Sodium in PDB 6se8: Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q
Enzymatic activity of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q
All present enzymatic activity of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q:
3.2.1.23;
Protein crystallography data
The structure of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q, PDB code: 6se8
was solved by
M.Rutkiewicz,
A.Bujacz,
G.Bujacz,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.56 /
1.84
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
136.859,
136.859,
127.082,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
13.5 /
16.5
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q
(pdb code 6se8). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the
Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q, PDB code: 6se8:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
Sodium binding site 1 out
of 6 in 6se8
Go back to
Sodium Binding Sites List in 6se8
Sodium binding site 1 out
of 6 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1117
b:32.4
occ:1.00
|
OD2
|
A:ASP584
|
2.3
|
30.6
|
1.0
|
O
|
A:PHE581
|
2.4
|
30.5
|
1.0
|
O
|
A:HOH1541
|
2.4
|
44.9
|
1.0
|
OD2
|
A:ASP207
|
2.4
|
33.4
|
1.0
|
O
|
A:HOH1640
|
2.5
|
34.1
|
1.0
|
CG
|
A:ASP207
|
3.3
|
35.6
|
1.0
|
CG
|
A:ASP584
|
3.3
|
28.9
|
1.0
|
CD1
|
A:PHE581
|
3.4
|
39.7
|
0.5
|
C
|
A:PHE581
|
3.4
|
30.0
|
1.0
|
OD1
|
A:ASP207
|
3.5
|
29.8
|
1.0
|
CE1
|
A:PHE581
|
3.8
|
47.7
|
0.5
|
OH
|
A:TYR108
|
3.8
|
30.2
|
1.0
|
NE1
|
A:TRP548
|
3.9
|
25.1
|
1.0
|
OD1
|
A:ASP584
|
4.0
|
28.7
|
1.0
|
O
|
A:HOH1298
|
4.0
|
36.7
|
1.0
|
CG
|
A:PHE581
|
4.0
|
38.3
|
0.5
|
CA
|
A:VAL582
|
4.2
|
28.8
|
1.0
|
N
|
A:VAL582
|
4.2
|
32.5
|
1.0
|
CB
|
A:ASP584
|
4.3
|
28.4
|
1.0
|
OE1
|
A:GLU549
|
4.4
|
25.7
|
1.0
|
CB
|
A:PHE581
|
4.4
|
29.2
|
0.5
|
CB
|
A:PHE581
|
4.4
|
29.3
|
0.5
|
CA
|
A:PHE581
|
4.4
|
29.1
|
0.5
|
CA
|
A:PHE581
|
4.4
|
29.1
|
0.5
|
NE2
|
A:HIS520
|
4.5
|
26.5
|
1.0
|
CB
|
A:ASP207
|
4.6
|
29.4
|
1.0
|
CZ
|
A:PHE581
|
4.6
|
55.0
|
0.5
|
CE2
|
A:TRP548
|
4.7
|
22.8
|
1.0
|
CD1
|
A:TRP548
|
4.8
|
26.0
|
1.0
|
O
|
A:ASP207
|
4.8
|
28.4
|
1.0
|
CD2
|
A:PHE581
|
4.8
|
35.0
|
0.5
|
C
|
A:VAL582
|
4.9
|
33.1
|
1.0
|
O
|
A:HOH1605
|
4.9
|
39.4
|
1.0
|
CZ
|
A:TYR108
|
4.9
|
29.2
|
1.0
|
CZ2
|
A:TRP548
|
4.9
|
25.1
|
1.0
|
|
Sodium binding site 2 out
of 6 in 6se8
Go back to
Sodium Binding Sites List in 6se8
Sodium binding site 2 out
of 6 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1118
b:29.7
occ:1.00
|
O
|
A:HOH1871
|
2.3
|
38.8
|
1.0
|
O
|
A:LEU542
|
2.4
|
26.7
|
1.0
|
O
|
A:PHE536
|
2.4
|
28.7
|
1.0
|
O
|
A:HOH1881
|
2.4
|
40.0
|
1.0
|
O
|
A:TYR539
|
2.6
|
28.2
|
1.0
|
C
|
A:LEU542
|
3.5
|
28.1
|
1.0
|
C
|
A:TYR539
|
3.5
|
26.8
|
1.0
|
C
|
A:PHE536
|
3.5
|
28.9
|
1.0
|
O
|
A:PRO540
|
3.9
|
28.1
|
1.0
|
CA
|
A:PRO540
|
3.9
|
27.2
|
1.0
|
C
|
A:PRO540
|
4.0
|
25.3
|
1.0
|
CB
|
A:LEU542
|
4.1
|
24.4
|
1.0
|
CA
|
A:LEU542
|
4.1
|
23.5
|
1.0
|
N
|
A:LEU542
|
4.1
|
24.4
|
1.0
|
N
|
A:PRO540
|
4.1
|
27.6
|
1.0
|
CA
|
A:PHE536
|
4.2
|
26.9
|
1.0
|
NE
|
A:ARG325
|
4.4
|
39.6
|
1.0
|
CD
|
A:ARG325
|
4.4
|
37.2
|
1.0
|
N
|
A:TYR539
|
4.4
|
26.5
|
1.0
|
CA
|
A:TYR539
|
4.6
|
28.0
|
1.0
|
N
|
A:GLU537
|
4.6
|
29.2
|
1.0
|
N
|
A:MET543
|
4.6
|
24.6
|
1.0
|
CD1
|
A:LEU327
|
4.7
|
27.6
|
1.0
|
CA
|
A:GLU537
|
4.8
|
31.2
|
1.0
|
C
|
A:GLU537
|
4.8
|
33.7
|
1.0
|
N
|
A:ARG541
|
4.9
|
26.8
|
1.0
|
O
|
A:LEU535
|
4.9
|
26.2
|
1.0
|
CB
|
A:PHE536
|
4.9
|
24.9
|
1.0
|
CA
|
A:MET543
|
5.0
|
23.6
|
1.0
|
O
|
A:GLU537
|
5.0
|
38.3
|
1.0
|
|
Sodium binding site 3 out
of 6 in 6se8
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Sodium Binding Sites List in 6se8
Sodium binding site 3 out
of 6 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1119
b:39.2
occ:1.00
|
OD2
|
A:ASP651
|
2.3
|
32.9
|
1.0
|
O
|
A:HOH1904
|
2.3
|
44.0
|
1.0
|
O
|
A:HOH1764
|
2.4
|
29.7
|
1.0
|
O
|
A:HOH1884
|
2.5
|
41.0
|
1.0
|
O
|
A:HOH2019
|
2.5
|
44.9
|
1.0
|
CG
|
A:ASP651
|
3.4
|
32.5
|
1.0
|
CA
|
A:ASP651
|
4.0
|
30.0
|
1.0
|
CB
|
A:ASP651
|
4.0
|
29.7
|
1.0
|
N
|
A:VAL652
|
4.0
|
29.3
|
1.0
|
O
|
A:HOH1438
|
4.2
|
31.2
|
1.0
|
O
|
A:VAL652
|
4.3
|
29.9
|
1.0
|
O
|
A:HOH1809
|
4.3
|
48.1
|
1.0
|
O
|
A:HOH1447
|
4.4
|
29.9
|
1.0
|
O
|
A:HOH1914
|
4.4
|
38.5
|
1.0
|
OD1
|
A:ASP651
|
4.4
|
35.4
|
1.0
|
C
|
A:ASP651
|
4.5
|
33.9
|
1.0
|
O
|
A:HOH1248
|
4.6
|
50.6
|
1.0
|
C
|
A:VAL652
|
4.8
|
30.7
|
1.0
|
O
|
A:HOH1842
|
4.9
|
44.3
|
1.0
|
|
Sodium binding site 4 out
of 6 in 6se8
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Sodium Binding Sites List in 6se8
Sodium binding site 4 out
of 6 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1120
b:78.2
occ:1.00
|
O
|
A:HOH1292
|
2.5
|
33.9
|
1.0
|
O
|
A:HOH1799
|
2.6
|
53.2
|
1.0
|
O
|
A:HOH1833
|
2.8
|
39.7
|
1.0
|
O
|
A:HOH1728
|
2.9
|
53.4
|
1.0
|
O
|
A:ALA44
|
2.9
|
33.7
|
1.0
|
O
|
A:HOH2018
|
3.4
|
58.8
|
1.0
|
O
|
A:HOH1211
|
3.5
|
52.4
|
1.0
|
C
|
A:ALA44
|
3.8
|
35.6
|
1.0
|
O
|
A:HOH1892
|
3.9
|
55.6
|
1.0
|
OXT
|
A:ACT1101
|
4.0
|
58.8
|
1.0
|
O
|
A:HOH1671
|
4.2
|
45.3
|
1.0
|
N
|
A:ALA44
|
4.2
|
31.4
|
1.0
|
O
|
A:LEU45
|
4.3
|
31.3
|
1.0
|
CA
|
A:ALA44
|
4.4
|
33.4
|
1.0
|
CB
|
A:ALA44
|
4.5
|
34.1
|
1.0
|
O
|
A:HOH1810
|
4.6
|
46.4
|
1.0
|
NH2
|
A:ARG422
|
4.6
|
33.2
|
1.0
|
C
|
A:LEU45
|
4.7
|
31.6
|
1.0
|
C
|
A:ACT1101
|
4.7
|
28.3
|
1.0
|
O
|
A:ACT1101
|
4.8
|
40.0
|
1.0
|
N
|
A:LEU45
|
4.9
|
34.6
|
1.0
|
|
Sodium binding site 5 out
of 6 in 6se8
Go back to
Sodium Binding Sites List in 6se8
Sodium binding site 5 out
of 6 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1121
b:29.6
occ:1.00
|
O
|
A:HOH1642
|
2.3
|
37.0
|
1.0
|
O
|
A:PRO914
|
2.6
|
28.9
|
1.0
|
O
|
A:ALA957
|
2.6
|
32.7
|
1.0
|
O
|
A:ASP955
|
2.7
|
33.1
|
1.0
|
O
|
A:LEU954
|
2.7
|
31.0
|
1.0
|
O
|
A:HOH1575
|
3.0
|
31.2
|
1.0
|
NH2
|
A:ARG913
|
3.3
|
27.7
|
1.0
|
C
|
A:ASP955
|
3.3
|
35.0
|
1.0
|
CA
|
A:ASP955
|
3.6
|
29.2
|
1.0
|
C
|
A:PRO914
|
3.6
|
28.0
|
1.0
|
C
|
A:ALA957
|
3.7
|
31.9
|
1.0
|
C
|
A:LEU954
|
3.8
|
31.7
|
1.0
|
N
|
A:ALA957
|
3.9
|
32.9
|
1.0
|
O
|
A:HOH1241
|
4.1
|
57.9
|
1.0
|
N
|
A:ASP955
|
4.2
|
31.0
|
1.0
|
CA
|
A:ALA957
|
4.3
|
35.0
|
1.0
|
N
|
A:ALA956
|
4.3
|
31.8
|
1.0
|
CZ
|
A:ARG913
|
4.4
|
30.1
|
1.0
|
C
|
A:ALA956
|
4.4
|
36.3
|
1.0
|
CG
|
A:ARG913
|
4.4
|
27.5
|
1.0
|
OD1
|
A:ASP955
|
4.4
|
36.5
|
1.0
|
CA
|
A:PRO914
|
4.5
|
27.2
|
1.0
|
CB
|
A:PRO914
|
4.5
|
32.1
|
1.0
|
O
|
A:HOH1965
|
4.5
|
61.5
|
1.0
|
N
|
A:PRO914
|
4.5
|
28.9
|
1.0
|
N
|
A:GLN915
|
4.5
|
26.3
|
1.0
|
CB
|
A:ALA957
|
4.6
|
37.3
|
1.0
|
CA
|
A:GLN915
|
4.7
|
25.6
|
1.0
|
N
|
A:ALA958
|
4.8
|
34.1
|
1.0
|
CD
|
A:PRO914
|
4.8
|
28.3
|
1.0
|
CA
|
A:ALA956
|
4.9
|
34.8
|
1.0
|
CD
|
A:ARG913
|
4.9
|
30.3
|
1.0
|
CB
|
A:ASP955
|
4.9
|
30.1
|
1.0
|
|
Sodium binding site 6 out
of 6 in 6se8
Go back to
Sodium Binding Sites List in 6se8
Sodium binding site 6 out
of 6 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1122
b:60.2
occ:1.00
|
OE1
|
A:GLN882
|
2.2
|
41.7
|
0.5
|
O
|
A:ALA895
|
2.5
|
39.6
|
1.0
|
O
|
A:GLY892
|
2.6
|
29.7
|
1.0
|
O
|
A:HOH1452
|
2.6
|
55.1
|
1.0
|
O
|
A:HOH1505
|
2.7
|
60.2
|
1.0
|
OE1
|
A:GLN882
|
3.2
|
41.2
|
0.5
|
CD
|
A:GLN882
|
3.2
|
40.6
|
0.5
|
C
|
A:ALA895
|
3.6
|
29.2
|
1.0
|
C
|
A:GLY892
|
3.6
|
28.4
|
1.0
|
O
|
A:HOH1613
|
3.8
|
26.9
|
0.5
|
NE2
|
A:GLN882
|
3.9
|
53.4
|
0.5
|
CB
|
A:ALA895
|
4.0
|
31.4
|
1.0
|
CD
|
A:GLN882
|
4.0
|
37.5
|
0.5
|
CA
|
A:ALA895
|
4.2
|
28.7
|
1.0
|
N
|
A:ALA895
|
4.2
|
28.3
|
1.0
|
O
|
A:GLN893
|
4.2
|
31.3
|
1.0
|
CG
|
A:GLN882
|
4.3
|
29.0
|
0.5
|
CB
|
A:GLN882
|
4.3
|
38.6
|
0.5
|
CA
|
A:GLN893
|
4.3
|
30.2
|
1.0
|
CG
|
A:GLN882
|
4.3
|
29.1
|
0.5
|
O
|
A:HOH1988
|
4.3
|
57.4
|
1.0
|
C
|
A:GLN893
|
4.3
|
27.9
|
1.0
|
N
|
A:GLN893
|
4.4
|
28.0
|
1.0
|
CB
|
A:GLN882
|
4.5
|
30.4
|
0.5
|
CA
|
A:GLY892
|
4.5
|
28.7
|
1.0
|
N
|
A:ARG896
|
4.7
|
31.9
|
1.0
|
O
|
A:HOH1709
|
4.9
|
43.8
|
1.0
|
|
Reference:
M.Rutkiewicz,
A.Bujacz,
M.Wanarska,
A.Wierzbicka-Wos,
H.Cieslinski.
Active Site Architecture and Reaction Mechanism Determination of Cold Adapted Beta-D-Galactosidase Fromarthrobactersp. 32CB. Int J Mol Sci V. 20 2019.
ISSN: ESSN 1422-0067
PubMed: 31484304
DOI: 10.3390/IJMS20174301
Page generated: Tue Oct 8 13:25:50 2024
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