER403 4.4 35.6 1.0 CA A:ILE402 4.4 34.4 1.0 C A:ASP395 4.5 38.9 1.0 OD2 A:ASP395 4.6 34.2 1.0 CB A:ASP395 4.6 35.8 1.0 N A:GLY398 4.7 41.8 1.0 N A:LYS396 4.7 39.4 1.0 OG A:SER403 4.7 45.7 1.0 CA A:ASP397 4.8 43.0 1.0 CA A:ASN399 4.8 40.4 1.0 CB A:TYR401 4.8 34.2 1.0 C A:ILE402 4.9 32.1 1.0 N A:GLY400 5.0 36.8 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Monomeric GCAMP6M


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 Monomeric GCAMP6M within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:51.5 occ:1.00 OD1 A:ASP435 2.3 51.6 1.0 OD1 A:ASP431 2.4 48.0 1.0 OD1 A:ASP433 2.4 65.8 1.0 O A:GLN437 2.4 46.3 1.0 O A:HOH674 2.4 39.9 1.0 OE1 A:GLU442 2.6 54.8 1.0 OE2 A:GLU442 2.6 51.9 1.0 CD A:GLU442 3.0 62.0 1.0 CG A:ASP433 3.3 67.3 1.0 CG A:ASP435 3.3 59.2 1.0 CG A:ASP431 3.4 51.2 1.0 C A:GLN437 3.5 41.5 1.0 OD2 A:ASP433 3.7 64.1 1.0 OD2 A:ASP431 3.9 46.2 1.0 N A:ASP435 4.0 51.5 1.0 OD2 A:ASP435 4.1 55.4 1.0 N A:GLY434 4.1 60.2 1.0 N A:GLN437 4.2 50.5 1.0 N A:ASP433 4.2 72.0 1.0 CB A:ASP435 4.3 47.2 1.0 N A:ILE432 4.4 62.6 1.0 N A:VAL438 4.4 39.9 1.0 CA A:ASP431 4.4 58.4 1.0 CA A:VAL438 4.4 43.1 1.0 CA A:GLN437 4.4 42.0 1.0 CB A:ASP431 4.4 56.0 1.0 CG A:GLU442 4.5 71.2 1.0 CA A:ASP435 4.6 32.3 1.0 CB A:ASP433 4.6 57.8 1.0 N A:ASN439 4.6 32.5 1.0 CA A:ASP433 4.7 56.5 1.0 N A:GLY436 4.7 49.2 1.0 ND2 A:ASN439 4.8 62.3 1.0 C A:ASP431 4.8 68.9 1.0 C A:ASP433 4.8 62.5 1.0 C A:GLY434 4.9 50.9 1.0 CG A:ASN439 4.9 56.4 1.0 CA A:GLY434 4.9 55.7 1.0 CB A:GLN437 4.9 36.3 1.0 C A:VAL438 4.9 37.0 1.0 C A:ASP435 5.0 39.1 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Monomeric GCAMP6M


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 Monomeric GCAMP6M within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:21.6 occ:1.00 OD1 A:ASP358 2.2 19.4 1.0 O A:HOH676 2.2 22.8 1.0 O A:THR364 2.3 20.5 1.0 OD1 A:ASP362 2.4 26.8 1.0 OD1 A:ASP360 2.4 31.0 1.0 OE1 A:GLU369 2.5 24.7 1.0 OE2 A:GLU369 2.6 23.1 1.0 CD A:GLU369 2.9 25.2 1.0 CG A:ASP360 3.2 37.0 1.0 CG A:ASP362 3.3 28.2 1.0 CG A:ASP358 3.4 21.8 1.0 C A:THR364 3.5 17.8 1.0 OD2 A:ASP360 3.5 31.0 1.0 OD2 A:ASP362 3.8 32.2 1.0 OD2 A:ASP366 4.1 51.5 1.0 N A:THR364 4.1 15.9 1.0 OG1 A:THR364 4.2 15.6 1.0 OD2 A:ASP358 4.2 14.6 1.0 N A:ASP366 4.2 13.2 1.0 N A:ASP362 4.2 21.5 1.0 CA A:ASP358 4.3 23.4 1.0 N A:ASP360 4.3 26.0 1.0 CB A:ASP362 4.3 19.7 1.0 CA A:THR364 4.3 21.5 1.0 CB A:ASP358 4.3 22.7 1.0 N A:ILE365 4.4 10.6 1.0 CG A:GLU369 4.4 15.7 1.0 CA A:ILE365 4.4 15.4 1.0 C A:ASP358 4.5 24.6 1.0 CG A:ASP366 4.5 39.2 1.0 CB A:ASP360 4.5 17.5 1.0 O A:HOH623 4.5 25.1 1.0 N A:ALA359 4.6 28.0 1.0 N A:GLY361 4.6 21.5 1.0 CA A:ASP362 4.7 24.5 1.0 N A:GLY363 4.7 19.2 1.0 CA A:ASP360 4.8 22.2 1.0 C A:ILE365 4.8 18.6 1.0 CB A:THR364 4.9 18.2 1.0 CB A:ASP366 4.9 18.8 1.0 C A:ASP360 5.0 22.5 1.0 C A:ASP362 5.0 18.6 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Monomeric GCAMP6M


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 Monomeric GCAMP6M within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:18.7 occ:1.00 OD1 A:ASP326 2.3 17.2 1.0 O A:THR328 2.3 17.4 1.0 O A:HOH675 2.4 30.6 1.0 OD1 A:ASP324 2.4 23.6 1.0 OD1 A:ASP322 2.5 15.6 1.0 OE1 A:GLU333 2.5 21.0 1.0 OE2 A:GLU333 2.6 26.8 1.0 CD A:GLU333 2.8 26.8 1.0 CG A:ASP326 3.3 22.5 1.0 CG A:ASP324 3.4 22.3 1.0 C A:THR328 3.5 14.1 1.0 OD2 A:ASP324 3.6 18.9 1.0 CG A:ASP322 3.6 18.7 1.0 OD2 A:ASP326 3.8 19.2 1.0 CA A:ASP322 4.2 22.9 1.0 N A:THR328 4.2 19.7 1.0 N A:ASP326 4.3 14.4 1.0 CG A:GLU333 4.3 15.6 1.0 CG2 A:THR328 4.3 17.8 1.0 CB A:ASP322 4.4 17.5 1.0 CB A:ASP326 4.4 18.1 1.0 CA A:THR328 4.4 16.2 1.0 N A:ILE329 4.5 15.5 1.0 OD2 A:ASP322 4.5 15.1 1.0 CA A:ILE329 4.5 10.0 1.0 C A:ASP322 4.6 26.2 1.0 N A:ASP324 4.7 19.1 1.0 CB A:ASP324 4.7 10.0 1.0 CA A:ASP326 4.7 14.9 1.0 N A:GLY325 4.8 12.2 1.0 N A:LYS323 4.8 20.2 1.0 O A:HOH649 4.8 30.6 1.0 N A:THR330 4.9 17.0 1.0 N A:GLY327 4.9 14.0 1.0

J.Ding, A.F.Luo, L.Hu, D.Wang, F.Shao. Structural Basis of the Ultrasensitive Calcium Indicator GCAMP6. Sci China Life Sci 2014.
ISSN: ESSN 1869-1889
PubMed: 24390420
DOI: 10.1007/S11427-013-4599-5