Calcium in PDB 6q3r: Aspergillus Aculeatus Galactanase
Enzymatic activity of Aspergillus Aculeatus Galactanase
All present enzymatic activity of Aspergillus Aculeatus Galactanase:
3.2.1.89;
Protein crystallography data
The structure of Aspergillus Aculeatus Galactanase, PDB code: 6q3r
was solved by
S.J.Muderspach,
S.Torpenholt,
L.Lo Leggio,
J.C.N.Poulsen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.17 /
2.69
|
Space group
|
I 41 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
200.200,
200.200,
106.830,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
14.5 /
21.1
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Aspergillus Aculeatus Galactanase
(pdb code 6q3r). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the
Aspergillus Aculeatus Galactanase, PDB code: 6q3r:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
Calcium binding site 1 out
of 7 in 6q3r
Go back to
Calcium Binding Sites List in 6q3r
Calcium binding site 1 out
of 7 in the Aspergillus Aculeatus Galactanase
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Aspergillus Aculeatus Galactanase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca508
b:51.8
occ:1.00
|
O
|
A:ASP38
|
2.2
|
42.9
|
1.0
|
O
|
A:HOH661
|
2.3
|
31.7
|
1.0
|
OD1
|
A:ASP38
|
2.5
|
54.6
|
1.0
|
O
|
A:HOH685
|
2.6
|
30.9
|
1.0
|
O
|
A:HOH696
|
2.7
|
30.6
|
1.0
|
C
|
A:ASP38
|
3.2
|
40.2
|
1.0
|
CA
|
A:ASP38
|
3.6
|
41.6
|
1.0
|
CG
|
A:ASP38
|
3.7
|
50.1
|
1.0
|
CB
|
A:ASP38
|
4.2
|
45.6
|
1.0
|
N
|
A:ALA39
|
4.4
|
39.2
|
1.0
|
O
|
A:HOH703
|
4.6
|
31.4
|
1.0
|
OD2
|
A:ASP38
|
4.7
|
48.0
|
1.0
|
O
|
A:ALA37
|
4.8
|
32.6
|
1.0
|
CA
|
A:ALA39
|
4.8
|
36.1
|
1.0
|
N
|
A:ASP38
|
4.9
|
38.7
|
1.0
|
N
|
A:GLY40
|
4.9
|
32.3
|
1.0
|
|
Calcium binding site 2 out
of 7 in 6q3r
Go back to
Calcium Binding Sites List in 6q3r
Calcium binding site 2 out
of 7 in the Aspergillus Aculeatus Galactanase
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Aspergillus Aculeatus Galactanase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca509
b:77.5
occ:1.00
|
O
|
A:HOH602
|
2.1
|
31.8
|
1.0
|
OE2
|
A:GLU64
|
2.8
|
39.0
|
1.0
|
OE1
|
A:GLU64
|
3.5
|
42.4
|
1.0
|
CD
|
A:GLU64
|
3.5
|
42.5
|
1.0
|
OE2
|
B:GLU286
|
3.7
|
88.7
|
1.0
|
OD1
|
A:ASP17
|
3.8
|
58.2
|
1.0
|
O
|
A:HOH692
|
3.9
|
26.0
|
1.0
|
N
|
B:ALA1
|
4.0
|
57.5
|
1.0
|
O
|
B:HOH508
|
4.3
|
32.2
|
1.0
|
OXT
|
B:LEU334
|
4.4
|
51.2
|
1.0
|
O
|
B:GLU333
|
4.5
|
53.6
|
1.0
|
OD2
|
A:ASP17
|
4.5
|
64.0
|
1.0
|
CG
|
A:ASP17
|
4.6
|
55.8
|
1.0
|
CD
|
B:GLU286
|
4.6
|
83.1
|
1.0
|
CA
|
B:ALA1
|
4.6
|
53.2
|
1.0
|
O
|
A:HOH684
|
4.7
|
30.1
|
1.0
|
OE1
|
B:GLU286
|
4.8
|
86.5
|
1.0
|
C
|
B:LEU334
|
4.8
|
53.2
|
1.0
|
|
Calcium binding site 3 out
of 7 in 6q3r
Go back to
Calcium Binding Sites List in 6q3r
Calcium binding site 3 out
of 7 in the Aspergillus Aculeatus Galactanase
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Aspergillus Aculeatus Galactanase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca510
b:80.5
occ:0.50
|
OE2
|
A:GLU329
|
3.1
|
66.8
|
1.0
|
CD
|
A:GLU329
|
3.9
|
59.8
|
1.0
|
OE1
|
A:GLU329
|
4.1
|
59.5
|
1.0
|
CD2
|
A:LEU25
|
5.0
|
40.5
|
1.0
|
|
Calcium binding site 4 out
of 7 in 6q3r
Go back to
Calcium Binding Sites List in 6q3r
Calcium binding site 4 out
of 7 in the Aspergillus Aculeatus Galactanase
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Aspergillus Aculeatus Galactanase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca511
b:72.3
occ:1.00
|
O
|
A:HOH709
|
2.7
|
49.0
|
1.0
|
OE1
|
A:GLU147
|
3.1
|
38.0
|
1.0
|
CD
|
A:GLU147
|
3.9
|
36.3
|
1.0
|
OE2
|
A:GLU147
|
4.0
|
38.4
|
1.0
|
O
|
A:HOH632
|
4.2
|
29.8
|
1.0
|
|
Calcium binding site 5 out
of 7 in 6q3r
Go back to
Calcium Binding Sites List in 6q3r
Calcium binding site 5 out
of 7 in the Aspergillus Aculeatus Galactanase
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Aspergillus Aculeatus Galactanase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca408
b:70.8
occ:1.00
|
O
|
B:HOH504
|
1.9
|
46.8
|
1.0
|
OD1
|
B:ASP17
|
2.9
|
54.3
|
1.0
|
O
|
B:HOH570
|
2.9
|
43.6
|
1.0
|
O
|
B:HOH565
|
3.1
|
45.1
|
1.0
|
OD2
|
B:ASP17
|
3.3
|
64.1
|
1.0
|
CG
|
B:ASP17
|
3.5
|
53.2
|
1.0
|
OE2
|
B:GLU64
|
3.8
|
33.1
|
1.0
|
OE1
|
B:GLU64
|
4.1
|
43.1
|
1.0
|
CD
|
B:GLU64
|
4.4
|
39.0
|
1.0
|
O
|
B:LEU13
|
4.7
|
40.3
|
1.0
|
CB
|
B:ASP17
|
5.0
|
51.0
|
1.0
|
|
Calcium binding site 6 out
of 7 in 6q3r
Go back to
Calcium Binding Sites List in 6q3r
Calcium binding site 6 out
of 7 in the Aspergillus Aculeatus Galactanase
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Aspergillus Aculeatus Galactanase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca409
b:64.7
occ:0.70
|
OD2
|
B:ASP102
|
2.4
|
60.5
|
1.0
|
O
|
B:HOH562
|
2.4
|
44.4
|
1.0
|
O
|
B:HOH554
|
2.5
|
31.1
|
1.0
|
CG
|
B:ASP102
|
3.2
|
48.6
|
1.0
|
OD1
|
B:ASP102
|
3.2
|
51.6
|
1.0
|
CB
|
B:ASP102
|
4.7
|
44.7
|
1.0
|
OG1
|
B:THR105
|
4.8
|
41.4
|
1.0
|
|
Calcium binding site 7 out
of 7 in 6q3r
Go back to
Calcium Binding Sites List in 6q3r
Calcium binding site 7 out
of 7 in the Aspergillus Aculeatus Galactanase
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Aspergillus Aculeatus Galactanase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca410
b:36.9
occ:0.50
|
O
|
B:HOH523
|
2.8
|
19.5
|
1.0
|
O3
|
B:GAL402
|
2.9
|
41.7
|
1.0
|
OE2
|
B:GLU246
|
2.9
|
39.1
|
1.0
|
OD2
|
B:ASP79
|
3.1
|
34.9
|
1.0
|
NE2
|
B:HIS81
|
3.1
|
35.6
|
1.0
|
OD1
|
B:ASN135
|
3.2
|
31.9
|
1.0
|
ND2
|
B:ASN135
|
3.4
|
33.4
|
1.0
|
O2
|
B:GAL402
|
3.4
|
37.6
|
1.0
|
CG
|
B:ASN135
|
3.5
|
32.4
|
1.0
|
NH1
|
B:ARG45
|
3.6
|
33.1
|
1.0
|
CE1
|
B:HIS81
|
3.6
|
34.7
|
1.0
|
NH2
|
B:ARG45
|
3.8
|
39.0
|
1.0
|
C3
|
B:GAL402
|
3.8
|
44.8
|
1.0
|
NE1
|
B:TRP297
|
3.9
|
29.9
|
1.0
|
CD
|
B:GLU246
|
4.0
|
38.5
|
1.0
|
CZ
|
B:ARG45
|
4.1
|
36.1
|
1.0
|
O
|
B:HOH512
|
4.2
|
45.5
|
1.0
|
CG
|
B:ASP79
|
4.3
|
34.2
|
1.0
|
C2
|
B:GAL402
|
4.3
|
43.0
|
1.0
|
CD2
|
B:HIS81
|
4.4
|
35.4
|
1.0
|
OE1
|
B:GLU246
|
4.6
|
37.2
|
1.0
|
CD1
|
B:TRP297
|
4.6
|
29.7
|
1.0
|
CE2
|
B:TRP297
|
4.6
|
30.5
|
1.0
|
CB
|
B:ASN135
|
4.7
|
33.8
|
1.0
|
OD1
|
B:ASP79
|
4.7
|
34.8
|
1.0
|
OD2
|
B:ASP8
|
4.8
|
31.9
|
1.0
|
CB
|
B:ARG47
|
4.8
|
30.4
|
1.0
|
CZ2
|
B:TRP297
|
4.9
|
30.7
|
1.0
|
ND1
|
B:HIS81
|
4.9
|
34.1
|
1.0
|
CG
|
B:GLU246
|
5.0
|
38.9
|
1.0
|
|
Reference:
S.Torpenholt,
J.C.N.Poulsen,
S.J.Muderspach,
L.De Maria,
L.Lo Leggio.
Structure of Aspergillus Aculeatus Beta-1,4-Galactanase in Complex with Galactobiose. Acta Crystallogr.,Sect.F V. 75 399 2019.
ISSN: ESSN 2053-230X
PubMed: 31204685
DOI: 10.1107/S2053230X19005612
Page generated: Tue Jul 16 13:15:46 2024
|