Sodium in PDB 6sea: Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Lactose Bound in Deep Mode
Enzymatic activity of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Lactose Bound in Deep Mode
All present enzymatic activity of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Lactose Bound in Deep Mode:
3.2.1.23;
Protein crystallography data
The structure of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Lactose Bound in Deep Mode, PDB code: 6sea
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)
|
46.89 /
1.87
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
138.613,
138.613,
127.347,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
18.2 /
20.5
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Lactose Bound in Deep Mode
(pdb code 6sea). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Lactose Bound in Deep Mode, PDB code: 6sea:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 6sea
Go back to
Sodium Binding Sites List in 6sea
Sodium binding site 1 out
of 4 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Lactose Bound in Deep Mode
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 in Complex with Lactose Bound in Deep Mode within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1102
b:45.5
occ:1.00
|
OD2
|
A:ASP584
|
2.3
|
40.1
|
1.0
|
O
|
A:PHE581
|
2.4
|
49.4
|
1.0
|
O
|
A:HOH1572
|
2.4
|
40.6
|
1.0
|
OD2
|
A:ASP207
|
2.4
|
40.0
|
1.0
|
O6
|
A:LAT1101
|
2.6
|
50.5
|
1.0
|
CG
|
A:ASP584
|
3.3
|
42.1
|
1.0
|
CG
|
A:ASP207
|
3.3
|
42.1
|
1.0
|
C
|
A:PHE581
|
3.5
|
49.0
|
1.0
|
OD1
|
A:ASP207
|
3.7
|
41.4
|
1.0
|
C6
|
A:LAT1101
|
3.8
|
48.9
|
1.0
|
CD2
|
A:PHE581
|
3.8
|
53.5
|
1.0
|
NE1
|
A:TRP548
|
3.9
|
38.7
|
1.0
|
OD1
|
A:ASP584
|
3.9
|
39.5
|
1.0
|
OH
|
A:TYR108
|
3.9
|
39.1
|
1.0
|
CA
|
A:VAL582
|
4.1
|
44.2
|
1.0
|
O4
|
A:LAT1101
|
4.1
|
41.5
|
1.0
|
N
|
A:VAL582
|
4.2
|
44.1
|
1.0
|
CB
|
A:ASP584
|
4.2
|
40.9
|
1.0
|
OE2
|
A:GLU549
|
4.3
|
35.8
|
1.0
|
C4
|
A:LAT1101
|
4.3
|
45.0
|
1.0
|
CB
|
A:ASP207
|
4.5
|
36.1
|
1.0
|
CB
|
A:PHE581
|
4.5
|
48.0
|
1.0
|
CA
|
A:PHE581
|
4.5
|
48.4
|
1.0
|
C5
|
A:LAT1101
|
4.6
|
48.3
|
1.0
|
CG
|
A:PHE581
|
4.6
|
50.0
|
1.0
|
CE2
|
A:PHE581
|
4.6
|
53.6
|
1.0
|
NE2
|
A:HIS520
|
4.7
|
38.6
|
1.0
|
CE2
|
A:TRP548
|
4.8
|
35.1
|
1.0
|
O
|
A:ASP207
|
4.8
|
35.5
|
1.0
|
C
|
A:VAL582
|
4.8
|
44.4
|
1.0
|
CD1
|
A:TRP548
|
4.9
|
36.6
|
1.0
|
CZ2
|
A:TRP548
|
4.9
|
35.1
|
1.0
|
|
Sodium binding site 2 out
of 4 in 6sea
Go back to
Sodium Binding Sites List in 6sea
Sodium binding site 2 out
of 4 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Lactose Bound in Deep Mode
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 in Complex with Lactose Bound in Deep Mode within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1103
b:56.4
occ:1.00
|
OE1
|
A:GLN951
|
2.6
|
51.0
|
1.0
|
OE1
|
A:GLU916
|
2.7
|
45.8
|
1.0
|
N
|
A:ALA763
|
2.9
|
45.3
|
1.0
|
O
|
A:HOH1330
|
3.4
|
43.9
|
1.0
|
CB
|
A:TRP762
|
3.4
|
48.3
|
1.0
|
CD
|
A:GLN951
|
3.5
|
51.7
|
1.0
|
CA
|
A:TRP762
|
3.5
|
47.4
|
1.0
|
CB
|
A:ALA763
|
3.6
|
46.8
|
1.0
|
C
|
A:TRP762
|
3.7
|
45.0
|
1.0
|
NH1
|
A:ARG947
|
3.7
|
47.9
|
1.0
|
CG
|
A:GLN951
|
3.7
|
52.1
|
1.0
|
CA
|
A:ALA763
|
3.8
|
46.4
|
1.0
|
CD
|
A:GLU916
|
3.8
|
46.1
|
1.0
|
CD2
|
A:LEU954
|
3.8
|
47.7
|
1.0
|
NH2
|
A:ARG947
|
3.9
|
46.8
|
1.0
|
CB
|
A:GLU916
|
3.9
|
45.2
|
1.0
|
CA
|
A:GLU916
|
4.1
|
45.4
|
1.0
|
CZ
|
A:ARG947
|
4.1
|
45.9
|
1.0
|
CB
|
A:GLN951
|
4.3
|
50.1
|
1.0
|
NH2
|
A:ARG863
|
4.3
|
44.3
|
1.0
|
CG
|
A:GLU916
|
4.4
|
45.0
|
1.0
|
CG
|
A:TRP762
|
4.6
|
48.8
|
1.0
|
O
|
A:ALA763
|
4.6
|
44.2
|
1.0
|
NE2
|
A:GLN951
|
4.7
|
52.8
|
1.0
|
N
|
A:GLU916
|
4.7
|
46.5
|
1.0
|
C
|
A:ALA763
|
4.7
|
43.9
|
1.0
|
CA
|
A:GLN951
|
4.8
|
51.6
|
1.0
|
OE2
|
A:GLU916
|
4.9
|
45.6
|
1.0
|
O
|
A:TRP762
|
4.9
|
44.5
|
1.0
|
N
|
A:TRP762
|
4.9
|
47.4
|
1.0
|
CG
|
A:LEU954
|
5.0
|
48.7
|
1.0
|
|
Sodium binding site 3 out
of 4 in 6sea
Go back to
Sodium Binding Sites List in 6sea
Sodium binding site 3 out
of 4 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Lactose Bound in Deep Mode
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 in Complex with Lactose Bound in Deep Mode within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1104
b:43.5
occ:1.00
|
O
|
A:PRO914
|
2.5
|
48.9
|
1.0
|
O
|
A:ALA957
|
2.6
|
52.9
|
1.0
|
O
|
A:LEU954
|
2.7
|
49.9
|
1.0
|
O
|
A:ASP955
|
2.8
|
52.1
|
1.0
|
O
|
A:HOH1444
|
3.0
|
43.5
|
1.0
|
O
|
A:HOH1759
|
3.1
|
48.6
|
1.0
|
C
|
A:ASP955
|
3.3
|
53.3
|
1.0
|
NH2
|
A:ARG913
|
3.3
|
42.5
|
1.0
|
CA
|
A:ASP955
|
3.5
|
51.3
|
1.0
|
C
|
A:PRO914
|
3.6
|
48.5
|
1.0
|
C
|
A:ALA957
|
3.7
|
51.9
|
1.0
|
C
|
A:LEU954
|
3.7
|
49.1
|
1.0
|
N
|
A:ALA957
|
3.9
|
51.8
|
1.0
|
N
|
A:ASP955
|
4.1
|
50.4
|
1.0
|
OD1
|
A:ASP955
|
4.3
|
48.9
|
1.0
|
CA
|
A:ALA957
|
4.3
|
52.2
|
1.0
|
N
|
A:ALA956
|
4.3
|
52.5
|
1.0
|
CA
|
A:PRO914
|
4.4
|
49.8
|
1.0
|
CB
|
A:PRO914
|
4.4
|
50.0
|
1.0
|
C
|
A:ALA956
|
4.4
|
52.4
|
1.0
|
CZ
|
A:ARG913
|
4.4
|
43.3
|
1.0
|
N
|
A:GLN915
|
4.5
|
44.1
|
1.0
|
N
|
A:PRO914
|
4.5
|
47.5
|
1.0
|
CG
|
A:ARG913
|
4.5
|
44.8
|
1.0
|
CB
|
A:ALA957
|
4.6
|
51.1
|
1.0
|
CA
|
A:GLN915
|
4.7
|
43.7
|
1.0
|
CD
|
A:PRO914
|
4.8
|
48.0
|
1.0
|
N
|
A:ALA958
|
4.9
|
53.8
|
1.0
|
O
|
A:HOH1669
|
4.9
|
50.3
|
1.0
|
CB
|
A:ASP955
|
4.9
|
49.1
|
1.0
|
CA
|
A:ALA956
|
4.9
|
52.8
|
1.0
|
CD
|
A:ARG913
|
4.9
|
44.1
|
1.0
|
O
|
A:ALA956
|
4.9
|
52.0
|
1.0
|
C
|
A:ARG913
|
5.0
|
44.8
|
1.0
|
|
Sodium binding site 4 out
of 4 in 6sea
Go back to
Sodium Binding Sites List in 6sea
Sodium binding site 4 out
of 4 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Lactose Bound in Deep Mode
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 in Complex with Lactose Bound in Deep Mode within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1105
b:43.8
occ:1.00
|
O
|
A:GLN206
|
2.6
|
39.5
|
1.0
|
O
|
A:HOH1475
|
2.8
|
44.7
|
1.0
|
OD1
|
A:ASP205
|
2.8
|
40.2
|
1.0
|
O
|
A:ASN110
|
2.9
|
41.0
|
1.0
|
O
|
A:THR109
|
3.0
|
43.2
|
1.0
|
OG1
|
A:THR109
|
3.1
|
44.6
|
1.0
|
C
|
A:GLN206
|
3.6
|
38.2
|
1.0
|
CZ2
|
A:TRP210
|
3.6
|
42.4
|
1.0
|
O
|
A:ASP205
|
3.7
|
40.4
|
1.0
|
NE1
|
A:TRP210
|
3.7
|
42.9
|
1.0
|
C
|
A:THR109
|
3.7
|
43.0
|
1.0
|
CE2
|
A:TRP210
|
3.8
|
42.9
|
1.0
|
C
|
A:ASN110
|
3.8
|
42.2
|
1.0
|
C
|
A:ASP205
|
3.8
|
40.9
|
1.0
|
CG
|
A:ASP205
|
3.9
|
40.0
|
1.0
|
CA
|
A:ASP205
|
4.2
|
38.2
|
1.0
|
CB
|
A:THR109
|
4.3
|
43.7
|
1.0
|
N
|
A:GLN206
|
4.3
|
39.5
|
1.0
|
N
|
A:ASN110
|
4.3
|
44.3
|
1.0
|
N
|
A:ASP207
|
4.3
|
38.3
|
1.0
|
CA
|
A:ASN110
|
4.4
|
44.3
|
1.0
|
CA
|
A:ASP207
|
4.4
|
37.1
|
1.0
|
O
|
A:MET208
|
4.4
|
39.9
|
1.0
|
O
|
A:GLN112
|
4.4
|
43.4
|
1.0
|
CA
|
A:THR109
|
4.5
|
42.8
|
1.0
|
N
|
A:MET208
|
4.5
|
36.8
|
1.0
|
O
|
A:HOH1642
|
4.5
|
38.6
|
1.0
|
CA
|
A:GLN206
|
4.6
|
41.0
|
1.0
|
CH2
|
A:TRP210
|
4.6
|
41.1
|
1.0
|
OD2
|
A:ASP205
|
4.6
|
39.5
|
1.0
|
CD1
|
A:TRP210
|
4.7
|
43.4
|
1.0
|
CB
|
A:ASP205
|
4.7
|
38.8
|
1.0
|
O
|
A:HOH1421
|
4.7
|
38.5
|
1.0
|
N
|
A:VAL111
|
4.8
|
43.7
|
1.0
|
O
|
A:VAL111
|
4.8
|
42.0
|
1.0
|
N
|
A:THR109
|
4.8
|
42.8
|
1.0
|
CD2
|
A:TRP210
|
4.9
|
43.1
|
1.0
|
C
|
A:VAL111
|
5.0
|
45.1
|
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 13:26:20 2024
|