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Calcium in PDB 3ekh: Calcium-Saturated GCAMP2 T116V/K378W Mutant Monomer

Protein crystallography data

The structure of Calcium-Saturated GCAMP2 T116V/K378W Mutant Monomer, PDB code: 3ekh 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) 23.41 / 2.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 121.648, 121.648, 97.327, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 22.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Calcium-Saturated GCAMP2 T116V/K378W Mutant Monomer (pdb code 3ekh). 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/K378W Mutant Monomer, PDB code: 3ekh:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3ekh

Go back to Calcium Binding Sites List in 3ekh
Calcium binding site 1 out of 4 in the Calcium-Saturated GCAMP2 T116V/K378W 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/K378W Mutant Monomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca453

b:17.7
occ:1.00
OD1 A:ASP323 2.3 20.1 1.0
OD1 A:ASP325 2.3 19.9 1.0
OD1 A:ASP327 2.3 20.8 1.0
O A:THR329 2.3 18.9 1.0
O A:HOH536 2.4 25.0 1.0
OE2 A:GLU334 2.5 20.7 1.0
OE1 A:GLU334 2.5 18.5 1.0
CD A:GLU334 2.8 22.4 1.0
CG A:ASP325 3.3 22.3 1.0
CG A:ASP327 3.4 18.9 1.0
CG A:ASP323 3.5 20.7 1.0
C A:THR329 3.6 19.2 1.0
OD2 A:ASP325 3.7 21.8 1.0
OD2 A:ASP327 4.0 19.9 1.0
CA A:ASP323 4.1 22.6 1.0
N A:ASP327 4.2 17.3 1.0
N A:THR329 4.2 18.5 1.0
CB A:ASP323 4.3 22.1 1.0
CG A:GLU334 4.3 21.9 1.0
C A:ASP323 4.4 22.6 1.0
N A:ASP325 4.4 22.4 1.0
OD2 A:ASP323 4.4 18.6 1.0
CB A:ASP327 4.4 17.5 1.0
CA A:THR329 4.5 19.2 1.0
O A:HOH522 4.5 25.8 1.0
N A:ILE330 4.5 18.8 1.0
CG2 A:THR329 4.5 20.4 1.0
CA A:ILE330 4.5 18.2 1.0
CB A:ASP325 4.6 22.1 1.0
N A:LYS324 4.6 22.9 1.0
CA A:ASP327 4.7 16.7 1.0
N A:GLY326 4.7 19.7 1.0
O A:HOH524 4.8 26.3 1.0
N A:GLY328 4.8 17.0 1.0
CA A:ASP325 4.8 21.8 1.0
O A:ASP323 4.8 21.3 1.0
C A:ASP325 4.9 20.9 1.0
C A:ASP327 4.9 17.1 1.0
N A:THR331 4.9 19.3 1.0
CG2 A:THR331 5.0 20.0 1.0
O A:HOH640 5.0 26.1 1.0

Calcium binding site 2 out of 4 in 3ekh

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Calcium binding site 2 out of 4 in the Calcium-Saturated GCAMP2 T116V/K378W 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/K378W Mutant Monomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca454

b:20.4
occ:1.00
OD2 A:ASP359 2.3 20.5 1.0
OE1 A:GLU370 2.4 18.9 1.0
O A:THR365 2.4 19.4 1.0
OD1 A:ASN363 2.4 22.1 1.0
OD1 A:ASP367 2.5 20.7 0.5
OD1 A:ASP361 2.5 26.0 1.0
OE2 A:GLU370 2.5 19.4 1.0
CD A:GLU370 2.8 19.8 1.0
CG A:ASP361 3.4 26.8 1.0
CG A:ASN363 3.4 24.0 1.0
CG A:ASP359 3.4 20.8 1.0
C A:THR365 3.6 19.8 1.0
CG A:ASP367 3.6 19.6 0.5
OD2 A:ASP361 3.8 30.4 1.0
ND2 A:ASN363 4.0 24.9 1.0
N A:ASP367 4.2 18.1 0.5
N A:ASP367 4.2 18.3 0.5
N A:THR365 4.2 20.5 1.0
OD1 A:ASP359 4.2 22.2 1.0
CA A:ASP359 4.2 20.6 1.0
N A:ASN363 4.3 24.5 1.0
CG A:GLU370 4.3 20.3 1.0
CB A:ASP359 4.3 19.9 1.0
OG1 A:THR365 4.4 21.4 1.0
N A:ASP361 4.4 25.0 1.0
OD2 A:ASP367 4.4 23.7 0.5
OD2 A:ASP367 4.5 17.5 0.5
CA A:THR365 4.5 20.0 1.0
CB A:ASP367 4.5 18.8 0.5
N A:ILE366 4.5 18.7 1.0
C A:ASP359 4.5 20.9 1.0
CA A:ILE366 4.5 18.6 1.0
CB A:ASN363 4.5 24.6 1.0
CG A:ASP367 4.5 17.9 0.5
CB A:ASP361 4.6 26.4 1.0
N A:GLY362 4.7 24.9 1.0
N A:ALA360 4.7 22.2 1.0
CA A:ASN363 4.8 24.4 1.0
N A:GLY364 4.8 22.7 1.0
C A:ILE366 4.8 18.2 1.0
CA A:ASP361 4.8 25.9 1.0
CB A:ASP367 4.8 18.1 0.5
OD1 A:ASP367 4.9 16.2 0.5
O A:HOH532 4.9 24.8 1.0
C A:ASN363 5.0 24.2 1.0
CA A:ASP367 5.0 18.3 0.5

Calcium binding site 3 out of 4 in 3ekh

Go back to Calcium Binding Sites List in 3ekh
Calcium binding site 3 out of 4 in the Calcium-Saturated GCAMP2 T116V/K378W 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/K378W Mutant Monomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca455

b:45.0
occ:1.00
O A:TYR402 2.1 47.5 1.0
OD1 A:ASN400 2.4 54.1 1.0
OD2 A:ASP396 2.4 45.2 1.0
OE2 A:GLU407 2.4 54.7 1.0
OE1 A:GLU407 2.6 56.0 1.0
OD2 A:ASP398 2.7 58.8 1.0
CD A:GLU407 2.9 57.3 1.0
C A:TYR402 3.3 47.5 1.0
CG A:ASP398 3.4 56.4 1.0
CG A:ASN400 3.6 53.3 1.0
CG A:ASP396 3.6 47.7 1.0
OD1 A:ASP398 3.6 58.1 1.0
N A:TYR402 4.2 47.5 1.0
CA A:ASP396 4.2 47.2 1.0
N A:ILE403 4.3 47.9 1.0
CA A:TYR402 4.3 47.2 1.0
CA A:ILE403 4.3 48.5 1.0
N A:ASN400 4.3 53.1 1.0
CG A:GLU407 4.4 57.7 1.0
ND2 A:ASN400 4.4 54.6 1.0
OD1 A:ASP396 4.4 47.6 1.0
N A:SER404 4.4 51.0 1.0
CB A:ASP396 4.5 47.0 1.0
CB A:ASN400 4.5 52.8 1.0
C A:ASP396 4.5 48.4 1.0
N A:ASP398 4.5 53.8 1.0
N A:GLY399 4.6 54.5 1.0
N A:LYS397 4.6 50.0 1.0
CB A:ASP398 4.8 55.0 1.0
CB A:TYR402 4.8 46.9 1.0
OG A:SER404 4.8 53.1 1.0
C A:ILE403 4.9 49.4 1.0
CA A:ASN400 4.9 52.4 1.0
N A:GLY401 5.0 50.1 1.0

Calcium binding site 4 out of 4 in 3ekh

Go back to Calcium Binding Sites List in 3ekh
Calcium binding site 4 out of 4 in the Calcium-Saturated GCAMP2 T116V/K378W 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/K378W Mutant Monomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca456

b:60.8
occ:1.00
OD1 A:ASP436 2.2 65.5 1.0
O A:GLN438 2.4 57.9 1.0
OE2 A:GLU443 2.5 59.3 1.0
OE1 A:GLU443 2.6 55.9 1.0
OD1 A:ASP432 2.7 71.0 1.0
OD2 A:ASP434 2.7 66.0 1.0
CD A:GLU443 2.9 55.3 1.0
CG A:ASP436 3.3 64.4 1.0
CG A:ASP432 3.4 71.2 1.0
CG A:ASP434 3.5 67.7 1.0
C A:GLN438 3.6 57.7 1.0
OD1 A:ASP434 3.8 67.2 1.0
OD2 A:ASP436 3.9 64.3 1.0
OD2 A:ASP432 4.0 70.3 1.0
CA A:ASP432 4.1 71.7 1.0
CB A:ASP432 4.2 71.6 1.0
N A:GLN438 4.4 59.3 1.0
N A:ASP434 4.4 69.3 1.0
CA A:VAL439 4.4 55.6 1.0
CB A:ASP436 4.4 63.8 1.0
N A:VAL439 4.4 56.6 1.0
CG A:GLU443 4.4 55.3 1.0
N A:ASP436 4.5 64.6 1.0
N A:ASN440 4.5 54.6 1.0
CA A:GLN438 4.5 58.3 1.0
N A:ILE433 4.5 70.9 1.0
C A:ASP432 4.6 71.4 1.0
C A:ASP434 4.7 67.9 1.0
OD1 A:ASN440 4.8 56.0 1.0
CB A:ASP434 4.8 68.4 1.0
CA A:ASP434 4.8 68.5 1.0
CA A:ASP436 4.9 63.7 1.0
C A:VAL439 4.9 54.9 1.0
O A:ASP434 4.9 67.8 1.0
CB A:GLN438 4.9 58.3 1.0
CG A:ASN440 4.9 55.1 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 Dec 12 04:10:16 2020

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