Calcium in PDB 3gqf: Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q
Enzymatic activity of Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q
All present enzymatic activity of Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q:
1.15.1.1;
Protein crystallography data
The structure of Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q, PDB code: 3gqf
was solved by
D.D.Winkler,
J.P.Schuermann,
P.J.Hart,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
28.07 /
2.20
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
112.576,
194.331,
143.179,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.5 /
24.2
|
Other elements in 3gqf:
The structure of Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q
(pdb code 3gqf). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the
Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q, PDB code: 3gqf:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
Calcium binding site 1 out
of 5 in 3gqf
Go back to
Calcium Binding Sites List in 3gqf
Calcium binding site 1 out
of 5 in the Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca154
b:63.6
occ:1.00
|
O
|
A:SER102
|
2.4
|
31.3
|
1.0
|
O
|
A:HOH493
|
2.4
|
60.2
|
1.0
|
O
|
A:HOH484
|
2.4
|
46.1
|
1.0
|
OD1
|
A:ASN26
|
2.4
|
52.3
|
1.0
|
O
|
A:HOH483
|
2.6
|
30.0
|
1.0
|
O
|
A:HOH492
|
2.6
|
54.6
|
1.0
|
O
|
A:ASN26
|
2.7
|
44.8
|
1.0
|
CG
|
A:ASN26
|
3.4
|
49.4
|
1.0
|
C
|
A:SER102
|
3.5
|
31.3
|
1.0
|
C
|
A:ASN26
|
3.5
|
44.5
|
1.0
|
CA
|
A:ASN26
|
4.0
|
45.8
|
1.0
|
O
|
A:GLY27
|
4.1
|
39.5
|
1.0
|
CA
|
A:SER102
|
4.2
|
31.8
|
1.0
|
ND2
|
A:ASN26
|
4.3
|
51.5
|
1.0
|
CB
|
A:ASN26
|
4.3
|
46.7
|
1.0
|
O
|
A:ILE104
|
4.3
|
28.6
|
1.0
|
N
|
A:VAL103
|
4.5
|
30.8
|
1.0
|
CB
|
A:SER102
|
4.5
|
32.4
|
1.0
|
O
|
A:VAL103
|
4.5
|
30.3
|
1.0
|
N
|
A:GLY27
|
4.6
|
42.9
|
1.0
|
CA
|
A:VAL103
|
4.6
|
29.9
|
1.0
|
C
|
A:GLY27
|
4.7
|
39.8
|
1.0
|
C
|
A:VAL103
|
4.7
|
30.0
|
1.0
|
|
Calcium binding site 2 out
of 5 in 3gqf
Go back to
Calcium Binding Sites List in 3gqf
Calcium binding site 2 out
of 5 in the Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca154
b:51.6
occ:1.00
|
O
|
B:HOH491
|
2.2
|
42.9
|
1.0
|
O
|
B:HOH485
|
2.4
|
28.9
|
1.0
|
O
|
B:SER102
|
2.5
|
30.7
|
1.0
|
O
|
B:HOH490
|
2.5
|
52.9
|
1.0
|
O
|
B:HOH486
|
2.6
|
33.8
|
1.0
|
O
|
B:ASN26
|
2.8
|
44.7
|
1.0
|
OD1
|
B:ASN26
|
3.1
|
52.6
|
1.0
|
C
|
B:ASN26
|
3.5
|
44.4
|
1.0
|
C
|
B:SER102
|
3.6
|
30.3
|
1.0
|
CA
|
B:ASN26
|
3.8
|
45.7
|
1.0
|
CG
|
B:ASN26
|
3.9
|
49.4
|
1.0
|
CB
|
B:ASN26
|
4.0
|
46.4
|
1.0
|
O
|
B:GLY27
|
4.2
|
39.1
|
1.0
|
CA
|
B:SER102
|
4.3
|
31.4
|
1.0
|
O
|
B:ILE104
|
4.4
|
27.6
|
1.0
|
CB
|
B:SER102
|
4.5
|
31.5
|
1.0
|
N
|
B:GLY27
|
4.6
|
42.7
|
1.0
|
N
|
B:VAL103
|
4.6
|
29.3
|
1.0
|
O
|
B:VAL103
|
4.6
|
28.3
|
1.0
|
CA
|
B:VAL103
|
4.7
|
28.2
|
1.0
|
C
|
B:GLY27
|
4.8
|
39.2
|
1.0
|
C
|
B:VAL103
|
4.9
|
28.2
|
1.0
|
|
Calcium binding site 3 out
of 5 in 3gqf
Go back to
Calcium Binding Sites List in 3gqf
Calcium binding site 3 out
of 5 in the Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca154
b:62.3
occ:1.00
|
O
|
C:HOH496
|
2.4
|
45.9
|
1.0
|
O
|
C:SER102
|
2.5
|
32.1
|
1.0
|
O
|
C:HOH494
|
2.6
|
42.3
|
1.0
|
OD1
|
C:ASN26
|
2.9
|
49.4
|
1.0
|
O
|
C:HOH495
|
2.9
|
43.0
|
1.0
|
O
|
C:HOH488
|
3.1
|
43.6
|
1.0
|
O
|
C:ASN26
|
3.2
|
44.9
|
1.0
|
C
|
C:SER102
|
3.7
|
31.8
|
1.0
|
CG
|
C:ASN26
|
4.0
|
49.3
|
1.0
|
C
|
C:ASN26
|
4.0
|
45.1
|
1.0
|
CA
|
C:ASN26
|
4.2
|
46.4
|
1.0
|
CB
|
C:ASN26
|
4.4
|
47.2
|
1.0
|
CA
|
C:SER102
|
4.5
|
32.5
|
1.0
|
CA
|
C:VAL103
|
4.6
|
31.0
|
1.0
|
N
|
C:VAL103
|
4.6
|
31.3
|
1.0
|
O
|
C:ILE104
|
4.6
|
29.9
|
1.0
|
O
|
C:VAL103
|
4.6
|
31.7
|
1.0
|
O
|
C:GLY27
|
4.7
|
40.9
|
1.0
|
CB
|
C:SER102
|
4.7
|
33.0
|
1.0
|
C
|
C:VAL103
|
4.7
|
31.3
|
1.0
|
|
Calcium binding site 4 out
of 5 in 3gqf
Go back to
Calcium Binding Sites List in 3gqf
Calcium binding site 4 out
of 5 in the Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca154
b:62.6
occ:1.00
|
OD1
|
D:ASN26
|
2.3
|
51.8
|
1.0
|
O
|
D:HOH497
|
2.3
|
51.8
|
1.0
|
O
|
D:HOH498
|
2.5
|
44.1
|
1.0
|
O
|
D:SER102
|
2.5
|
32.3
|
1.0
|
O
|
D:HOH489
|
2.5
|
38.1
|
1.0
|
O
|
D:ASN26
|
2.7
|
46.1
|
1.0
|
CG
|
D:ASN26
|
3.4
|
49.8
|
1.0
|
C
|
D:SER102
|
3.6
|
31.9
|
1.0
|
C
|
D:ASN26
|
3.7
|
45.7
|
1.0
|
CA
|
D:ASN26
|
4.0
|
46.7
|
1.0
|
ND2
|
D:ASN26
|
4.2
|
50.5
|
1.0
|
O
|
D:GLY27
|
4.3
|
41.0
|
1.0
|
CB
|
D:ASN26
|
4.3
|
47.5
|
1.0
|
CA
|
D:SER102
|
4.4
|
32.7
|
1.0
|
O
|
D:ILE104
|
4.5
|
30.2
|
1.0
|
N
|
D:VAL103
|
4.6
|
31.3
|
1.0
|
CB
|
D:SER102
|
4.6
|
33.1
|
1.0
|
O
|
D:VAL103
|
4.7
|
30.4
|
1.0
|
CA
|
D:VAL103
|
4.7
|
30.6
|
1.0
|
C
|
D:VAL103
|
4.8
|
30.7
|
1.0
|
N
|
D:GLY27
|
4.8
|
44.2
|
1.0
|
C
|
D:GLY27
|
4.9
|
41.4
|
1.0
|
|
Calcium binding site 5 out
of 5 in 3gqf
Go back to
Calcium Binding Sites List in 3gqf
Calcium binding site 5 out
of 5 in the Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca154
b:56.0
occ:1.00
|
O
|
F:SER102
|
2.4
|
29.8
|
1.0
|
O
|
F:HOH170
|
2.6
|
24.3
|
1.0
|
O
|
F:HOH460
|
2.6
|
46.7
|
1.0
|
OD1
|
F:ASN26
|
2.7
|
48.5
|
1.0
|
O
|
F:ASN26
|
2.9
|
43.1
|
1.0
|
O
|
F:HOH424
|
2.9
|
40.4
|
0.5
|
O
|
F:HOH181
|
3.2
|
42.0
|
1.0
|
CG
|
F:ASN26
|
3.4
|
46.5
|
1.0
|
C
|
F:SER102
|
3.6
|
29.3
|
1.0
|
C
|
F:ASN26
|
3.7
|
42.7
|
1.0
|
ND2
|
F:ASN26
|
4.0
|
47.3
|
1.0
|
CA
|
F:ASN26
|
4.1
|
43.9
|
1.0
|
CB
|
F:ASN26
|
4.3
|
44.2
|
1.0
|
CA
|
F:SER102
|
4.4
|
29.9
|
1.0
|
O
|
F:GLY27
|
4.4
|
37.6
|
1.0
|
O
|
F:ILE104
|
4.5
|
26.4
|
1.0
|
N
|
F:VAL103
|
4.5
|
28.1
|
1.0
|
CA
|
F:VAL103
|
4.6
|
27.5
|
1.0
|
CB
|
F:SER102
|
4.7
|
30.2
|
1.0
|
O
|
F:VAL103
|
4.7
|
27.5
|
1.0
|
N
|
F:GLY27
|
4.8
|
41.3
|
1.0
|
C
|
F:VAL103
|
4.8
|
27.8
|
1.0
|
C
|
F:GLY27
|
4.9
|
38.2
|
1.0
|
O
|
F:HOH399
|
5.0
|
48.2
|
1.0
|
|
Reference:
D.D.Winkler,
J.P.Schuermann,
X.Cao,
S.P.Holloway,
D.R.Borchelt,
M.C.Carroll,
J.B.Proescher,
V.C.Culotta,
P.J.Hart.
Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q. Biochemistry V. 48 3436 2009.
ISSN: ISSN 0006-2960
PubMed: 19227972
DOI: 10.1021/BI8021735
Page generated: Sat Jul 13 10:46:22 2024
|