Calcium in PDB 3wlc: Crystal Structure of Dimeric GCAMP6M

The structure of Crystal Structure of Dimeric GCAMP6M, PDB code: 3wlc 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)	20.08 / 2.49
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	124.440, 46.860, 68.340, 90.00, 99.36, 90.00
R / Rfree (%)	17.7 / 22.5

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

Calcium binding site 1 out of 4 in the Crystal Structure of Dimeric 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 Dimeric GCAMP6M within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:12.4 occ:1.00 O A:TYR401 2.3 15.3 1.0 OD1 A:ASP397 2.3 17.5 1.0 OD1 A:ASN399 2.4 18.5 1.0 OD1 A:ASP395 2.4 15.7 1.0 OE1 A:GLU406 2.5 9.6 1.0 OE2 A:GLU406 2.6 12.7 1.0 O A:HOH623 2.7 21.7 1.0 CD A:GLU406 2.8 13.0 1.0 CG A:ASP397 3.1 19.9 1.0 CG A:ASN399 3.2 16.6 1.0 OD2 A:ASP397 3.3 9.9 1.0 C A:TYR401 3.6 12.4 1.0 CG A:ASP395 3.7 14.0 1.0 ND2 A:ASN399 3.9 8.7 1.0 N A:ASN399 4.3 13.5 1.0 CB A:ASN399 4.3 10.4 1.0 N A:TYR401 4.3 12.8 1.0 CG A:GLU406 4.3 7.4 1.0 N A:ASP397 4.3 19.3 1.0 OD2 A:ASP395 4.4 11.7 1.0 CA A:TYR401 4.4 12.2 1.0 CB A:ASP397 4.5 13.7 1.0 N A:ILE402 4.5 11.2 1.0 CA A:ASP395 4.5 15.2 1.0 CA A:ILE402 4.5 9.6 1.0 N A:SER403 4.5 14.0 1.0 CB A:ASP395 4.6 11.7 1.0 N A:LYS396 4.7 12.7 1.0 N A:GLY398 4.7 14.9 1.0 C A:ASP395 4.7 13.8 1.0 CA A:ASN399 4.7 8.8 1.0 OE1 A:GLN437 4.7 22.3 1.0 CA A:ASP397 4.8 19.6 1.0 O A:HOH636 4.8 13.7 1.0 CB A:TYR401 4.9 11.3 1.0 N A:GLY400 5.0 9.9 1.0 C A:ASP397 5.0 18.7 1.0 C A:ILE402 5.0 9.8 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Dimeric 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 Dimeric GCAMP6M within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:10.4 occ:1.00 OD1 A:ASP435 2.3 16.0 1.0 OD1 A:ASP433 2.4 10.2 1.0 O A:GLN437 2.4 9.6 1.0 OD1 A:ASP431 2.5 13.5 1.0 O A:HOH613 2.5 13.5 1.0 OE1 A:GLU442 2.5 11.8 1.0 OE2 A:GLU442 2.6 13.7 1.0 CD A:GLU442 2.9 14.4 1.0 CG A:ASP433 3.3 11.4 1.0 CG A:ASP435 3.3 14.8 1.0 C A:GLN437 3.5 8.8 1.0 CG A:ASP431 3.6 12.7 1.0 OD2 A:ASP433 3.6 15.0 1.0 OD2 A:ASP435 3.8 12.6 1.0 CA A:ASP431 4.2 13.8 1.0 N A:ASP435 4.2 7.2 1.0 CA A:VAL438 4.2 9.2 1.0 N A:VAL438 4.3 6.6 1.0 N A:ASN439 4.3 9.8 1.0 N A:ASP433 4.3 13.0 1.0 N A:GLN437 4.3 10.0 1.0 OD2 A:ASP431 4.4 12.3 1.0 CB A:ASP431 4.4 10.4 1.0 N A:ILE432 4.4 11.2 1.0 CB A:ASP435 4.4 10.1 1.0 CG A:GLU442 4.4 12.7 1.0 N A:GLY434 4.5 9.8 1.0 CA A:GLN437 4.5 7.6 1.0 C A:ASP431 4.6 11.0 1.0 CB A:ASP433 4.6 6.5 1.0 C A:VAL438 4.7 8.1 1.0 CA A:ASP435 4.8 9.7 1.0 CA A:ASP433 4.8 10.1 1.0 CG A:ASN439 4.8 10.6 1.0 ND2 A:ASN439 4.9 14.8 1.0 N A:GLY436 4.9 9.2 1.0 C A:ASP433 4.9 13.7 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Dimeric 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 Dimeric GCAMP6M within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:35.2 occ:1.00 OD1 A:ASP358 2.3 27.3 1.0 OD1 A:ASP362 2.4 33.4 1.0 OE1 A:GLU369 2.4 41.8 1.0 OE2 A:GLU369 2.5 29.8 1.0 OD1 A:ASP360 2.5 47.0 1.0 O A:THR364 2.6 25.0 1.0 CD A:GLU369 2.8 28.6 1.0 OD2 A:ASP362 2.8 34.6 1.0 CG A:ASP362 2.8 39.1 1.0 CG A:ASP358 3.4 30.0 1.0 CG A:ASP360 3.5 47.8 1.0 C A:THR364 3.6 29.0 1.0 OD2 A:ASP360 3.8 44.4 1.0 N A:ASP362 4.0 32.8 1.0 CB A:ASP362 4.2 31.1 1.0 OD2 A:ASP358 4.2 36.2 1.0 CG A:GLU369 4.3 31.6 1.0 CA A:ASP358 4.3 28.5 1.0 OG1 A:THR364 4.3 30.0 1.0 N A:GLY361 4.3 29.7 1.0 N A:THR364 4.3 29.4 1.0 CA A:ILE365 4.3 24.5 1.0 CB A:ASP358 4.4 30.1 1.0 N A:ILE365 4.4 27.0 1.0 OD2 A:ASP366 4.4 32.4 1.0 N A:ASP366 4.5 27.7 1.0 CA A:ASP362 4.5 31.0 1.0 CA A:THR364 4.5 27.5 1.0 N A:ASP360 4.6 38.0 1.0 C A:ASP358 4.6 28.7 1.0 CB A:ASP360 4.7 46.7 1.0 C A:GLY361 4.7 34.2 1.0 N A:ALA359 4.8 27.4 1.0 C A:ASP360 4.8 37.1 1.0 CG A:ASP366 4.8 29.6 1.0 N A:GLY363 4.9 34.4 1.0 C A:ASP362 4.9 30.7 1.0 CA A:GLY361 4.9 36.4 1.0 CA A:ASP360 4.9 45.0 1.0 C A:ILE365 4.9 27.6 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Dimeric 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 Dimeric GCAMP6M within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:18.7 occ:1.00 OD1 A:ASP326 2.4 23.9 1.0 O A:THR328 2.4 16.0 1.0 OD1 A:ASP324 2.4 18.9 1.0 OD1 A:ASP322 2.4 19.5 1.0 OE2 A:GLU333 2.4 15.9 1.0 O A:HOH617 2.5 14.0 1.0 OE1 A:GLU333 2.5 17.7 1.0 CD A:GLU333 2.8 15.7 1.0 CG A:ASP326 3.3 18.4 1.0 CG A:ASP324 3.4 17.2 1.0 C A:THR328 3.6 21.1 1.0 OD2 A:ASP324 3.7 17.2 1.0 CG A:ASP322 3.7 16.8 1.0 OD2 A:ASP326 3.9 23.2 1.0 N A:ASP326 4.2 17.8 1.0 CG A:GLU333 4.3 20.0 1.0 N A:ASP324 4.3 10.2 1.0 CA A:ASP322 4.3 15.2 1.0 N A:THR328 4.3 20.3 1.0 N A:LYS323 4.4 15.9 1.0 CB A:ASP326 4.4 12.4 1.0 N A:GLY325 4.5 15.5 1.0 CG2 A:THR328 4.5 14.8 1.0 C A:ASP322 4.5 17.7 1.0 OD2 A:ASP322 4.5 14.8 1.0 CB A:ASP322 4.5 15.0 1.0 CA A:THR328 4.5 20.0 1.0 N A:ILE329 4.6 20.4 1.0 CA A:ILE329 4.6 20.9 1.0 CB A:ASP324 4.6 13.3 1.0 CA A:ASP326 4.8 14.3 1.0 N A:THR330 4.8 16.3 1.0 CA A:ASP324 4.8 13.2 1.0 CG2 A:THR330 4.8 13.2 1.0 O A:HOH712 4.9 29.5 1.0 N A:GLY327 4.9 18.9 1.0 C A:ASP324 5.0 16.3 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