Sodium in PDB 6tbg: 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: 6tbg
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)
|
115.98 /
1.50
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
99.285,
115.735,
115.981,
90.12,
90.00,
90.03
|
R / Rfree (%)
|
13.8 /
18.2
|
Sodium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
30;
Binding sites:
The binding sites of Sodium atom in the Structure of A Beta Galactosidase with Inhibitor
(pdb code 6tbg). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 30 binding sites of Sodium where determined in the
Structure of A Beta Galactosidase with Inhibitor, PDB code: 6tbg:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 30 in 6tbg
Go back to
Sodium Binding Sites List in 6tbg
Sodium binding site 1 out
of 30 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:33.4
occ:1.00
|
O
|
A:GLY466
|
2.3
|
30.1
|
1.0
|
O
|
A:HOH1071
|
2.3
|
45.1
|
1.0
|
O
|
A:HOH798
|
2.4
|
44.0
|
1.0
|
OG
|
A:SER518
|
2.5
|
38.1
|
1.0
|
OD1
|
A:ASP464
|
2.5
|
30.0
|
1.0
|
OE1
|
A:GLN519
|
2.5
|
34.5
|
0.7
|
CG
|
A:ASP464
|
3.3
|
29.9
|
1.0
|
C
|
A:GLY466
|
3.3
|
27.5
|
1.0
|
CB
|
A:SER518
|
3.3
|
35.9
|
1.0
|
OD2
|
A:ASP464
|
3.4
|
33.2
|
1.0
|
NA
|
A:NA606
|
3.5
|
39.8
|
1.0
|
CD
|
A:GLN519
|
3.6
|
40.2
|
0.7
|
CA
|
A:GLY466
|
3.6
|
27.8
|
1.0
|
N
|
A:GLY466
|
3.9
|
27.8
|
1.0
|
NE2
|
A:GLN519
|
4.0
|
41.2
|
0.7
|
OD1
|
A:ASP469
|
4.5
|
29.3
|
1.0
|
N
|
A:LEU467
|
4.5
|
27.2
|
1.0
|
CB
|
A:ASP464
|
4.6
|
26.6
|
1.0
|
CA
|
A:SER518
|
4.6
|
32.0
|
1.0
|
O
|
A:HOH944
|
4.8
|
39.6
|
1.0
|
CG
|
A:GLN519
|
4.9
|
42.3
|
0.7
|
C
|
A:SER518
|
5.0
|
36.1
|
1.0
|
|
Sodium binding site 2 out
of 30 in 6tbg
Go back to
Sodium Binding Sites List in 6tbg
Sodium binding site 2 out
of 30 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:Na604
b:27.1
occ:1.00
|
O
|
A:HOH906
|
2.5
|
22.5
|
1.0
|
OE2
|
A:GLU533
|
2.5
|
21.8
|
1.0
|
O
|
A:HOH800
|
2.5
|
37.5
|
1.0
|
OE1
|
A:GLU544
|
2.7
|
26.0
|
1.0
|
O
|
A:HOH1122
|
2.7
|
43.1
|
1.0
|
O
|
A:HOH736
|
3.0
|
32.5
|
1.0
|
CD
|
A:GLU533
|
3.4
|
20.4
|
1.0
|
CD
|
A:GLU544
|
3.6
|
26.1
|
1.0
|
CG
|
A:GLU533
|
3.6
|
19.4
|
1.0
|
OE2
|
A:GLU544
|
3.8
|
27.4
|
1.0
|
O
|
A:HOH960
|
3.8
|
22.3
|
1.0
|
O
|
A:HOH1064
|
4.1
|
33.5
|
1.0
|
O
|
B:HOH953
|
4.1
|
47.3
|
1.0
|
O
|
A:PRO562
|
4.3
|
21.1
|
1.0
|
O
|
A:GLY534
|
4.5
|
22.6
|
1.0
|
OE1
|
A:GLU533
|
4.6
|
19.9
|
1.0
|
O
|
A:HOH1083
|
4.6
|
27.6
|
1.0
|
ND1
|
A:HIS563
|
4.6
|
20.7
|
1.0
|
CA
|
A:HIS563
|
4.6
|
18.5
|
1.0
|
O
|
A:HOH1142
|
4.7
|
26.6
|
1.0
|
O
|
A:HOH1172
|
4.7
|
28.6
|
1.0
|
N
|
A:LEU564
|
4.9
|
18.6
|
1.0
|
CG
|
A:GLU544
|
5.0
|
24.0
|
1.0
|
|
Sodium binding site 3 out
of 30 in 6tbg
Go back to
Sodium Binding Sites List in 6tbg
Sodium binding site 3 out
of 30 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:Na605
b:33.0
occ:1.00
|
O
|
A:HIS49
|
2.4
|
26.2
|
1.0
|
O
|
A:GLY367
|
2.6
|
24.0
|
1.0
|
OG
|
A:SER417
|
2.9
|
38.8
|
1.0
|
O
|
A:HOH1020
|
2.9
|
37.3
|
1.0
|
O
|
A:HOH899
|
3.3
|
29.5
|
1.0
|
C
|
A:GLY367
|
3.4
|
21.3
|
1.0
|
CA
|
A:GLY367
|
3.6
|
23.5
|
1.0
|
C
|
A:HIS49
|
3.6
|
24.4
|
1.0
|
CB
|
A:SER417
|
3.8
|
30.6
|
1.0
|
C
|
A:SER417
|
3.9
|
36.5
|
1.0
|
N
|
A:TYR418
|
3.9
|
28.7
|
1.0
|
O
|
A:SER417
|
4.0
|
43.2
|
1.0
|
CA
|
A:TYR418
|
4.2
|
29.2
|
1.0
|
N
|
A:HIS49
|
4.3
|
25.9
|
1.0
|
O
|
A:HOH914
|
4.4
|
26.3
|
1.0
|
O
|
A:HOH1030
|
4.4
|
47.1
|
1.0
|
CA
|
A:SER417
|
4.4
|
28.6
|
1.0
|
CA
|
A:HIS49
|
4.4
|
25.9
|
1.0
|
N
|
A:ALA50
|
4.6
|
24.4
|
1.0
|
O
|
A:GLY368
|
4.6
|
23.8
|
1.0
|
O
|
A:HOH883
|
4.6
|
23.9
|
1.0
|
N
|
A:GLY368
|
4.6
|
21.9
|
1.0
|
CB
|
A:TYR418
|
4.6
|
26.9
|
1.0
|
CA
|
A:ALA50
|
4.7
|
26.0
|
1.0
|
CG2
|
A:ILE369
|
4.7
|
26.2
|
1.0
|
C
|
A:GLY368
|
4.8
|
21.1
|
1.0
|
CB
|
A:HIS49
|
4.8
|
26.3
|
1.0
|
O
|
A:HOH939
|
4.9
|
31.1
|
1.0
|
O
|
A:HOH834
|
4.9
|
28.9
|
1.0
|
|
Sodium binding site 4 out
of 30 in 6tbg
Go back to
Sodium Binding Sites List in 6tbg
Sodium binding site 4 out
of 30 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:Na606
b:39.8
occ:1.00
|
O
|
A:HOH1062
|
2.1
|
52.4
|
1.0
|
O
|
A:HOH944
|
2.2
|
39.6
|
1.0
|
O
|
A:SER518
|
2.4
|
40.3
|
1.0
|
O
|
A:HOH798
|
2.5
|
44.0
|
1.0
|
OG
|
A:SER518
|
2.6
|
38.1
|
1.0
|
OE1
|
A:GLN519
|
2.8
|
34.5
|
0.7
|
C
|
A:SER518
|
3.2
|
36.1
|
1.0
|
NA
|
A:NA601
|
3.5
|
33.4
|
1.0
|
CB
|
A:SER518
|
3.5
|
35.9
|
1.0
|
CD
|
A:GLN519
|
3.7
|
40.2
|
0.7
|
CA
|
A:SER518
|
3.7
|
32.0
|
1.0
|
CG
|
A:GLN519
|
4.0
|
42.3
|
0.7
|
N
|
A:GLN519
|
4.2
|
40.1
|
1.0
|
OD2
|
A:ASP469
|
4.3
|
33.5
|
1.0
|
OD1
|
A:ASP469
|
4.4
|
29.3
|
1.0
|
OD2
|
A:ASP464
|
4.6
|
33.2
|
1.0
|
CA
|
A:GLN519
|
4.7
|
38.5
|
1.0
|
OD1
|
A:ASP464
|
4.7
|
30.0
|
1.0
|
NE2
|
A:GLN519
|
4.8
|
41.2
|
0.7
|
CG
|
A:ASP464
|
4.8
|
29.9
|
1.0
|
CG
|
A:ASP469
|
4.8
|
26.4
|
1.0
|
CB
|
A:GLN519
|
4.9
|
40.5
|
1.0
|
O
|
A:HOH703
|
5.0
|
44.1
|
1.0
|
|
Sodium binding site 5 out
of 30 in 6tbg
Go back to
Sodium Binding Sites List in 6tbg
Sodium binding site 5 out
of 30 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:34.8
occ:1.00
|
O
|
B:GLY466
|
2.3
|
31.2
|
1.0
|
O
|
B:HOH1032
|
2.3
|
39.9
|
1.0
|
OG
|
B:SER518
|
2.4
|
38.7
|
1.0
|
O
|
B:HOH1132
|
2.5
|
43.6
|
1.0
|
OD1
|
B:ASP464
|
2.5
|
30.8
|
1.0
|
O
|
B:HOH1111
|
2.7
|
48.9
|
1.0
|
CG
|
B:ASP464
|
3.3
|
32.5
|
1.0
|
CB
|
B:SER518
|
3.3
|
37.9
|
1.0
|
O
|
B:HOH708
|
3.3
|
31.0
|
1.0
|
C
|
B:GLY466
|
3.3
|
29.4
|
1.0
|
OD2
|
B:ASP464
|
3.4
|
34.1
|
1.0
|
CA
|
B:GLY466
|
3.7
|
28.0
|
1.0
|
N
|
B:GLY466
|
4.0
|
28.0
|
1.0
|
OD1
|
B:ASP469
|
4.5
|
28.8
|
1.0
|
O
|
B:HOH1244
|
4.5
|
51.5
|
1.0
|
N
|
B:LEU467
|
4.6
|
27.0
|
1.0
|
CB
|
B:ASP464
|
4.6
|
29.9
|
1.0
|
CA
|
B:SER518
|
4.6
|
34.8
|
1.0
|
O
|
B:HOH855
|
4.7
|
45.3
|
1.0
|
C
|
B:SER518
|
4.9
|
38.8
|
1.0
|
O
|
B:SER518
|
4.9
|
38.5
|
1.0
|
|
Sodium binding site 6 out
of 30 in 6tbg
Go back to
Sodium Binding Sites List in 6tbg
Sodium binding site 6 out
of 30 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:Na605
b:27.9
occ:0.50
|
O
|
B:HOH1112
|
2.1
|
34.7
|
0.5
|
O
|
B:HOH1146
|
2.2
|
36.5
|
0.5
|
O
|
B:HOH960
|
2.3
|
30.4
|
0.5
|
O
|
B:HOH940
|
2.5
|
24.4
|
1.0
|
O
|
B:THR488
|
2.6
|
25.3
|
1.0
|
O
|
B:HOH1028
|
2.8
|
38.6
|
1.0
|
C
|
B:THR488
|
3.5
|
24.2
|
1.0
|
O
|
B:HOH735
|
3.6
|
42.2
|
1.0
|
N
|
B:THR488
|
4.0
|
22.3
|
1.0
|
N
|
B:PRO489
|
4.1
|
23.9
|
1.0
|
CD
|
B:PRO489
|
4.1
|
24.2
|
1.0
|
NZ
|
B:LYS510
|
4.1
|
26.0
|
1.0
|
CA
|
B:THR488
|
4.4
|
24.6
|
1.0
|
O
|
B:HOH1038
|
4.5
|
24.8
|
1.0
|
O
|
B:PRO489
|
4.6
|
23.0
|
1.0
|
CB
|
B:ASN487
|
4.8
|
20.2
|
1.0
|
O
|
B:HOH1149
|
4.9
|
35.3
|
1.0
|
C
|
B:ASN487
|
5.0
|
21.5
|
1.0
|
|
Sodium binding site 7 out
of 30 in 6tbg
Go back to
Sodium Binding Sites List in 6tbg
Sodium binding site 7 out
of 30 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
|
C:Na601
b:45.5
occ:1.00
|
O
|
C:HOH960
|
2.1
|
41.0
|
0.7
|
OG
|
C:SER518
|
2.4
|
42.6
|
1.0
|
O
|
C:SER518
|
2.6
|
43.2
|
1.0
|
O
|
C:HOH996
|
2.7
|
46.1
|
1.0
|
C
|
C:SER518
|
3.2
|
44.0
|
1.0
|
NA
|
C:NA602
|
3.4
|
39.5
|
1.0
|
CB
|
C:SER518
|
3.5
|
42.0
|
1.0
|
CA
|
C:SER518
|
3.7
|
39.7
|
1.0
|
N
|
C:GLN519
|
4.2
|
43.1
|
1.0
|
OD2
|
C:ASP469
|
4.4
|
36.6
|
1.0
|
OD1
|
C:ASP469
|
4.4
|
33.9
|
1.0
|
OD2
|
C:ASP464
|
4.5
|
40.9
|
1.0
|
CA
|
C:GLN519
|
4.7
|
45.3
|
1.0
|
CG
|
C:ASP464
|
4.7
|
34.9
|
1.0
|
OD1
|
C:ASP464
|
4.7
|
34.1
|
1.0
|
CG
|
C:ASP469
|
4.8
|
32.3
|
1.0
|
|
Sodium binding site 8 out
of 30 in 6tbg
Go back to
Sodium Binding Sites List in 6tbg
Sodium binding site 8 out
of 30 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:Na602
b:39.5
occ:1.00
|
O
|
C:GLY466
|
2.3
|
34.1
|
1.0
|
OG
|
C:SER518
|
2.4
|
42.6
|
1.0
|
OD1
|
C:ASP464
|
2.5
|
34.1
|
1.0
|
O
|
C:HOH996
|
2.7
|
46.1
|
1.0
|
CG
|
C:ASP464
|
3.3
|
34.9
|
1.0
|
CB
|
C:SER518
|
3.3
|
42.0
|
1.0
|
C
|
C:GLY466
|
3.3
|
31.3
|
1.0
|
OD2
|
C:ASP464
|
3.4
|
40.9
|
1.0
|
NA
|
C:NA601
|
3.4
|
45.5
|
1.0
|
CA
|
C:GLY466
|
3.6
|
31.4
|
1.0
|
N
|
C:GLY466
|
3.9
|
31.1
|
1.0
|
OD1
|
C:ASP469
|
4.4
|
33.9
|
1.0
|
O
|
C:HOH960
|
4.5
|
41.0
|
0.7
|
N
|
C:LEU467
|
4.5
|
32.2
|
1.0
|
CB
|
C:ASP464
|
4.6
|
30.1
|
1.0
|
CA
|
C:SER518
|
4.6
|
39.7
|
1.0
|
C
|
C:SER518
|
5.0
|
44.0
|
1.0
|
|
Sodium binding site 9 out
of 30 in 6tbg
Go back to
Sodium Binding Sites List in 6tbg
Sodium binding site 9 out
of 30 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:Na605
b:25.7
occ:1.00
|
OE2
|
C:GLU533
|
2.5
|
22.1
|
1.0
|
O
|
C:HOH866
|
2.5
|
22.4
|
1.0
|
OE1
|
C:GLU544
|
2.6
|
25.6
|
1.0
|
O
|
C:HOH900
|
2.8
|
36.5
|
1.0
|
O
|
C:HOH742
|
3.0
|
35.6
|
1.0
|
O
|
C:HOH1177
|
3.0
|
50.4
|
1.0
|
CD
|
C:GLU533
|
3.4
|
22.0
|
1.0
|
O
|
C:HOH1158
|
3.4
|
49.2
|
1.0
|
CD
|
C:GLU544
|
3.5
|
23.0
|
1.0
|
CG
|
C:GLU533
|
3.6
|
19.6
|
1.0
|
OE2
|
C:GLU544
|
3.7
|
25.7
|
1.0
|
O
|
C:HOH1004
|
3.8
|
22.9
|
1.0
|
O
|
C:HOH1094
|
4.1
|
34.9
|
1.0
|
O
|
C:PRO562
|
4.4
|
21.6
|
1.0
|
O
|
C:GLY534
|
4.5
|
22.8
|
1.0
|
OE1
|
C:GLU533
|
4.6
|
21.3
|
1.0
|
O
|
A:HOH744
|
4.6
|
52.5
|
1.0
|
ND1
|
C:HIS563
|
4.6
|
20.6
|
1.0
|
CA
|
C:HIS563
|
4.7
|
19.4
|
1.0
|
O
|
C:HOH1113
|
4.8
|
25.3
|
1.0
|
O
|
C:HOH1221
|
4.8
|
26.6
|
1.0
|
O
|
C:HOH1190
|
4.8
|
27.2
|
1.0
|
CG
|
C:GLU544
|
4.9
|
21.9
|
1.0
|
N
|
C:LEU564
|
4.9
|
20.2
|
1.0
|
N
|
C:GLY534
|
5.0
|
19.3
|
1.0
|
|
Sodium binding site 10 out
of 30 in 6tbg
Go back to
Sodium Binding Sites List in 6tbg
Sodium binding site 10 out
of 30 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:Na606
b:31.0
occ:1.00
|
O
|
C:SER417
|
2.3
|
23.7
|
0.5
|
O
|
C:HIS49
|
2.3
|
26.5
|
1.0
|
O
|
C:GLY367
|
2.5
|
23.4
|
1.0
|
O
|
C:HOH1069
|
2.6
|
27.9
|
1.0
|
OG
|
C:SER417
|
2.7
|
32.3
|
0.5
|
C
|
C:GLY367
|
3.4
|
20.6
|
1.0
|
C
|
C:SER417
|
3.4
|
24.3
|
0.5
|
C
|
C:HIS49
|
3.5
|
24.6
|
1.0
|
CA
|
C:GLY367
|
3.6
|
19.8
|
1.0
|
O
|
C:HOH887
|
3.6
|
29.9
|
1.0
|
CB
|
C:SER417
|
3.8
|
29.9
|
0.5
|
C
|
C:SER417
|
3.9
|
31.1
|
0.5
|
O
|
C:SER417
|
4.0
|
32.5
|
0.5
|
N
|
C:TYR418
|
4.1
|
24.7
|
1.0
|
N
|
C:HIS49
|
4.1
|
26.0
|
1.0
|
OG
|
C:SER417
|
4.1
|
25.8
|
0.5
|
O
|
C:HOH1058
|
4.2
|
39.4
|
1.0
|
CA
|
C:TYR418
|
4.2
|
28.5
|
1.0
|
CB
|
C:SER417
|
4.3
|
25.9
|
0.5
|
CA
|
C:HIS49
|
4.3
|
25.3
|
1.0
|
O
|
C:HOH946
|
4.4
|
25.1
|
1.0
|
CA
|
C:SER417
|
4.4
|
26.5
|
0.5
|
CA
|
C:SER417
|
4.5
|
30.6
|
0.5
|
N
|
C:ALA50
|
4.5
|
23.7
|
1.0
|
N
|
C:GLY368
|
4.6
|
21.6
|
1.0
|
O
|
C:GLY368
|
4.6
|
23.0
|
1.0
|
CB
|
C:HIS49
|
4.7
|
25.8
|
1.0
|
O
|
C:HOH844
|
4.7
|
23.2
|
1.0
|
O
|
C:HOH899
|
4.7
|
28.7
|
1.0
|
CA
|
C:ALA50
|
4.7
|
25.6
|
1.0
|
CB
|
C:TYR418
|
4.7
|
27.1
|
1.0
|
CG2
|
C:ILE369
|
4.8
|
25.0
|
1.0
|
C
|
C:GLY368
|
4.8
|
20.6
|
1.0
|
|
Reference:
W.Offen,
G.Davies.
Structure of A Beta Galactosidase with Inhibitor To Be Published.
Page generated: Tue Oct 8 13:39:29 2024
|