Sodium in PDB 6tbk: Structure of A Beta Galactosidase with Inhibitor
Enzymatic activity of Structure of A Beta Galactosidase with Inhibitor
All present enzymatic activity of Structure of A Beta Galactosidase with Inhibitor:
3.2.1.23;
Protein crystallography data
The structure of Structure of A Beta Galactosidase with Inhibitor, PDB code: 6tbk
was solved by
W.Offen,
G.Davies,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
63.20 /
1.60
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
98.952,
116.052,
115.576,
89.84,
90.07,
89.98
|
R / Rfree (%)
|
15.2 /
21.2
|
Sodium Binding Sites:
Sodium binding site 1 out
of 32 in 6tbk
Go back to
Sodium Binding Sites List in 6tbk
Sodium binding site 1 out
of 32 in the Structure of A Beta Galactosidase with Inhibitor
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Structure of A Beta Galactosidase with Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na601
b:37.5
occ:1.00
|
O
|
A:HOH916
|
2.2
|
46.7
|
1.0
|
O
|
A:GLY466
|
2.4
|
32.4
|
1.0
|
OD1
|
A:ASP464
|
2.5
|
29.0
|
1.0
|
OG
|
A:SER518
|
2.5
|
40.6
|
1.0
|
O
|
A:HOH751
|
2.5
|
40.0
|
1.0
|
OE1
|
A:GLN519
|
2.6
|
51.0
|
1.0
|
CB
|
A:SER518
|
3.2
|
44.1
|
1.0
|
CG
|
A:ASP464
|
3.2
|
35.8
|
1.0
|
NA
|
A:NA602
|
3.3
|
40.2
|
1.0
|
C
|
A:GLY466
|
3.4
|
27.1
|
1.0
|
OD2
|
A:ASP464
|
3.4
|
39.0
|
1.0
|
CD
|
A:GLN519
|
3.5
|
63.3
|
1.0
|
NE2
|
A:GLN519
|
3.7
|
59.0
|
1.0
|
CA
|
A:GLY466
|
3.8
|
30.0
|
1.0
|
N
|
A:GLY466
|
3.9
|
27.3
|
1.0
|
OD1
|
A:ASP469
|
4.4
|
39.5
|
1.0
|
N
|
A:LEU467
|
4.6
|
29.0
|
1.0
|
CA
|
A:SER518
|
4.6
|
38.6
|
1.0
|
O
|
A:HOH828
|
4.6
|
40.7
|
1.0
|
CB
|
A:ASP464
|
4.6
|
29.7
|
1.0
|
C
|
A:SER518
|
4.9
|
42.6
|
1.0
|
CG
|
A:GLN519
|
5.0
|
60.7
|
1.0
|
|
Sodium binding site 2 out
of 32 in 6tbk
Go back to
Sodium Binding Sites List in 6tbk
Sodium binding site 2 out
of 32 in the Structure of A Beta Galactosidase with Inhibitor
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Structure of A Beta Galactosidase with Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na602
b:40.2
occ:1.00
|
O
|
A:HOH828
|
2.2
|
40.7
|
1.0
|
O
|
A:HOH751
|
2.6
|
40.0
|
1.0
|
O
|
A:SER518
|
2.6
|
44.3
|
1.0
|
OE1
|
A:GLN519
|
2.6
|
51.0
|
1.0
|
OG
|
A:SER518
|
2.7
|
40.6
|
1.0
|
C
|
A:SER518
|
3.2
|
42.6
|
1.0
|
NA
|
A:NA601
|
3.3
|
37.5
|
1.0
|
CB
|
A:SER518
|
3.5
|
44.1
|
1.0
|
CD
|
A:GLN519
|
3.6
|
63.3
|
1.0
|
CA
|
A:SER518
|
3.7
|
38.6
|
1.0
|
CG
|
A:GLN519
|
4.2
|
60.7
|
1.0
|
N
|
A:GLN519
|
4.2
|
43.6
|
1.0
|
OD2
|
A:ASP469
|
4.4
|
31.2
|
1.0
|
OD1
|
A:ASP469
|
4.4
|
39.5
|
1.0
|
OD1
|
A:ASP464
|
4.4
|
29.0
|
1.0
|
NE2
|
A:GLN519
|
4.6
|
59.0
|
1.0
|
OD2
|
A:ASP464
|
4.6
|
39.0
|
1.0
|
CG
|
A:ASP464
|
4.7
|
35.8
|
1.0
|
CA
|
A:GLN519
|
4.7
|
51.0
|
1.0
|
CG
|
A:ASP469
|
4.8
|
32.2
|
1.0
|
O
|
A:HOH916
|
4.8
|
46.7
|
1.0
|
|
Sodium binding site 3 out
of 32 in 6tbk
Go back to
Sodium Binding Sites List in 6tbk
Sodium binding site 3 out
of 32 in the Structure of A Beta Galactosidase with Inhibitor
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Structure of A Beta Galactosidase with Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na603
b:33.4
occ:1.00
|
O
|
A:HOH810
|
2.4
|
24.3
|
1.0
|
OE2
|
A:GLU533
|
2.5
|
28.0
|
1.0
|
OE1
|
A:GLU544
|
2.6
|
28.8
|
1.0
|
O
|
A:HOH827
|
3.1
|
37.2
|
1.0
|
CD
|
A:GLU533
|
3.4
|
33.6
|
1.0
|
CD
|
A:GLU544
|
3.6
|
30.9
|
1.0
|
CG
|
A:GLU533
|
3.7
|
22.5
|
1.0
|
OE2
|
A:GLU544
|
3.8
|
35.5
|
1.0
|
O
|
A:HOH849
|
3.9
|
28.0
|
1.0
|
O
|
A:HOH912
|
4.1
|
38.1
|
1.0
|
O
|
A:PRO562
|
4.4
|
25.0
|
1.0
|
O
|
A:GLY534
|
4.4
|
26.6
|
1.0
|
OE1
|
A:GLU533
|
4.5
|
25.9
|
1.0
|
CA
|
A:HIS563
|
4.6
|
23.2
|
1.0
|
O
|
A:HOH936
|
4.6
|
31.7
|
1.0
|
O
|
A:HOH920
|
4.7
|
28.2
|
1.0
|
ND1
|
A:HIS563
|
4.7
|
24.2
|
1.0
|
O
|
A:HOH929
|
4.9
|
33.9
|
1.0
|
N
|
A:LEU564
|
4.9
|
19.5
|
1.0
|
O
|
A:HOH753
|
4.9
|
33.0
|
1.0
|
N
|
A:GLY534
|
5.0
|
22.0
|
1.0
|
CG
|
A:GLU544
|
5.0
|
25.5
|
1.0
|
C
|
A:GLY534
|
5.0
|
30.1
|
1.0
|
|
Sodium binding site 4 out
of 32 in 6tbk
Go back to
Sodium Binding Sites List in 6tbk
Sodium binding site 4 out
of 32 in the Structure of A Beta Galactosidase with Inhibitor
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Structure of A Beta Galactosidase with Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na604
b:39.8
occ:1.00
|
O
|
A:HIS49
|
2.5
|
27.8
|
1.0
|
O
|
A:GLY367
|
2.5
|
29.1
|
1.0
|
O
|
A:HOH868
|
3.0
|
35.8
|
1.0
|
O
|
A:HOH872
|
3.2
|
36.4
|
1.0
|
C
|
A:GLY367
|
3.4
|
25.1
|
1.0
|
C
|
A:HIS49
|
3.6
|
27.2
|
1.0
|
CA
|
A:GLY367
|
3.7
|
24.5
|
1.0
|
OG
|
A:SER417
|
3.7
|
50.4
|
1.0
|
CB
|
A:SER417
|
3.8
|
38.2
|
1.0
|
C
|
A:SER417
|
3.9
|
35.5
|
1.0
|
N
|
A:TYR418
|
4.0
|
27.1
|
1.0
|
O
|
A:SER417
|
4.0
|
41.3
|
1.0
|
CA
|
A:TYR418
|
4.2
|
25.5
|
1.0
|
N
|
A:HIS49
|
4.3
|
31.1
|
1.0
|
O
|
A:HOH853
|
4.4
|
27.7
|
1.0
|
O
|
A:GLY368
|
4.4
|
23.7
|
1.0
|
CA
|
A:SER417
|
4.5
|
27.6
|
1.0
|
CA
|
A:HIS49
|
4.5
|
27.7
|
1.0
|
O
|
A:HOH858
|
4.5
|
24.3
|
1.0
|
N
|
A:ALA50
|
4.6
|
27.3
|
1.0
|
CA
|
A:ALA50
|
4.6
|
27.7
|
1.0
|
O
|
A:HOH857
|
4.6
|
30.2
|
1.0
|
CG2
|
A:ILE369
|
4.6
|
29.4
|
1.0
|
N
|
A:GLY368
|
4.6
|
23.1
|
1.0
|
C
|
A:GLY368
|
4.6
|
24.8
|
1.0
|
CB
|
A:TYR418
|
4.7
|
28.6
|
1.0
|
CB
|
A:HIS49
|
4.8
|
31.2
|
1.0
|
O
|
A:HOH846
|
4.8
|
33.3
|
1.0
|
|
Sodium binding site 5 out
of 32 in 6tbk
Go back to
Sodium Binding Sites List in 6tbk
Sodium binding site 5 out
of 32 in the Structure of A Beta Galactosidase with Inhibitor
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Structure of A Beta Galactosidase with Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na601
b:38.3
occ:1.00
|
O
|
B:HOH963
|
2.2
|
38.5
|
1.0
|
O
|
B:GLY466
|
2.3
|
31.4
|
1.0
|
OG
|
B:SER518
|
2.4
|
36.5
|
1.0
|
OD1
|
B:ASP464
|
2.5
|
34.9
|
1.0
|
CG
|
B:ASP464
|
3.3
|
36.7
|
1.0
|
CB
|
B:SER518
|
3.3
|
49.6
|
1.0
|
O
|
B:HOH703
|
3.3
|
32.4
|
1.0
|
C
|
B:GLY466
|
3.4
|
33.7
|
1.0
|
OD2
|
B:ASP464
|
3.4
|
42.0
|
1.0
|
CA
|
B:GLY466
|
3.8
|
29.1
|
1.0
|
N
|
B:GLY466
|
4.0
|
34.1
|
1.0
|
OD1
|
B:ASP469
|
4.4
|
33.6
|
1.0
|
NE2
|
B:GLN519
|
4.5
|
48.4
|
0.5
|
N
|
B:LEU467
|
4.6
|
30.8
|
1.0
|
CB
|
B:ASP464
|
4.6
|
30.1
|
1.0
|
CA
|
B:SER518
|
4.6
|
39.7
|
1.0
|
O
|
B:HOH794
|
4.7
|
37.6
|
1.0
|
O
|
B:SER518
|
5.0
|
41.0
|
1.0
|
C
|
B:SER518
|
5.0
|
42.8
|
1.0
|
|
Sodium binding site 6 out
of 32 in 6tbk
Go back to
Sodium Binding Sites List in 6tbk
Sodium binding site 6 out
of 32 in the Structure of A Beta Galactosidase with Inhibitor
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Structure of A Beta Galactosidase with Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na602
b:34.1
occ:1.00
|
OE1
|
B:GLU544
|
2.4
|
29.2
|
1.0
|
OE2
|
B:GLU533
|
2.5
|
27.4
|
1.0
|
O
|
B:HOH754
|
2.6
|
25.5
|
1.0
|
O
|
B:HOH732
|
3.2
|
35.2
|
1.0
|
CD
|
B:GLU533
|
3.4
|
22.5
|
1.0
|
CD
|
B:GLU544
|
3.5
|
28.2
|
1.0
|
CG
|
B:GLU533
|
3.6
|
21.5
|
1.0
|
O
|
B:HOH882
|
3.7
|
29.5
|
1.0
|
OE2
|
B:GLU544
|
3.8
|
31.6
|
1.0
|
O
|
H:HOH828
|
4.2
|
49.0
|
1.0
|
O
|
B:GLY534
|
4.4
|
25.5
|
1.0
|
O
|
B:PRO562
|
4.5
|
22.8
|
1.0
|
OE1
|
B:GLU533
|
4.5
|
25.1
|
1.0
|
ND1
|
B:HIS563
|
4.7
|
23.4
|
1.0
|
O
|
B:HOH736
|
4.7
|
36.4
|
1.0
|
O
|
B:HOH977
|
4.8
|
29.1
|
1.0
|
CA
|
B:HIS563
|
4.8
|
20.8
|
1.0
|
O
|
B:HOH998
|
4.8
|
32.2
|
1.0
|
CG
|
B:GLU544
|
4.8
|
24.1
|
1.0
|
O
|
B:HOH994
|
4.9
|
31.1
|
1.0
|
|
Sodium binding site 7 out
of 32 in 6tbk
Go back to
Sodium Binding Sites List in 6tbk
Sodium binding site 7 out
of 32 in the Structure of A Beta Galactosidase with Inhibitor
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Structure of A Beta Galactosidase with Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na603
b:36.1
occ:1.00
|
O
|
B:HIS49
|
2.4
|
29.6
|
1.0
|
O
|
B:GLY367
|
2.6
|
24.8
|
1.0
|
OG
|
B:SER417
|
2.9
|
40.6
|
1.0
|
O
|
B:HOH950
|
2.9
|
37.5
|
1.0
|
O
|
B:HOH946
|
3.1
|
33.2
|
1.0
|
C
|
B:GLY367
|
3.5
|
25.8
|
1.0
|
C
|
B:HIS49
|
3.6
|
24.7
|
1.0
|
CA
|
B:GLY367
|
3.7
|
24.5
|
1.0
|
CB
|
B:SER417
|
3.8
|
28.4
|
1.0
|
C
|
B:SER417
|
3.9
|
40.6
|
1.0
|
N
|
B:TYR418
|
4.1
|
28.6
|
1.0
|
O
|
B:SER417
|
4.1
|
49.4
|
1.0
|
N
|
B:HIS49
|
4.3
|
25.9
|
1.0
|
CA
|
B:TYR418
|
4.3
|
30.4
|
1.0
|
O
|
B:HOH891
|
4.4
|
41.8
|
1.0
|
CA
|
B:HIS49
|
4.4
|
26.5
|
1.0
|
CA
|
B:SER417
|
4.5
|
24.1
|
1.0
|
O
|
B:HOH896
|
4.5
|
26.1
|
1.0
|
N
|
B:ALA50
|
4.5
|
23.6
|
1.0
|
O
|
B:HOH838
|
4.6
|
23.0
|
1.0
|
O
|
B:GLY368
|
4.6
|
23.6
|
1.0
|
CA
|
B:ALA50
|
4.6
|
26.5
|
1.0
|
N
|
B:GLY368
|
4.7
|
23.3
|
1.0
|
CG2
|
B:ILE369
|
4.7
|
29.8
|
1.0
|
C
|
B:GLY368
|
4.8
|
21.9
|
1.0
|
CB
|
B:HIS49
|
4.8
|
25.0
|
1.0
|
O
|
B:HOH807
|
4.8
|
28.1
|
1.0
|
CB
|
B:TYR418
|
4.8
|
30.2
|
1.0
|
O
|
B:HOH812
|
5.0
|
38.7
|
1.0
|
|
Sodium binding site 8 out
of 32 in 6tbk
Go back to
Sodium Binding Sites List in 6tbk
Sodium binding site 8 out
of 32 in the Structure of A Beta Galactosidase with Inhibitor
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of Structure of A Beta Galactosidase with Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na601
b:33.9
occ:1.00
|
O
|
C:HOH855
|
2.4
|
25.2
|
1.0
|
OE2
|
C:GLU533
|
2.5
|
28.0
|
1.0
|
OE1
|
C:GLU544
|
2.6
|
28.3
|
1.0
|
O
|
C:HOH706
|
2.6
|
39.2
|
1.0
|
O
|
C:HOH812
|
3.2
|
37.0
|
1.0
|
CD
|
C:GLU533
|
3.3
|
27.1
|
1.0
|
CD
|
C:GLU544
|
3.5
|
30.0
|
1.0
|
CG
|
C:GLU533
|
3.6
|
20.6
|
1.0
|
OE2
|
C:GLU544
|
3.8
|
32.0
|
1.0
|
O
|
C:HOH897
|
3.8
|
29.0
|
1.0
|
O
|
C:HOH905
|
4.0
|
46.4
|
1.0
|
O
|
C:PRO562
|
4.3
|
26.7
|
1.0
|
O
|
C:GLY534
|
4.4
|
23.6
|
1.0
|
OE1
|
C:GLU533
|
4.5
|
26.7
|
1.0
|
ND1
|
C:HIS563
|
4.6
|
25.8
|
1.0
|
O
|
C:HOH950
|
4.7
|
26.0
|
1.0
|
CA
|
C:HIS563
|
4.7
|
20.6
|
1.0
|
O
|
C:HOH979
|
4.7
|
26.9
|
1.0
|
CG
|
C:GLU544
|
4.9
|
28.3
|
1.0
|
N
|
C:LEU564
|
4.9
|
22.8
|
1.0
|
N
|
C:GLY534
|
4.9
|
24.7
|
1.0
|
O
|
C:HOH973
|
5.0
|
34.4
|
1.0
|
CB
|
C:GLU533
|
5.0
|
20.9
|
1.0
|
|
Sodium binding site 9 out
of 32 in 6tbk
Go back to
Sodium Binding Sites List in 6tbk
Sodium binding site 9 out
of 32 in the Structure of A Beta Galactosidase with Inhibitor
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 9 of Structure of A Beta Galactosidase with Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na602
b:39.3
occ:1.00
|
O
|
C:HIS49
|
2.3
|
30.3
|
1.0
|
O
|
C:GLY367
|
2.5
|
28.2
|
1.0
|
O
|
C:HOH927
|
2.7
|
32.8
|
1.0
|
OG
|
C:SER417
|
3.1
|
49.4
|
1.0
|
C
|
C:GLY367
|
3.4
|
25.7
|
1.0
|
O
|
C:HOH763
|
3.5
|
31.5
|
0.7
|
C
|
C:HIS49
|
3.6
|
31.5
|
1.0
|
CA
|
C:GLY367
|
3.6
|
24.4
|
1.0
|
O
|
C:SER417
|
3.6
|
61.8
|
1.0
|
C
|
C:SER417
|
3.8
|
42.1
|
1.0
|
CB
|
C:SER417
|
4.0
|
38.2
|
1.0
|
N
|
C:TYR418
|
4.1
|
29.7
|
1.0
|
CA
|
C:TYR418
|
4.2
|
36.1
|
1.0
|
N
|
C:HIS49
|
4.2
|
25.0
|
1.0
|
O
|
C:HOH895
|
4.3
|
38.4
|
1.0
|
O
|
C:HOH835
|
4.4
|
27.7
|
1.0
|
CA
|
C:HIS49
|
4.4
|
28.3
|
1.0
|
CA
|
C:SER417
|
4.5
|
28.9
|
1.0
|
N
|
C:ALA50
|
4.5
|
26.1
|
1.0
|
O
|
C:GLY368
|
4.6
|
24.0
|
1.0
|
N
|
C:GLY368
|
4.6
|
22.6
|
1.0
|
O
|
C:HOH851
|
4.6
|
22.8
|
1.0
|
CA
|
C:ALA50
|
4.7
|
27.5
|
1.0
|
CB
|
C:HIS49
|
4.7
|
26.9
|
1.0
|
CG2
|
C:ILE369
|
4.8
|
29.9
|
1.0
|
CB
|
C:TYR418
|
4.8
|
29.4
|
1.0
|
C
|
C:GLY368
|
4.8
|
24.4
|
1.0
|
O
|
C:HOH839
|
4.9
|
32.7
|
1.0
|
O
|
C:HOH747
|
4.9
|
29.9
|
1.0
|
|
Sodium binding site 10 out
of 32 in 6tbk
Go back to
Sodium Binding Sites List in 6tbk
Sodium binding site 10 out
of 32 in the Structure of A Beta Galactosidase with Inhibitor
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 10 of Structure of A Beta Galactosidase with Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na603
b:48.0
occ:1.00
|
O
|
C:GLY466
|
2.3
|
36.8
|
1.0
|
OD1
|
C:ASP464
|
2.5
|
37.4
|
1.0
|
OG
|
C:SER518
|
2.5
|
44.0
|
1.0
|
O
|
C:HOH941
|
2.6
|
42.1
|
1.0
|
NA
|
C:NA604
|
3.1
|
50.6
|
1.0
|
CB
|
C:SER518
|
3.2
|
47.9
|
1.0
|
CG
|
C:ASP464
|
3.2
|
41.0
|
1.0
|
OD2
|
C:ASP464
|
3.3
|
48.9
|
1.0
|
C
|
C:GLY466
|
3.4
|
31.9
|
1.0
|
CA
|
C:GLY466
|
3.8
|
37.1
|
1.0
|
N
|
C:GLY466
|
3.9
|
35.9
|
1.0
|
OD1
|
C:ASP469
|
4.3
|
44.6
|
1.0
|
CA
|
C:SER518
|
4.6
|
42.2
|
1.0
|
N
|
C:LEU467
|
4.6
|
36.5
|
1.0
|
O
|
C:HOH776
|
4.6
|
36.5
|
0.5
|
CB
|
C:ASP464
|
4.6
|
37.3
|
1.0
|
C
|
C:SER518
|
4.9
|
52.3
|
1.0
|
|
Reference:
W.Offen,
G.Davies.
Structure of A Beta Galactosidase with Inhibitor To Be Published.
Page generated: Tue Oct 8 13:39:54 2024
|