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Calcium in PDB 3ek8: Calcium-Saturated GCAMP2 T116V/G87R Mutant Monomer

Protein crystallography data

The structure of Calcium-Saturated GCAMP2 T116V/G87R Mutant Monomer, PDB code: 3ek8 was solved by J.Akerboom, J.D.Velez Rivera, L.L.Looger, E.R.Schreiter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.30 / 2.80
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 120.800, 120.800, 97.350, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 26.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Calcium-Saturated GCAMP2 T116V/G87R Mutant Monomer (pdb code 3ek8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Calcium-Saturated GCAMP2 T116V/G87R Mutant Monomer, PDB code: 3ek8:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3ek8

Go back to Calcium Binding Sites List in 3ek8
Calcium binding site 1 out of 4 in the Calcium-Saturated GCAMP2 T116V/G87R Mutant Monomer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Calcium-Saturated GCAMP2 T116V/G87R Mutant Monomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca452

b:28.8
occ:1.00
OD1 A:ASP327 2.3 23.4 1.0
OE2 A:GLU334 2.3 30.6 1.0
OD1 A:ASP325 2.4 28.8 1.0
OD1 A:ASP323 2.4 25.4 1.0
O A:THR329 2.5 24.0 1.0
OE1 A:GLU334 2.6 32.4 1.0
CD A:GLU334 2.7 31.3 1.0
CG A:ASP325 3.3 26.7 1.0
CG A:ASP327 3.3 23.6 1.0
OD2 A:ASP325 3.5 26.9 1.0
CG A:ASP323 3.6 26.9 1.0
C A:THR329 3.7 24.0 1.0
OD2 A:ASP327 3.9 23.8 1.0
CG A:GLU334 4.2 30.0 1.0
CB A:ASP327 4.3 23.3 1.0
CA A:ASP323 4.3 28.4 1.0
N A:ASP327 4.3 23.4 1.0
N A:THR329 4.4 23.8 1.0
CB A:ASP323 4.4 28.1 1.0
N A:ASP325 4.5 26.8 1.0
OD2 A:ASP323 4.6 26.6 1.0
CB A:ASP325 4.6 26.0 1.0
C A:ASP323 4.6 28.6 1.0
N A:ILE330 4.6 24.1 1.0
CA A:ILE330 4.6 24.4 1.0
CA A:THR329 4.6 24.0 1.0
CA A:ASP327 4.7 23.1 1.0
N A:GLY326 4.8 25.3 1.0
N A:LYS324 4.8 28.2 1.0
N A:THR331 4.8 25.6 1.0
CG2 A:THR329 4.8 23.8 1.0
CA A:ASP325 4.9 26.1 1.0
N A:GLY328 4.9 22.9 1.0
C A:ASP327 4.9 23.0 1.0

Calcium binding site 2 out of 4 in 3ek8

Go back to Calcium Binding Sites List in 3ek8
Calcium binding site 2 out of 4 in the Calcium-Saturated GCAMP2 T116V/G87R Mutant Monomer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Calcium-Saturated GCAMP2 T116V/G87R Mutant Monomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca453

b:29.0
occ:1.00
OE1 A:GLU370 2.3 25.9 1.0
OD2 A:ASP359 2.3 26.2 1.0
O A:THR365 2.4 24.4 1.0
OD1 A:ASP361 2.4 29.9 1.0
OE2 A:GLU370 2.5 27.1 1.0
OD1 A:ASP367 2.5 29.9 1.0
OD1 A:ASN363 2.6 28.5 1.0
CD A:GLU370 2.7 26.4 1.0
CG A:ASP361 3.2 29.2 1.0
CG A:ASN363 3.2 26.6 1.0
CG A:ASP359 3.5 25.4 1.0
OD2 A:ASP361 3.5 31.3 1.0
ND2 A:ASN363 3.6 26.0 1.0
C A:THR365 3.6 24.4 1.0
CG A:ASP367 3.8 29.1 1.0
N A:ASP367 4.1 25.4 1.0
N A:ASN363 4.1 26.1 1.0
CG A:GLU370 4.3 25.2 1.0
N A:ASP361 4.3 26.7 1.0
CA A:ASP359 4.3 25.3 1.0
OD1 A:ASP359 4.3 26.3 1.0
N A:THR365 4.4 24.1 1.0
CB A:ASN363 4.4 25.9 1.0
OG1 A:THR365 4.4 23.1 1.0
CB A:ASP359 4.4 25.2 1.0
CB A:ASP367 4.4 26.5 1.0
CB A:ASP361 4.5 27.2 1.0
N A:GLY362 4.5 26.6 1.0
C A:ASP359 4.5 25.8 1.0
N A:ALA360 4.5 26.4 1.0
N A:ILE366 4.6 24.1 1.0
CA A:ILE366 4.6 24.2 1.0
CA A:THR365 4.6 24.1 1.0
CA A:ASN363 4.7 25.9 1.0
CA A:ASP361 4.7 27.1 1.0
OD2 A:ASP367 4.7 31.7 1.0
C A:ILE366 4.8 24.8 1.0
C A:ASP361 4.8 26.8 1.0
N A:GLY364 4.8 25.3 1.0
CA A:ASP367 4.9 25.9 1.0
C A:ASN363 4.9 25.6 1.0

Calcium binding site 3 out of 4 in 3ek8

Go back to Calcium Binding Sites List in 3ek8
Calcium binding site 3 out of 4 in the Calcium-Saturated GCAMP2 T116V/G87R Mutant Monomer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Calcium-Saturated GCAMP2 T116V/G87R Mutant Monomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca454

b:47.7
occ:1.00
O A:TYR402 2.3 55.3 1.0
OD1 A:ASN400 2.3 57.7 1.0
OE1 A:GLU407 2.4 62.7 1.0
OE2 A:GLU407 2.5 61.7 1.0
OD2 A:ASP396 2.5 57.4 1.0
OD2 A:ASP398 2.7 59.8 1.0
CD A:GLU407 2.7 64.9 1.0
CG A:ASN400 3.2 57.4 1.0
CG A:ASP398 3.3 58.6 1.0
OD1 A:ASP398 3.3 59.0 1.0
C A:TYR402 3.5 55.6 1.0
CG A:ASP396 3.6 55.3 1.0
ND2 A:ASN400 4.0 56.7 1.0
CA A:ASP396 4.1 54.3 1.0
CB A:ASN400 4.2 57.1 1.0
CG A:GLU407 4.2 65.4 1.0
N A:ASN400 4.2 56.8 1.0
N A:TYR402 4.3 55.3 1.0
C A:ASP396 4.4 54.6 1.0
CB A:ASP396 4.4 54.5 1.0
CA A:TYR402 4.4 55.2 1.0
OD1 A:ASP396 4.4 55.3 1.0
N A:GLY399 4.4 57.0 1.0
N A:SER404 4.5 58.9 1.0
N A:ILE403 4.5 56.1 1.0
N A:ASP398 4.5 57.4 1.0
CA A:ILE403 4.6 56.8 1.0
N A:LYS397 4.7 55.4 1.0
CB A:ASP398 4.7 57.7 1.0
CA A:ASN400 4.7 56.8 1.0
O A:ASP396 4.8 54.7 1.0
CB A:TYR402 4.9 54.8 1.0
N A:GLY401 4.9 56.2 1.0
CA A:ASP398 5.0 57.5 1.0
CB A:SER404 5.0 60.0 1.0

Calcium binding site 4 out of 4 in 3ek8

Go back to Calcium Binding Sites List in 3ek8
Calcium binding site 4 out of 4 in the Calcium-Saturated GCAMP2 T116V/G87R Mutant Monomer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Calcium-Saturated GCAMP2 T116V/G87R Mutant Monomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca455

b:60.0
occ:1.00
OD1 A:ASP432 2.2 75.6 1.0
O A:GLN438 2.5 60.9 1.0
OD1 A:ASP436 2.5 67.5 1.0
OE2 A:GLU443 2.6 65.6 1.0
OD2 A:ASP434 2.7 69.5 1.0
OE1 A:GLU443 2.8 66.2 1.0
CD A:GLU443 3.1 66.0 1.0
CG A:ASP436 3.1 67.1 1.0
CG A:ASP432 3.4 76.1 1.0
OD2 A:ASP436 3.5 67.2 1.0
N A:ASP436 3.5 67.6 1.0
C A:GLN438 3.6 61.1 1.0
CG A:ASP434 3.6 70.4 1.0
OD1 A:ASN440 3.8 63.7 1.0
N A:GLY435 3.9 70.3 1.0
OD1 A:ASP434 4.0 69.5 1.0
N A:GLN438 4.0 62.2 1.0
OD2 A:ASP432 4.1 75.2 1.0
CB A:ASP436 4.1 66.7 1.0
CA A:ASP436 4.2 66.4 1.0
CA A:ASP432 4.3 76.5 1.0
CA A:GLN438 4.4 61.3 1.0
N A:GLY437 4.4 64.4 1.0
CB A:ASP432 4.5 76.4 1.0
N A:VAL439 4.5 61.0 1.0
CA A:GLY435 4.5 69.2 1.0
C A:GLY435 4.5 68.5 1.0
N A:ASP434 4.5 73.1 1.0
CG A:GLU443 4.6 66.1 1.0
C A:ASP436 4.6 65.4 1.0
CA A:VAL439 4.6 61.0 1.0
N A:ILE433 4.7 75.5 1.0
C A:ASP432 4.7 76.1 1.0
CB A:ASP434 4.9 71.5 1.0
C A:ASP434 4.9 71.2 1.0
N A:ASN440 4.9 61.8 1.0
CA A:ASP434 5.0 71.8 1.0
CG A:ASN440 5.0 62.9 1.0
CB A:GLN438 5.0 61.2 1.0

Reference:

J.Akerboom, J.D.Rivera, M.M.Guilbe, E.C.Malave, H.H.Hernandez, L.Tian, S.A.Hires, J.S.Marvin, L.L.Looger, E.R.Schreiter. Crystal Structures of the Gcamp Calcium Sensor Reveal the Mechanism of Fluorescence Signal Change and Aid Rational Design J.Biol.Chem. V. 284 6455 2009.
ISSN: ISSN 0021-9258
PubMed: 19098007
DOI: 10.1074/JBC.M807657200
Page generated: Sat Jul 13 09:28:20 2024

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