Calcium in PDB 3ek4: Calcium-Saturated GCAMP2 Monomer
Protein crystallography data
The structure of Calcium-Saturated GCAMP2 Monomer, PDB code: 3ek4
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)
|
45.45 /
2.65
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.498,
117.260,
68.801,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22.2 /
28
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Calcium-Saturated GCAMP2 Monomer
(pdb code 3ek4). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the
Calcium-Saturated GCAMP2 Monomer, PDB code: 3ek4:
Jump to Calcium binding site number:
1;
2;
3;
Calcium binding site 1 out
of 3 in 3ek4
Go back to
Calcium Binding Sites List in 3ek4
Calcium binding site 1 out
of 3 in the Calcium-Saturated GCAMP2 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 Monomer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca452
b:55.6
occ:1.00
|
OD1
|
A:ASP323
|
2.1
|
62.4
|
1.0
|
O
|
A:THR329
|
2.3
|
56.1
|
1.0
|
OD1
|
A:ASP327
|
2.4
|
60.5
|
1.0
|
OE1
|
A:GLU334
|
2.7
|
54.9
|
1.0
|
OE2
|
A:GLU334
|
2.7
|
53.8
|
1.0
|
CD
|
A:GLU334
|
3.1
|
54.0
|
1.0
|
CG
|
A:ASP323
|
3.2
|
64.0
|
1.0
|
OD1
|
A:ASP325
|
3.2
|
63.8
|
1.0
|
OD2
|
A:ASP325
|
3.3
|
63.1
|
1.0
|
CG
|
A:ASP327
|
3.5
|
60.2
|
1.0
|
CG
|
A:ASP325
|
3.5
|
62.8
|
1.0
|
C
|
A:THR329
|
3.5
|
55.9
|
1.0
|
OD2
|
A:ASP323
|
3.9
|
64.8
|
1.0
|
N
|
A:ASP327
|
4.1
|
60.3
|
1.0
|
CB
|
A:ASP323
|
4.1
|
64.1
|
1.0
|
OG1
|
A:THR329
|
4.1
|
57.0
|
1.0
|
CA
|
A:ASP323
|
4.1
|
64.2
|
1.0
|
OD2
|
A:ASP327
|
4.2
|
59.9
|
1.0
|
N
|
A:THR329
|
4.2
|
57.4
|
1.0
|
CA
|
A:THR329
|
4.4
|
56.6
|
1.0
|
CB
|
A:ASP327
|
4.5
|
59.9
|
1.0
|
N
|
A:ILE330
|
4.5
|
55.0
|
1.0
|
CA
|
A:ILE330
|
4.5
|
53.8
|
1.0
|
C
|
A:ASP323
|
4.6
|
63.7
|
1.0
|
CG
|
A:GLU334
|
4.6
|
52.8
|
1.0
|
N
|
A:GLY326
|
4.6
|
61.6
|
1.0
|
CA
|
A:ASP327
|
4.7
|
60.0
|
1.0
|
N
|
A:ASP325
|
4.7
|
62.4
|
1.0
|
CB
|
A:ASP325
|
4.8
|
62.3
|
1.0
|
N
|
A:GLY328
|
4.9
|
59.3
|
1.0
|
C
|
A:ASP325
|
4.9
|
62.0
|
1.0
|
C
|
A:ASP327
|
4.9
|
59.7
|
1.0
|
N
|
A:THR331
|
4.9
|
52.5
|
1.0
|
N
|
A:LYS324
|
4.9
|
63.2
|
1.0
|
CB
|
A:THR329
|
5.0
|
56.8
|
1.0
|
|
Calcium binding site 2 out
of 3 in 3ek4
Go back to
Calcium Binding Sites List in 3ek4
Calcium binding site 2 out
of 3 in the Calcium-Saturated GCAMP2 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 Monomer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca453
b:51.2
occ:1.00
|
OE1
|
A:GLU370
|
2.3
|
49.7
|
1.0
|
OD1
|
A:ASP361
|
2.4
|
43.1
|
1.0
|
OD2
|
A:ASP359
|
2.4
|
39.0
|
1.0
|
O
|
A:THR365
|
2.4
|
45.4
|
1.0
|
OD1
|
A:ASN363
|
2.5
|
42.4
|
1.0
|
OE2
|
A:GLU370
|
2.5
|
48.4
|
1.0
|
CD
|
A:GLU370
|
2.7
|
49.7
|
1.0
|
CG
|
A:ASP361
|
3.1
|
42.9
|
1.0
|
OD2
|
A:ASP361
|
3.2
|
43.7
|
1.0
|
CG
|
A:ASN363
|
3.3
|
41.5
|
1.0
|
OD2
|
A:ASP367
|
3.4
|
53.7
|
1.0
|
C
|
A:THR365
|
3.6
|
45.0
|
1.0
|
CG
|
A:ASP359
|
3.6
|
40.1
|
1.0
|
ND2
|
A:ASN363
|
3.8
|
38.6
|
1.0
|
CG
|
A:GLU370
|
4.2
|
50.5
|
1.0
|
N
|
A:THR365
|
4.3
|
43.4
|
1.0
|
N
|
A:ASN363
|
4.3
|
42.5
|
1.0
|
OD1
|
A:ASP359
|
4.3
|
41.1
|
1.0
|
N
|
A:ASP367
|
4.3
|
48.8
|
1.0
|
N
|
A:ASP361
|
4.3
|
41.3
|
1.0
|
CB
|
A:ASP361
|
4.4
|
41.6
|
1.0
|
CG
|
A:ASP367
|
4.4
|
52.0
|
1.0
|
CB
|
A:ASN363
|
4.4
|
42.0
|
1.0
|
N
|
A:ILE366
|
4.5
|
46.0
|
1.0
|
OG1
|
A:THR365
|
4.5
|
44.5
|
1.0
|
CA
|
A:THR365
|
4.5
|
44.4
|
1.0
|
CA
|
A:ILE366
|
4.5
|
46.8
|
1.0
|
N
|
A:GLY362
|
4.6
|
41.7
|
1.0
|
CA
|
A:ASP359
|
4.7
|
39.5
|
1.0
|
CB
|
A:ASP359
|
4.7
|
39.6
|
1.0
|
CA
|
A:ASP361
|
4.7
|
41.7
|
1.0
|
CA
|
A:ASN363
|
4.8
|
42.3
|
1.0
|
C
|
A:ASP359
|
4.8
|
39.3
|
1.0
|
N
|
A:ALA360
|
4.9
|
39.7
|
1.0
|
N
|
A:GLY364
|
4.9
|
42.5
|
1.0
|
C
|
A:ASN363
|
4.9
|
42.5
|
1.0
|
C
|
A:ASP361
|
4.9
|
41.7
|
1.0
|
C
|
A:ILE366
|
4.9
|
47.8
|
1.0
|
CB
|
A:GLU370
|
5.0
|
51.7
|
1.0
|
|
Calcium binding site 3 out
of 3 in 3ek4
Go back to
Calcium Binding Sites List in 3ek4
Calcium binding site 3 out
of 3 in the Calcium-Saturated GCAMP2 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 Monomer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca454
b:0.3
occ:1.00
|
O
|
A:TYR402
|
2.3
|
0.8
|
1.0
|
OD1
|
A:ASN400
|
2.4
|
0.3
|
1.0
|
OE2
|
A:GLU407
|
2.6
|
96.8
|
1.0
|
OD2
|
A:ASP398
|
2.8
|
0.1
|
1.0
|
OD2
|
A:ASP396
|
3.0
|
98.8
|
1.0
|
CG
|
A:ASN400
|
3.2
|
0.8
|
1.0
|
CD
|
A:GLU407
|
3.3
|
97.0
|
1.0
|
OE1
|
A:GLU407
|
3.3
|
96.4
|
1.0
|
OD1
|
A:ASP396
|
3.3
|
99.0
|
1.0
|
ND2
|
A:ASN400
|
3.4
|
0.7
|
1.0
|
CG
|
A:ASP396
|
3.4
|
98.9
|
1.0
|
C
|
A:TYR402
|
3.4
|
0.8
|
1.0
|
CG
|
A:ASP398
|
3.6
|
0.7
|
1.0
|
OD1
|
A:ASP398
|
3.6
|
0.8
|
1.0
|
CA
|
A:ILE403
|
3.8
|
0.6
|
1.0
|
N
|
A:SER404
|
3.8
|
0.2
|
1.0
|
N
|
A:ILE403
|
4.1
|
0.7
|
1.0
|
C
|
A:ILE403
|
4.2
|
0.4
|
1.0
|
OG
|
A:SER404
|
4.2
|
99.5
|
1.0
|
CB
|
A:ASN400
|
4.5
|
0.9
|
1.0
|
CG
|
A:GLU407
|
4.6
|
97.4
|
1.0
|
CA
|
A:TYR402
|
4.7
|
0.8
|
1.0
|
CB
|
A:SER404
|
4.7
|
99.9
|
1.0
|
CB
|
A:ASP396
|
4.8
|
98.8
|
1.0
|
N
|
A:ASN400
|
4.8
|
0.8
|
1.0
|
N
|
A:TYR402
|
4.8
|
0.8
|
1.0
|
CA
|
A:SER404
|
4.9
|
100.0
|
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 09:27:04 2024
|