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Calcium in PDB 3sg3: Crystal Structure of GCAMP3-D380Y

Protein crystallography data

The structure of Crystal Structure of GCAMP3-D380Y, PDB code: 3sg3 was solved by E.R.Schreiter, J.Akerboom, L.L.Looger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.80 / 2.10
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 120.444, 120.444, 98.000, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 19.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of GCAMP3-D380Y (pdb code 3sg3). 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 GCAMP3-D380Y, PDB code: 3sg3:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3sg3

Go back to Calcium Binding Sites List in 3sg3
Calcium binding site 1 out of 4 in the Crystal Structure of GCAMP3-D380Y


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 GCAMP3-D380Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca451

b:17.9
occ:1.00
OD1 A:ASP322 2.2 19.1 1.0
O A:HOH494 2.3 25.5 1.0
O A:THR328 2.3 19.7 1.0
OD1 A:ASP326 2.4 17.0 1.0
OD1 A:ASP324 2.4 21.5 1.0
OE1 A:GLU333 2.5 22.4 1.0
OE2 A:GLU333 2.5 22.5 1.0
CD A:GLU333 2.9 27.1 1.0
CG A:ASP326 3.3 18.4 1.0
CG A:ASP324 3.3 21.4 1.0
CG A:ASP322 3.4 18.0 1.0
C A:THR328 3.5 19.8 1.0
OD2 A:ASP324 3.7 19.0 1.0
OD2 A:ASP326 3.9 19.1 1.0
CA A:ASP322 4.1 20.9 1.0
N A:ASP326 4.2 19.1 1.0
N A:THR328 4.2 17.2 1.0
CB A:ASP322 4.2 19.3 1.0
OD2 A:ASP322 4.3 17.6 1.0
O A:HOH543 4.3 29.0 1.0
N A:ASP324 4.3 20.3 1.0
C A:ASP322 4.4 22.2 1.0
CB A:ASP326 4.4 18.3 1.0
CG A:GLU333 4.4 23.6 1.0
CA A:THR328 4.4 20.2 1.0
N A:ILE329 4.4 17.2 1.0
CA A:ILE329 4.5 18.1 1.0
N A:LYS323 4.6 24.1 1.0
CB A:ASP324 4.6 21.8 1.0
CA A:ASP326 4.6 17.4 1.0
CG2 A:THR328 4.6 19.6 1.0
N A:GLY325 4.7 21.2 1.0
O A:HOH528 4.8 24.9 1.0
CA A:ASP324 4.8 20.6 1.0
N A:GLY327 4.8 16.5 1.0
C A:ASP324 4.9 19.1 1.0
C A:ASP326 4.9 17.3 1.0
O A:ASP322 4.9 22.1 1.0
N A:THR330 4.9 18.5 1.0
O A:HOH554 4.9 31.5 1.0

Calcium binding site 2 out of 4 in 3sg3

Go back to Calcium Binding Sites List in 3sg3
Calcium binding site 2 out of 4 in the Crystal Structure of GCAMP3-D380Y


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 GCAMP3-D380Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca452

b:20.3
occ:1.00
OD2 A:ASP358 2.2 18.7 1.0
O A:HOH714 2.3 26.2 1.0
OD1 A:ASP362 2.3 23.4 1.0
O A:THR364 2.4 18.4 1.0
OE1 A:GLU369 2.4 18.8 1.0
OD1 A:ASP360 2.4 23.6 1.0
OE2 A:GLU369 2.6 19.6 1.0
CD A:GLU369 2.9 18.3 1.0
CG A:ASP362 3.3 27.6 1.0
CG A:ASP360 3.3 24.3 1.0
CG A:ASP358 3.4 21.7 1.0
C A:THR364 3.5 18.7 1.0
OD2 A:ASP360 3.7 28.0 1.0
OD2 A:ASP362 3.8 26.7 1.0
OG1 A:THR364 4.1 19.3 1.0
N A:THR364 4.1 19.4 1.0
OD1 A:ASP358 4.2 17.7 1.0
N A:ASP362 4.2 24.8 1.0
N A:ASP360 4.3 25.3 1.0
CA A:ASP358 4.3 19.9 1.0
N A:ASP366 4.3 18.5 1.0
CA A:THR364 4.3 19.2 1.0
CB A:ASP358 4.4 19.1 1.0
CG A:GLU369 4.4 18.6 1.0
CB A:ASP362 4.4 27.1 1.0
N A:ILE365 4.5 19.0 1.0
CA A:ILE365 4.5 17.1 1.0
N A:GLY361 4.5 25.4 1.0
C A:ASP358 4.5 20.6 1.0
CB A:ASP360 4.6 26.0 1.0
OD2 A:ASP366 4.6 30.8 1.0
N A:GLY363 4.7 24.6 1.0
N A:ALA359 4.7 20.8 1.0
CG A:ASP366 4.7 27.8 1.0
CA A:ASP362 4.7 26.9 1.0
CA A:ASP360 4.8 25.7 1.0
O A:HOH578 4.8 31.8 1.0
CB A:THR364 4.9 21.0 1.0
C A:ILE365 4.9 19.5 1.0
C A:ASP362 4.9 28.7 1.0
C A:ASP360 4.9 28.1 1.0
CB A:ASP366 5.0 22.4 1.0

Calcium binding site 3 out of 4 in 3sg3

Go back to Calcium Binding Sites List in 3sg3
Calcium binding site 3 out of 4 in the Crystal Structure of GCAMP3-D380Y


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 GCAMP3-D380Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca453

b:41.0
occ:1.00
OD1 A:ASN399 2.2 45.4 1.0
O A:TYR401 2.2 40.0 1.0
OE1 A:GLU406 2.3 34.3 1.0
OE2 A:GLU406 2.4 36.0 1.0
OD2 A:ASP395 2.5 38.2 1.0
O A:HOH655 2.5 38.7 1.0
OD2 A:ASP397 2.5 57.7 1.0
CD A:GLU406 2.7 34.5 1.0
CG A:ASP397 3.1 61.3 1.0
OD1 A:ASP397 3.2 62.3 1.0
CG A:ASN399 3.4 49.2 1.0
C A:TYR401 3.4 37.4 1.0
CG A:ASP395 3.6 43.1 1.0
N A:TYR401 4.1 37.2 1.0
CG A:GLU406 4.2 38.0 1.0
ND2 A:ASN399 4.2 55.7 1.0
CA A:TYR401 4.3 37.2 1.0
N A:ASP397 4.3 55.6 1.0
O A:HOH674 4.3 45.7 1.0
CA A:ASP395 4.3 38.6 1.0
N A:ASN399 4.3 38.9 1.0
CB A:ASN399 4.3 48.6 1.0
N A:ILE402 4.4 38.5 1.0
CB A:ASP397 4.4 56.2 1.0
C A:ASP395 4.5 39.7 1.0
OD1 A:ASP395 4.5 37.8 1.0
CB A:ASP395 4.5 40.0 1.0
CA A:ILE402 4.5 41.5 1.0
N A:SER403 4.6 45.6 1.0
N A:GLY398 4.6 45.4 1.0
CB A:TYR401 4.7 39.5 1.0
N A:LYS396 4.7 39.4 1.0
CA A:ASP397 4.7 55.4 1.0
N A:GLY400 4.7 42.0 1.0
CA A:ASN399 4.8 42.6 1.0
O A:ASP395 4.8 39.8 1.0
C A:ASP397 4.8 48.8 1.0
C A:ILE402 5.0 40.4 1.0

Calcium binding site 4 out of 4 in 3sg3

Go back to Calcium Binding Sites List in 3sg3
Calcium binding site 4 out of 4 in the Crystal Structure of GCAMP3-D380Y


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 GCAMP3-D380Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca454

b:45.3
occ:1.00
O A:HOH576 2.2 43.3 1.0
OD1 A:ASP431 2.2 40.7 1.0
OD1 A:ASP435 2.4 46.6 1.0
O A:GLN437 2.4 40.3 1.0
OE2 A:GLU442 2.4 55.2 1.0
OE1 A:GLU442 2.6 53.5 1.0
OD2 A:ASP433 2.6 47.9 1.0
CD A:GLU442 2.8 56.8 1.0
CG A:ASP431 3.3 41.7 1.0
CG A:ASP433 3.3 46.6 1.0
CG A:ASP435 3.3 53.9 1.0
C A:GLN437 3.5 39.1 1.0
OD1 A:ASP433 3.5 42.3 1.0
OD2 A:ASP435 3.8 49.7 1.0
OD2 A:ASP431 4.0 47.3 1.0
N A:ASP435 4.0 43.2 1.0
CA A:ASP431 4.1 51.3 1.0
N A:GLN437 4.1 42.0 1.0
CB A:ASP431 4.2 47.4 1.0
N A:ASP433 4.3 56.0 1.0
CG A:GLU442 4.3 56.8 1.0
CA A:GLN437 4.4 40.7 1.0
CA A:VAL438 4.4 39.1 1.0
N A:VAL438 4.4 39.4 1.0
CB A:ASP435 4.4 49.4 1.0
N A:GLY434 4.5 56.5 1.0
N A:ASN439 4.5 38.0 1.0
N A:ILE432 4.5 54.0 1.0
CB A:ASP433 4.5 46.8 1.0
C A:ASP431 4.5 51.0 1.0
C A:ASP433 4.6 52.2 1.0
CA A:ASP435 4.6 42.3 1.0
CA A:ASP433 4.7 52.9 1.0
N A:GLY436 4.7 41.7 1.0
C A:VAL438 4.9 31.8 1.0
CB A:GLN437 4.9 41.6 1.0
C A:ASP435 4.9 45.9 1.0

Reference:

J.Akerboom, T.W.Chen, T.J.Wardill, L.Tian, J.S.Marvin, S.Mutlu, N.C.Calderon, F.Esposti, B.G.Borghuis, X.R.Sun, A.Gordus, M.B.Orger, R.Portugues, F.Engert, J.J.Macklin, A.Filosa, A.Aggarwal, R.A.Kerr, R.Takagi, S.Kracun, E.Shigetomi, B.S.Khakh, H.Baier, L.Lagnado, S.S.Wang, C.I.Bargmann, B.E.Kimmel, V.Jayaraman, K.Svoboda, D.S.Kim, E.R.Schreiter, L.L.Looger. Optimization of A Gcamp Calcium Indicator For Neural Activity Imaging. J.Neurosci. V. 32 13819 2012.
ISSN: ISSN 0270-6474
PubMed: 23035093
DOI: 10.1523/JNEUROSCI.2601-12.2012
Page generated: Sat Dec 12 04:29:53 2020

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