Sodium in PDB 3t09: E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex
Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex
All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex:
3.2.1.23;
Protein crystallography data
The structure of E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex, PDB code: 3t09
was solved by
L.J.Jancewicz,
R.W.Wheatley,
G.Sutendra,
M.Lee,
M.Fraser,
R.E.Huber,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
128.40 /
1.75
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
126.881,
151.197,
131.808,
90.00,
103.05,
90.00
|
|
R / Rfree (%)
|
21.5 /
25.4
|
Other elements in 3t09:
The structure of E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex also contains other interesting chemical elements:
Sodium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
16;
Binding sites:
The binding sites of Sodium atom in the E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex
(pdb code 3t09). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 16 binding sites of Sodium where determined in the
E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex, PDB code: 3t09:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 16 in 3t09
Go back to
Sodium Binding Sites List in 3t09
Sodium binding site 1 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3101
b:12.8
occ:1.00
|
O
|
A:HOH4264
|
2.2
|
14.0
|
1.0
|
|
OD1
|
A:ASN604
|
2.4
|
21.4
|
1.0
|
|
OD2
|
A:ASP201
|
2.4
|
10.7
|
1.0
|
|
O
|
A:PHE601
|
2.4
|
12.7
|
1.0
|
|
O6
|
A:1492001
|
2.4
|
16.5
|
1.0
|
|
CG
|
A:ASP201
|
3.3
|
12.1
|
1.0
|
|
CD2
|
A:PHE601
|
3.3
|
8.9
|
1.0
|
|
CG
|
A:ASN604
|
3.4
|
18.5
|
1.0
|
|
CE2
|
A:PHE601
|
3.5
|
8.7
|
1.0
|
|
C
|
A:PHE601
|
3.6
|
15.9
|
1.0
|
|
C6
|
A:1492001
|
3.6
|
13.2
|
1.0
|
|
OD1
|
A:ASP201
|
3.6
|
14.1
|
1.0
|
|
OH
|
A:TYR100
|
3.7
|
15.9
|
1.0
|
|
ND2
|
A:ASN604
|
3.8
|
11.4
|
1.0
|
|
CG
|
A:PHE601
|
4.0
|
13.6
|
1.0
|
|
O4
|
A:1492001
|
4.1
|
13.6
|
1.0
|
|
C4
|
A:1492001
|
4.1
|
18.0
|
1.0
|
|
CZ
|
A:PHE601
|
4.1
|
15.8
|
1.0
|
|
NE1
|
A:TRP568
|
4.2
|
18.9
|
1.0
|
|
CA
|
A:CYS602
|
4.3
|
16.6
|
1.0
|
|
N
|
A:CYS602
|
4.3
|
16.6
|
1.0
|
|
C5
|
A:1492001
|
4.4
|
14.3
|
1.0
|
|
CB
|
A:ASP201
|
4.5
|
9.4
|
1.0
|
|
O
|
A:HOH4049
|
4.5
|
18.1
|
1.0
|
|
CD1
|
A:PHE601
|
4.6
|
14.5
|
1.0
|
|
NE2
|
A:HIS540
|
4.6
|
18.2
|
1.0
|
|
CA
|
A:PHE601
|
4.6
|
16.7
|
1.0
|
|
CB
|
A:PHE601
|
4.6
|
16.3
|
1.0
|
|
CE1
|
A:PHE601
|
4.7
|
12.4
|
1.0
|
|
O
|
A:ASP201
|
4.7
|
15.3
|
1.0
|
|
CB
|
A:ASN604
|
4.8
|
14.7
|
1.0
|
|
C
|
A:CYS602
|
4.8
|
12.9
|
1.0
|
|
CZ
|
A:TYR100
|
4.9
|
15.9
|
1.0
|
|
CE2
|
A:TRP568
|
5.0
|
14.8
|
1.0
|
|
Sodium binding site 2 out
of 16 in 3t09
Go back to
Sodium Binding Sites List in 3t09
Sodium binding site 2 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3102
b:17.1
occ:1.00
|
O
|
A:HOH4594
|
2.2
|
36.2
|
1.0
|
|
O
|
A:PHE556
|
2.3
|
13.4
|
1.0
|
|
O
|
A:TYR559
|
2.4
|
14.6
|
1.0
|
|
O
|
A:LEU562
|
2.4
|
13.1
|
1.0
|
|
O
|
A:HOH4383
|
2.9
|
26.2
|
1.0
|
|
O
|
A:PRO560
|
3.2
|
14.9
|
1.0
|
|
C
|
A:TYR559
|
3.3
|
15.1
|
1.0
|
|
C
|
A:LEU562
|
3.5
|
12.7
|
1.0
|
|
C
|
A:PHE556
|
3.5
|
14.4
|
1.0
|
|
C
|
A:PRO560
|
3.6
|
11.9
|
1.0
|
|
CA
|
A:PRO560
|
3.7
|
17.4
|
1.0
|
|
N
|
A:PRO560
|
3.9
|
12.9
|
1.0
|
|
O
|
A:HOH4270
|
4.0
|
18.2
|
1.0
|
|
N
|
A:LEU562
|
4.1
|
10.2
|
1.0
|
|
O
|
A:HOH4754
|
4.2
|
32.5
|
1.0
|
|
CA
|
A:PHE556
|
4.2
|
11.8
|
1.0
|
|
CA
|
A:LEU562
|
4.3
|
10.5
|
1.0
|
|
N
|
A:GLN563
|
4.4
|
10.8
|
1.0
|
|
CA
|
A:TYR559
|
4.4
|
14.7
|
1.0
|
|
N
|
A:TYR559
|
4.4
|
11.1
|
1.0
|
|
CA
|
A:GLN563
|
4.5
|
11.8
|
1.0
|
|
CB
|
A:LEU562
|
4.5
|
7.2
|
1.0
|
|
N
|
A:ARG557
|
4.5
|
10.4
|
1.0
|
|
N
|
A:ARG561
|
4.6
|
14.3
|
1.0
|
|
CA
|
A:ARG557
|
4.7
|
10.5
|
1.0
|
|
CG
|
A:GLN563
|
4.7
|
10.1
|
1.0
|
|
CD1
|
A:LEU350
|
4.7
|
16.3
|
1.0
|
|
C
|
A:ARG557
|
4.7
|
11.5
|
1.0
|
|
O
|
A:HOH4763
|
4.7
|
30.1
|
1.0
|
|
O
|
A:ARG557
|
4.8
|
15.1
|
1.0
|
|
CB
|
A:PHE556
|
4.8
|
10.3
|
1.0
|
|
C
|
A:ARG561
|
4.9
|
11.4
|
1.0
|
|
Sodium binding site 3 out
of 16 in 3t09
Go back to
Sodium Binding Sites List in 3t09
Sodium binding site 3 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3103
b:27.4
occ:1.00
|
O
|
A:PRO932
|
2.4
|
21.2
|
1.0
|
|
O
|
A:LEU967
|
2.4
|
21.8
|
1.0
|
|
O
|
A:THR970
|
2.7
|
23.9
|
1.0
|
|
O
|
A:HOH4198
|
2.8
|
21.6
|
1.0
|
|
C
|
A:PRO932
|
3.4
|
17.8
|
1.0
|
|
C
|
A:LEU967
|
3.6
|
23.2
|
1.0
|
|
O
|
A:HOH4686
|
3.6
|
31.3
|
1.0
|
|
CZ
|
A:PHE931
|
3.6
|
21.7
|
1.0
|
|
O
|
A:HOH4515
|
3.7
|
40.6
|
1.0
|
|
C
|
A:THR970
|
3.8
|
22.3
|
1.0
|
|
CE1
|
A:PHE931
|
3.9
|
24.0
|
1.0
|
|
CE2
|
A:PHE931
|
3.9
|
20.9
|
1.0
|
|
CA
|
A:MET968
|
3.9
|
26.9
|
1.0
|
|
CB
|
A:PRO932
|
3.9
|
15.0
|
1.0
|
|
CA
|
A:PRO932
|
4.0
|
17.9
|
1.0
|
|
N
|
A:PRO932
|
4.1
|
17.2
|
1.0
|
|
C
|
A:MET968
|
4.1
|
25.4
|
1.0
|
|
CD
|
A:PRO932
|
4.1
|
17.4
|
1.0
|
|
O
|
A:MET968
|
4.1
|
28.4
|
1.0
|
|
N
|
A:MET968
|
4.2
|
23.4
|
1.0
|
|
N
|
A:THR970
|
4.3
|
20.9
|
1.0
|
|
N
|
A:SER933
|
4.4
|
19.3
|
1.0
|
|
CD1
|
A:PHE931
|
4.4
|
21.1
|
1.0
|
|
CD2
|
A:PHE931
|
4.4
|
21.8
|
1.0
|
|
CG
|
A:PRO932
|
4.5
|
17.9
|
1.0
|
|
CA
|
A:THR970
|
4.7
|
22.3
|
1.0
|
|
CG
|
A:PHE931
|
4.7
|
15.2
|
1.0
|
|
N
|
A:GLU969
|
4.7
|
22.7
|
1.0
|
|
CA
|
A:LEU967
|
4.7
|
19.8
|
1.0
|
|
CA
|
A:SER933
|
4.8
|
20.2
|
1.0
|
|
N
|
A:SER971
|
4.8
|
24.0
|
1.0
|
|
C
|
A:PHE931
|
4.8
|
17.4
|
1.0
|
|
CA
|
A:SER971
|
4.9
|
20.3
|
1.0
|
|
Sodium binding site 4 out
of 16 in 3t09
Go back to
Sodium Binding Sites List in 3t09
Sodium binding site 4 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3104
b:32.2
occ:1.00
|
O
|
A:HOH5051
|
2.3
|
33.3
|
1.0
|
|
O
|
A:DMS8022
|
2.3
|
37.2
|
1.0
|
|
O
|
A:HOH4833
|
2.3
|
34.2
|
1.0
|
|
O
|
A:LEU670
|
2.4
|
23.6
|
1.0
|
|
O
|
A:SER647
|
2.5
|
19.6
|
1.0
|
|
O
|
A:GLU650
|
2.8
|
18.4
|
1.0
|
|
C
|
A:LEU670
|
3.6
|
21.1
|
1.0
|
|
N
|
A:GLU650
|
3.6
|
20.8
|
1.0
|
|
C
|
A:SER647
|
3.7
|
25.4
|
1.0
|
|
C
|
A:GLU650
|
3.8
|
16.5
|
1.0
|
|
S
|
A:DMS8022
|
4.0
|
48.0
|
1.0
|
|
C
|
A:ASP648
|
4.0
|
23.9
|
1.0
|
|
N
|
A:LEU670
|
4.0
|
29.1
|
1.0
|
|
CA
|
A:ASP648
|
4.1
|
24.8
|
1.0
|
|
CA
|
A:GLU650
|
4.1
|
17.9
|
1.0
|
|
N
|
A:ASN649
|
4.1
|
19.4
|
1.0
|
|
O
|
A:HOH4964
|
4.2
|
27.8
|
1.0
|
|
CA
|
A:LEU670
|
4.2
|
24.2
|
1.0
|
|
N
|
A:ASP648
|
4.4
|
21.3
|
1.0
|
|
CB
|
A:GLU650
|
4.4
|
18.6
|
1.0
|
|
O
|
A:ASP648
|
4.4
|
23.8
|
1.0
|
|
C1
|
A:DMS8022
|
4.4
|
44.1
|
1.0
|
|
OG
|
A:SER647
|
4.4
|
19.5
|
1.0
|
|
CB
|
A:LEU670
|
4.5
|
28.5
|
1.0
|
|
C
|
A:ASN649
|
4.7
|
16.6
|
1.0
|
|
N
|
A:ASP671
|
4.7
|
21.9
|
1.0
|
|
CA
|
A:ASN649
|
4.8
|
19.8
|
1.0
|
|
CB
|
A:SER647
|
4.8
|
21.8
|
1.0
|
|
CA
|
A:SER647
|
4.9
|
19.9
|
1.0
|
|
CA
|
A:ASP671
|
5.0
|
26.0
|
1.0
|
|
C
|
A:PRO669
|
5.0
|
29.5
|
1.0
|
|
Sodium binding site 5 out
of 16 in 3t09
Go back to
Sodium Binding Sites List in 3t09
Sodium binding site 5 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3101
b:15.1
occ:1.00
|
O
|
B:HOH4288
|
2.3
|
16.7
|
1.0
|
|
O
|
B:PHE601
|
2.4
|
17.3
|
1.0
|
|
OD1
|
B:ASN604
|
2.4
|
18.2
|
1.0
|
|
O6
|
B:1492001
|
2.4
|
16.2
|
1.0
|
|
OD2
|
B:ASP201
|
2.4
|
18.0
|
1.0
|
|
CG
|
B:ASP201
|
3.3
|
10.6
|
1.0
|
|
CD2
|
B:PHE601
|
3.4
|
17.0
|
1.0
|
|
CG
|
B:ASN604
|
3.4
|
20.4
|
1.0
|
|
CE2
|
B:PHE601
|
3.5
|
15.0
|
1.0
|
|
C
|
B:PHE601
|
3.6
|
19.6
|
1.0
|
|
C6
|
B:1492001
|
3.6
|
13.5
|
1.0
|
|
OD1
|
B:ASP201
|
3.7
|
18.5
|
1.0
|
|
OH
|
B:TYR100
|
3.7
|
18.3
|
1.0
|
|
ND2
|
B:ASN604
|
3.7
|
13.4
|
1.0
|
|
CG
|
B:PHE601
|
4.0
|
15.0
|
1.0
|
|
C4
|
B:1492001
|
4.1
|
13.4
|
1.0
|
|
CZ
|
B:PHE601
|
4.1
|
20.2
|
1.0
|
|
O4
|
B:1492001
|
4.1
|
13.4
|
1.0
|
|
NE1
|
B:TRP568
|
4.2
|
13.9
|
1.0
|
|
CA
|
B:CYS602
|
4.3
|
16.6
|
1.0
|
|
N
|
B:CYS602
|
4.3
|
18.3
|
1.0
|
|
C5
|
B:1492001
|
4.3
|
16.7
|
1.0
|
|
O
|
B:HOH4071
|
4.4
|
23.5
|
1.0
|
|
CB
|
B:ASP201
|
4.4
|
12.6
|
1.0
|
|
NE2
|
B:HIS540
|
4.6
|
15.5
|
1.0
|
|
CD1
|
B:PHE601
|
4.6
|
16.8
|
1.0
|
|
CA
|
B:PHE601
|
4.6
|
15.0
|
1.0
|
|
CE1
|
B:PHE601
|
4.6
|
17.0
|
1.0
|
|
CB
|
B:PHE601
|
4.6
|
17.6
|
1.0
|
|
O
|
B:ASP201
|
4.7
|
15.7
|
1.0
|
|
CB
|
B:ASN604
|
4.8
|
17.5
|
1.0
|
|
C
|
B:CYS602
|
4.8
|
16.6
|
1.0
|
|
CZ
|
B:TYR100
|
4.9
|
16.5
|
1.0
|
|
CE2
|
B:TRP568
|
5.0
|
18.4
|
1.0
|
|
Sodium binding site 6 out
of 16 in 3t09
Go back to
Sodium Binding Sites List in 3t09
Sodium binding site 6 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3102
b:17.2
occ:1.00
|
O
|
B:HOH4977
|
2.2
|
27.9
|
1.0
|
|
O
|
B:HOH4620
|
2.3
|
26.0
|
1.0
|
|
O
|
B:PHE556
|
2.4
|
13.4
|
1.0
|
|
O
|
B:TYR559
|
2.4
|
13.4
|
1.0
|
|
O
|
B:LEU562
|
2.4
|
17.5
|
1.0
|
|
O
|
B:PRO560
|
3.2
|
17.4
|
1.0
|
|
C
|
B:TYR559
|
3.3
|
15.4
|
1.0
|
|
C
|
B:LEU562
|
3.4
|
11.0
|
1.0
|
|
C
|
B:PHE556
|
3.5
|
12.2
|
1.0
|
|
C
|
B:PRO560
|
3.6
|
13.6
|
1.0
|
|
CA
|
B:PRO560
|
3.7
|
15.1
|
1.0
|
|
N
|
B:PRO560
|
3.9
|
12.9
|
1.0
|
|
N
|
B:LEU562
|
4.0
|
13.4
|
1.0
|
|
O
|
B:HOH4295
|
4.1
|
17.3
|
1.0
|
|
CA
|
B:LEU562
|
4.2
|
13.7
|
1.0
|
|
O
|
B:HOH5028
|
4.2
|
33.9
|
1.0
|
|
CA
|
B:PHE556
|
4.3
|
15.4
|
1.0
|
|
N
|
B:GLN563
|
4.3
|
11.9
|
1.0
|
|
O
|
B:HOH4969
|
4.3
|
29.4
|
1.0
|
|
CA
|
B:GLN563
|
4.4
|
11.4
|
1.0
|
|
CA
|
B:TYR559
|
4.5
|
13.7
|
1.0
|
|
CB
|
B:LEU562
|
4.5
|
13.5
|
1.0
|
|
N
|
B:TYR559
|
4.5
|
12.1
|
1.0
|
|
O
|
B:HOH4786
|
4.5
|
35.0
|
1.0
|
|
N
|
B:ARG561
|
4.6
|
11.9
|
1.0
|
|
N
|
B:ARG557
|
4.6
|
13.6
|
1.0
|
|
CG
|
B:GLN563
|
4.7
|
13.8
|
1.0
|
|
CA
|
B:ARG557
|
4.7
|
16.8
|
1.0
|
|
CD1
|
B:LEU350
|
4.8
|
16.2
|
1.0
|
|
C
|
B:ARG557
|
4.8
|
18.8
|
1.0
|
|
CB
|
B:PHE556
|
4.8
|
10.6
|
1.0
|
|
O
|
B:ARG557
|
4.9
|
18.4
|
1.0
|
|
C
|
B:ARG561
|
4.9
|
10.2
|
1.0
|
|
Sodium binding site 7 out
of 16 in 3t09
Go back to
Sodium Binding Sites List in 3t09
Sodium binding site 7 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3103
b:25.9
occ:1.00
|
O
|
B:HOH4709
|
2.3
|
38.3
|
1.0
|
|
O
|
B:LEU967
|
2.4
|
22.4
|
1.0
|
|
O
|
B:PRO932
|
2.4
|
19.6
|
1.0
|
|
O
|
B:THR970
|
2.8
|
25.0
|
1.0
|
|
O
|
B:HOH4220
|
2.8
|
23.6
|
1.0
|
|
C
|
B:PRO932
|
3.4
|
17.6
|
1.0
|
|
C
|
B:LEU967
|
3.5
|
19.4
|
1.0
|
|
CZ
|
B:PHE931
|
3.7
|
20.7
|
1.0
|
|
O
|
B:HOH4541
|
3.7
|
40.7
|
1.0
|
|
CE2
|
B:PHE931
|
3.8
|
22.8
|
1.0
|
|
C
|
B:THR970
|
3.9
|
23.2
|
1.0
|
|
CA
|
B:MET968
|
3.9
|
22.5
|
1.0
|
|
CB
|
B:PRO932
|
4.0
|
17.6
|
1.0
|
|
O
|
B:MET968
|
4.0
|
23.6
|
1.0
|
|
C
|
B:MET968
|
4.0
|
23.4
|
1.0
|
|
CA
|
B:PRO932
|
4.1
|
18.4
|
1.0
|
|
CE1
|
B:PHE931
|
4.1
|
28.3
|
1.0
|
|
CD
|
B:PRO932
|
4.2
|
18.9
|
1.0
|
|
N
|
B:PRO932
|
4.2
|
18.3
|
1.0
|
|
N
|
B:MET968
|
4.2
|
19.3
|
1.0
|
|
N
|
B:THR970
|
4.3
|
24.1
|
1.0
|
|
CD2
|
B:PHE931
|
4.4
|
17.8
|
1.0
|
|
N
|
B:SER933
|
4.4
|
15.0
|
1.0
|
|
CG
|
B:PRO932
|
4.5
|
19.3
|
1.0
|
|
O
|
B:HOH4951
|
4.6
|
39.6
|
1.0
|
|
CA
|
B:THR970
|
4.6
|
23.6
|
1.0
|
|
CD1
|
B:PHE931
|
4.7
|
22.6
|
1.0
|
|
CA
|
B:LEU967
|
4.7
|
17.2
|
1.0
|
|
N
|
B:GLU969
|
4.7
|
22.9
|
1.0
|
|
CA
|
B:SER933
|
4.8
|
15.4
|
1.0
|
|
N
|
B:SER971
|
4.8
|
21.7
|
1.0
|
|
CG
|
B:PHE931
|
4.8
|
23.2
|
1.0
|
|
CA
|
B:SER971
|
4.8
|
24.4
|
1.0
|
|
C
|
B:PHE931
|
4.9
|
19.3
|
1.0
|
|
Sodium binding site 8 out
of 16 in 3t09
Go back to
Sodium Binding Sites List in 3t09
Sodium binding site 8 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3104
b:36.5
occ:1.00
|
O
|
B:HOH4925
|
2.2
|
47.4
|
1.0
|
|
O
|
B:DMS8020
|
2.4
|
50.6
|
1.0
|
|
O
|
B:HOH4722
|
2.4
|
35.4
|
1.0
|
|
O
|
B:SER647
|
2.6
|
19.9
|
1.0
|
|
O
|
B:LEU670
|
2.7
|
24.5
|
1.0
|
|
O
|
B:GLU650
|
2.8
|
20.2
|
1.0
|
|
N
|
B:GLU650
|
3.5
|
19.5
|
1.0
|
|
S
|
B:DMS8020
|
3.7
|
55.3
|
1.0
|
|
C
|
B:GLU650
|
3.8
|
19.3
|
1.0
|
|
C
|
B:SER647
|
3.8
|
18.2
|
1.0
|
|
C
|
B:LEU670
|
3.8
|
22.7
|
1.0
|
|
C1
|
B:DMS8020
|
3.9
|
57.0
|
1.0
|
|
N
|
B:ASN649
|
3.9
|
16.7
|
1.0
|
|
C
|
B:ASP648
|
4.0
|
22.1
|
1.0
|
|
CA
|
B:ASP648
|
4.0
|
18.6
|
1.0
|
|
O
|
B:HOH4868
|
4.0
|
36.6
|
1.0
|
|
CA
|
B:GLU650
|
4.1
|
19.0
|
1.0
|
|
N
|
B:LEU670
|
4.1
|
24.1
|
1.0
|
|
O
|
B:HOH4823
|
4.3
|
33.6
|
1.0
|
|
N
|
B:ASP648
|
4.3
|
22.5
|
1.0
|
|
CA
|
B:LEU670
|
4.4
|
22.7
|
1.0
|
|
CB
|
B:GLU650
|
4.5
|
19.7
|
1.0
|
|
O
|
B:HOH4869
|
4.5
|
49.8
|
1.0
|
|
C
|
B:ASN649
|
4.6
|
15.6
|
1.0
|
|
O
|
B:ASP648
|
4.6
|
22.9
|
1.0
|
|
CA
|
B:ASN649
|
4.6
|
18.7
|
1.0
|
|
OG
|
B:SER647
|
4.7
|
19.3
|
1.0
|
|
CB
|
B:LEU670
|
4.7
|
26.3
|
1.0
|
|
C2
|
B:DMS8020
|
4.9
|
55.0
|
1.0
|
|
N
|
B:ASP671
|
5.0
|
23.6
|
1.0
|
|
N
|
B:LEU651
|
5.0
|
16.4
|
1.0
|
|
Sodium binding site 9 out
of 16 in 3t09
Go back to
Sodium Binding Sites List in 3t09
Sodium binding site 9 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 9 of E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na3101
b:17.6
occ:1.00
|
O
|
C:HOH4998
|
2.2
|
17.6
|
1.0
|
|
O
|
C:PHE601
|
2.4
|
16.9
|
1.0
|
|
OD1
|
C:ASN604
|
2.4
|
15.2
|
1.0
|
|
O6
|
C:1492001
|
2.4
|
13.0
|
1.0
|
|
OD2
|
C:ASP201
|
2.4
|
14.2
|
1.0
|
|
CG
|
C:ASP201
|
3.3
|
13.5
|
1.0
|
|
CG
|
C:ASN604
|
3.4
|
15.3
|
1.0
|
|
CD2
|
C:PHE601
|
3.4
|
17.2
|
1.0
|
|
CE2
|
C:PHE601
|
3.5
|
10.1
|
1.0
|
|
C
|
C:PHE601
|
3.5
|
17.4
|
1.0
|
|
C6
|
C:1492001
|
3.6
|
12.4
|
1.0
|
|
ND2
|
C:ASN604
|
3.7
|
13.9
|
1.0
|
|
OD1
|
C:ASP201
|
3.7
|
17.0
|
1.0
|
|
OH
|
C:TYR100
|
3.8
|
17.3
|
1.0
|
|
CG
|
C:PHE601
|
3.9
|
15.1
|
1.0
|
|
CZ
|
C:PHE601
|
4.1
|
17.3
|
1.0
|
|
O4
|
C:1492001
|
4.1
|
14.0
|
1.0
|
|
NE1
|
C:TRP568
|
4.1
|
13.4
|
1.0
|
|
C4
|
C:1492001
|
4.2
|
7.3
|
1.0
|
|
CA
|
C:CYS602
|
4.3
|
18.1
|
1.0
|
|
N
|
C:CYS602
|
4.3
|
16.3
|
1.0
|
|
C5
|
C:1492001
|
4.4
|
11.3
|
1.0
|
|
CD1
|
C:PHE601
|
4.5
|
13.5
|
1.0
|
|
O
|
C:HOH4084
|
4.5
|
16.2
|
1.0
|
|
NE2
|
C:HIS540
|
4.5
|
14.7
|
1.0
|
|
CB
|
C:ASP201
|
4.5
|
11.7
|
1.0
|
|
CA
|
C:PHE601
|
4.6
|
14.6
|
1.0
|
|
CE1
|
C:PHE601
|
4.6
|
18.6
|
1.0
|
|
CB
|
C:PHE601
|
4.6
|
16.1
|
1.0
|
|
CB
|
C:ASN604
|
4.7
|
17.1
|
1.0
|
|
C
|
C:CYS602
|
4.8
|
16.1
|
1.0
|
|
O
|
C:ASP201
|
4.8
|
15.6
|
1.0
|
|
CE2
|
C:TRP568
|
4.9
|
10.2
|
1.0
|
|
CZ
|
C:TYR100
|
4.9
|
15.7
|
1.0
|
|
CE1
|
C:HIS540
|
5.0
|
15.2
|
1.0
|
|
Sodium binding site 10 out
of 16 in 3t09
Go back to
Sodium Binding Sites List in 3t09
Sodium binding site 10 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 10 of E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na3102
b:17.6
occ:1.00
|
O
|
C:HOH4632
|
2.2
|
34.2
|
1.0
|
|
O
|
C:PHE556
|
2.4
|
14.7
|
1.0
|
|
O
|
C:LEU562
|
2.4
|
16.5
|
1.0
|
|
O
|
C:TYR559
|
2.4
|
16.9
|
1.0
|
|
O
|
C:HOH4421
|
2.9
|
30.5
|
1.0
|
|
O
|
C:PRO560
|
3.2
|
17.8
|
1.0
|
|
C
|
C:TYR559
|
3.4
|
12.5
|
1.0
|
|
C
|
C:LEU562
|
3.4
|
16.3
|
1.0
|
|
C
|
C:PHE556
|
3.5
|
16.7
|
1.0
|
|
C
|
C:PRO560
|
3.6
|
17.1
|
1.0
|
|
CA
|
C:PRO560
|
3.7
|
12.9
|
1.0
|
|
N
|
C:PRO560
|
4.0
|
12.9
|
1.0
|
|
O
|
C:HOH4307
|
4.0
|
19.7
|
1.0
|
|
O
|
C:HOH4782
|
4.0
|
38.0
|
1.0
|
|
N
|
C:LEU562
|
4.1
|
13.3
|
1.0
|
|
O
|
C:HOH4826
|
4.2
|
25.7
|
1.0
|
|
CA
|
C:LEU562
|
4.2
|
13.1
|
1.0
|
|
CA
|
C:PHE556
|
4.3
|
9.3
|
1.0
|
|
N
|
C:GLN563
|
4.3
|
16.0
|
1.0
|
|
CA
|
C:GLN563
|
4.3
|
17.2
|
1.0
|
|
CB
|
C:LEU562
|
4.4
|
13.8
|
1.0
|
|
CA
|
C:TYR559
|
4.5
|
15.2
|
1.0
|
|
N
|
C:ARG561
|
4.5
|
14.7
|
1.0
|
|
N
|
C:TYR559
|
4.5
|
14.7
|
1.0
|
|
N
|
C:ARG557
|
4.6
|
11.8
|
1.0
|
|
CA
|
C:ARG557
|
4.7
|
13.6
|
1.0
|
|
CG
|
C:GLN563
|
4.7
|
12.6
|
1.0
|
|
CD1
|
C:LEU350
|
4.8
|
19.9
|
1.0
|
|
C
|
C:ARG557
|
4.8
|
15.5
|
1.0
|
|
O
|
C:ARG557
|
4.8
|
17.4
|
1.0
|
|
C
|
C:ARG561
|
4.9
|
14.5
|
1.0
|
|
CB
|
C:PHE556
|
4.9
|
12.6
|
1.0
|
|
O
|
C:HOH4791
|
5.0
|
29.7
|
1.0
|
|
Reference:
L.J.Jancewicz,
R.W.Wheatley,
G.Sutendra,
M.Lee,
M.E.Fraser,
R.E.Huber.
Ser-796 of Beta-Galactosidase (E. Coli) Plays A Key Role in Maintaining An Optimum Balance Between the Opened and Closed Conformations of the Catalytically Important Active Site Loop Arch.Biochem.Biophys. V. 517 111 2012.
ISSN: ISSN 0003-9861
PubMed: 22155115
DOI: 10.1016/J.ABB.2011.11.017
Page generated: Tue Dec 15 06:25:26 2020
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