Calcium in PDB 3fz3: Crystal Structure of Almond PRU1 Protein
Protein crystallography data
The structure of Crystal Structure of Almond PRU1 Protein, PDB code: 3fz3
was solved by
T.C.Jin,
Y.Z.Zhang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
36.08 /
2.40
|
Space group
|
P 41
|
Cell size a, b, c (Å), α, β, γ (°)
|
151.021,
151.021,
165.367,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.2 /
22.9
|
Other elements in 3fz3:
The structure of Crystal Structure of Almond PRU1 Protein also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Almond PRU1 Protein
(pdb code 3fz3). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Crystal Structure of Almond PRU1 Protein, PDB code: 3fz3:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 3fz3
Go back to
Calcium Binding Sites List in 3fz3
Calcium binding site 1 out
of 6 in the Crystal Structure of Almond PRU1 Protein
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 Almond PRU1 Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1
b:52.7
occ:1.00
|
NH2
|
A:ARG194
|
3.0
|
44.3
|
1.0
|
N
|
A:LEU378
|
3.7
|
34.1
|
1.0
|
CG
|
A:ARG377
|
3.9
|
39.6
|
1.0
|
CA
|
A:ARG377
|
4.0
|
36.4
|
1.0
|
CD
|
A:ARG194
|
4.0
|
39.4
|
1.0
|
CG
|
A:ARG194
|
4.1
|
37.5
|
1.0
|
N
|
A:LYS379
|
4.2
|
35.6
|
1.0
|
CZ
|
A:ARG194
|
4.2
|
41.7
|
1.0
|
CG
|
A:LYS379
|
4.2
|
39.1
|
1.0
|
CB
|
A:ARG377
|
4.4
|
36.5
|
1.0
|
C
|
A:ARG377
|
4.4
|
35.1
|
1.0
|
O
|
A:LEU376
|
4.4
|
39.3
|
1.0
|
CE
|
A:LYS192
|
4.5
|
42.0
|
1.0
|
NZ
|
A:LYS379
|
4.5
|
44.4
|
1.0
|
NE
|
A:ARG194
|
4.6
|
40.7
|
1.0
|
CA
|
A:LEU378
|
4.6
|
34.7
|
1.0
|
O
|
A:HOH676
|
4.7
|
38.4
|
1.0
|
CB
|
A:LEU378
|
4.7
|
34.5
|
1.0
|
NZ
|
A:LYS192
|
4.8
|
44.0
|
1.0
|
C
|
A:LEU378
|
4.9
|
34.8
|
1.0
|
O
|
A:LYS379
|
4.9
|
36.9
|
1.0
|
CD
|
A:ARG377
|
5.0
|
42.3
|
1.0
|
CB
|
A:ARG194
|
5.0
|
36.2
|
1.0
|
|
Calcium binding site 2 out
of 6 in 3fz3
Go back to
Calcium Binding Sites List in 3fz3
Calcium binding site 2 out
of 6 in the Crystal Structure of Almond PRU1 Protein
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 Almond PRU1 Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca2
b:53.7
occ:1.00
|
NH2
|
B:ARG194
|
3.0
|
47.5
|
1.0
|
O
|
B:HOH683
|
3.4
|
45.2
|
1.0
|
N
|
B:LEU378
|
3.5
|
33.1
|
1.0
|
CD
|
B:ARG194
|
3.5
|
36.6
|
1.0
|
CE
|
B:LYS379
|
3.8
|
40.6
|
1.0
|
N
|
B:LYS379
|
3.9
|
31.9
|
1.0
|
CA
|
B:ARG377
|
4.0
|
35.6
|
1.0
|
CZ
|
B:ARG194
|
4.0
|
44.3
|
1.0
|
CG
|
B:ARG377
|
4.1
|
39.3
|
1.0
|
CG
|
B:ARG194
|
4.1
|
34.6
|
1.0
|
NE
|
B:ARG194
|
4.2
|
41.2
|
1.0
|
C
|
B:ARG377
|
4.3
|
34.1
|
1.0
|
CA
|
B:LEU378
|
4.4
|
31.8
|
1.0
|
NZ
|
B:LYS379
|
4.4
|
42.6
|
1.0
|
CB
|
B:LEU378
|
4.4
|
30.8
|
1.0
|
CG
|
B:LYS379
|
4.5
|
36.8
|
1.0
|
CB
|
B:ARG377
|
4.6
|
36.4
|
1.0
|
O
|
B:LYS379
|
4.6
|
34.0
|
1.0
|
O
|
B:LEU376
|
4.6
|
38.2
|
1.0
|
C
|
B:LEU378
|
4.6
|
31.4
|
1.0
|
CB
|
B:LYS379
|
4.7
|
34.9
|
1.0
|
CA
|
B:LYS379
|
4.7
|
34.0
|
1.0
|
CD
|
B:LYS379
|
4.8
|
39.5
|
1.0
|
O
|
E:HOH569
|
4.8
|
38.8
|
1.0
|
CD
|
B:ARG377
|
4.8
|
45.9
|
1.0
|
CB
|
B:ARG194
|
4.9
|
34.0
|
1.0
|
CE
|
B:LYS192
|
5.0
|
38.0
|
1.0
|
|
Calcium binding site 3 out
of 6 in 3fz3
Go back to
Calcium Binding Sites List in 3fz3
Calcium binding site 3 out
of 6 in the Crystal Structure of Almond PRU1 Protein
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 Almond PRU1 Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca3
b:45.3
occ:1.00
|
NE
|
C:ARG194
|
3.1
|
34.0
|
1.0
|
N
|
C:LEU378
|
3.5
|
30.9
|
1.0
|
CD
|
C:ARG194
|
3.5
|
35.2
|
1.0
|
CG
|
C:LYS379
|
3.6
|
35.9
|
1.0
|
N
|
C:LYS379
|
3.8
|
32.5
|
1.0
|
CA
|
C:ARG377
|
3.9
|
29.5
|
1.0
|
O
|
D:HOH890
|
4.0
|
51.5
|
1.0
|
CG
|
C:ARG377
|
4.1
|
29.1
|
1.0
|
CZ
|
C:ARG194
|
4.2
|
34.8
|
1.0
|
CG
|
C:ARG194
|
4.2
|
34.5
|
1.0
|
C
|
C:ARG377
|
4.2
|
30.1
|
1.0
|
CA
|
C:LEU378
|
4.4
|
31.0
|
1.0
|
NH2
|
C:ARG194
|
4.4
|
38.7
|
1.0
|
O
|
C:LEU376
|
4.4
|
31.4
|
1.0
|
CB
|
C:LEU378
|
4.5
|
30.8
|
1.0
|
NZ
|
C:LYS192
|
4.5
|
45.8
|
1.0
|
CB
|
C:ARG377
|
4.5
|
28.1
|
1.0
|
C
|
C:LEU378
|
4.6
|
31.6
|
1.0
|
CE
|
C:LYS379
|
4.6
|
43.0
|
1.0
|
CB
|
C:LYS379
|
4.6
|
34.0
|
1.0
|
CA
|
C:LYS379
|
4.7
|
32.7
|
1.0
|
CD
|
C:LYS379
|
4.7
|
41.3
|
1.0
|
CE
|
C:LYS192
|
4.8
|
41.8
|
1.0
|
O
|
C:LYS379
|
4.8
|
32.7
|
1.0
|
CB
|
C:ARG194
|
4.9
|
33.0
|
1.0
|
CD
|
C:ARG377
|
4.9
|
38.4
|
1.0
|
N
|
C:ARG377
|
5.0
|
29.6
|
1.0
|
|
Calcium binding site 4 out
of 6 in 3fz3
Go back to
Calcium Binding Sites List in 3fz3
Calcium binding site 4 out
of 6 in the Crystal Structure of Almond PRU1 Protein
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 Almond PRU1 Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca4
b:45.6
occ:1.00
|
O
|
D:HOH729
|
3.3
|
39.1
|
1.0
|
NE
|
D:ARG194
|
3.3
|
33.4
|
1.0
|
N
|
D:LEU378
|
3.6
|
31.7
|
1.0
|
CG
|
D:LYS379
|
3.6
|
37.7
|
1.0
|
CD
|
D:ARG194
|
3.8
|
34.0
|
1.0
|
O
|
C:HOH580
|
3.8
|
31.3
|
1.0
|
N
|
D:LYS379
|
3.9
|
33.6
|
1.0
|
CA
|
D:ARG377
|
3.9
|
30.1
|
1.0
|
CG
|
D:ARG377
|
3.9
|
31.2
|
1.0
|
CG
|
D:ARG194
|
4.1
|
34.9
|
1.0
|
C
|
D:ARG377
|
4.3
|
31.0
|
1.0
|
CZ
|
D:ARG194
|
4.3
|
32.3
|
1.0
|
CB
|
D:ARG377
|
4.4
|
29.1
|
1.0
|
CA
|
D:LEU378
|
4.4
|
31.1
|
1.0
|
CB
|
D:LEU378
|
4.5
|
29.7
|
1.0
|
NZ
|
D:LYS379
|
4.5
|
41.2
|
1.0
|
O
|
D:LEU376
|
4.5
|
29.6
|
1.0
|
NH2
|
D:ARG194
|
4.5
|
32.4
|
1.0
|
CE
|
D:LYS192
|
4.6
|
39.1
|
1.0
|
CD
|
D:LYS379
|
4.6
|
41.9
|
1.0
|
C
|
D:LEU378
|
4.6
|
32.0
|
1.0
|
CB
|
D:LYS379
|
4.7
|
35.1
|
1.0
|
NZ
|
D:LYS192
|
4.7
|
38.4
|
1.0
|
O
|
D:HOH563
|
4.7
|
38.0
|
1.0
|
CA
|
D:LYS379
|
4.7
|
34.2
|
1.0
|
CD
|
D:ARG377
|
4.8
|
38.6
|
1.0
|
O
|
D:LYS379
|
4.8
|
33.4
|
1.0
|
O
|
D:HOH1016
|
4.8
|
45.2
|
1.0
|
N
|
D:ARG377
|
4.9
|
29.3
|
1.0
|
CB
|
D:ARG194
|
5.0
|
34.0
|
1.0
|
|
Calcium binding site 5 out
of 6 in 3fz3
Go back to
Calcium Binding Sites List in 3fz3
Calcium binding site 5 out
of 6 in the Crystal Structure of Almond PRU1 Protein
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of Almond PRU1 Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca5
b:51.1
occ:1.00
|
NH2
|
E:ARG194
|
2.9
|
44.7
|
1.0
|
N
|
E:LEU378
|
3.7
|
31.2
|
1.0
|
CD
|
E:ARG194
|
3.9
|
40.3
|
1.0
|
CG
|
E:ARG194
|
4.0
|
39.0
|
1.0
|
CG
|
E:ARG377
|
4.0
|
35.6
|
1.0
|
CZ
|
E:ARG194
|
4.1
|
41.3
|
1.0
|
CA
|
E:ARG377
|
4.1
|
33.3
|
1.0
|
CE
|
E:LYS379
|
4.1
|
39.0
|
1.0
|
N
|
E:LYS379
|
4.1
|
34.1
|
1.0
|
C
|
E:ARG377
|
4.4
|
31.6
|
1.0
|
CB
|
E:ARG377
|
4.5
|
33.7
|
1.0
|
CG
|
E:LYS379
|
4.5
|
35.8
|
1.0
|
NE
|
E:ARG194
|
4.5
|
40.5
|
1.0
|
CA
|
E:LEU378
|
4.5
|
32.4
|
1.0
|
O
|
E:LEU376
|
4.6
|
37.2
|
1.0
|
CD
|
E:ARG377
|
4.6
|
40.3
|
1.0
|
NZ
|
E:LYS192
|
4.6
|
44.6
|
1.0
|
CB
|
E:LEU378
|
4.7
|
32.7
|
1.0
|
CD
|
E:LYS379
|
4.8
|
37.3
|
1.0
|
C
|
E:LEU378
|
4.8
|
33.0
|
1.0
|
NZ
|
E:LYS379
|
4.9
|
37.5
|
1.0
|
O
|
E:LYS379
|
4.9
|
34.9
|
1.0
|
O
|
E:HOH560
|
4.9
|
37.7
|
1.0
|
|
Calcium binding site 6 out
of 6 in 3fz3
Go back to
Calcium Binding Sites List in 3fz3
Calcium binding site 6 out
of 6 in the Crystal Structure of Almond PRU1 Protein
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Crystal Structure of Almond PRU1 Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca6
b:51.3
occ:1.00
|
O
|
F:HOH705
|
3.3
|
47.2
|
1.0
|
CD
|
F:ARG194
|
3.3
|
36.7
|
1.0
|
N
|
F:LEU378
|
3.4
|
32.0
|
1.0
|
NH2
|
F:ARG194
|
3.7
|
43.5
|
1.0
|
N
|
F:LYS379
|
3.8
|
32.4
|
1.0
|
CG
|
F:ARG377
|
3.9
|
39.2
|
1.0
|
CG
|
F:LYS379
|
3.9
|
37.5
|
1.0
|
CG
|
F:ARG194
|
4.0
|
35.2
|
1.0
|
CE
|
F:LYS379
|
4.0
|
39.5
|
1.0
|
CA
|
F:ARG377
|
4.0
|
34.8
|
1.0
|
C
|
F:ARG377
|
4.2
|
32.9
|
1.0
|
CA
|
F:LEU378
|
4.2
|
30.9
|
1.0
|
CB
|
F:LEU378
|
4.3
|
30.8
|
1.0
|
NE
|
F:ARG194
|
4.3
|
40.9
|
1.0
|
CZ
|
F:ARG194
|
4.5
|
42.5
|
1.0
|
CD
|
F:LYS379
|
4.5
|
38.6
|
1.0
|
C
|
F:LEU378
|
4.5
|
30.8
|
1.0
|
CB
|
F:ARG377
|
4.5
|
35.4
|
1.0
|
O
|
F:LYS379
|
4.6
|
33.6
|
1.0
|
NZ
|
F:LYS379
|
4.6
|
41.7
|
1.0
|
CD
|
F:ARG377
|
4.7
|
47.8
|
1.0
|
O
|
F:LEU376
|
4.7
|
36.3
|
1.0
|
CB
|
F:LYS379
|
4.7
|
34.9
|
1.0
|
CA
|
F:LYS379
|
4.7
|
34.2
|
1.0
|
CB
|
F:ARG194
|
5.0
|
34.8
|
1.0
|
|
Reference:
T.Jin,
S.M.Albillos,
F.Guo,
A.Howard,
T.J.Fu,
M.H.Kothary,
Y.Z.Zhang.
Crystal Structure of Prunin-1, A Major Component of the Almond (Prunus Dulcis) Allergen Amandin. J.Agric.Food Chem. V. 57 8643 2009.
ISSN: ISSN 0021-8561
PubMed: 19694440
DOI: 10.1021/JF9017355
Page generated: Sat Jul 13 10:27:50 2024
|