Sodium in PDB 3i3e: E. Coli (Lacz) Beta-Galactosidase (M542A)
Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (M542A)
All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (M542A):
3.2.1.23;
Protein crystallography data
The structure of E. Coli (Lacz) Beta-Galactosidase (M542A), PDB code: 3i3e
was solved by
M.L.Dugdale,
D.Dymianiw,
B.Minhas,
R.E.Huber,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
17.70 /
2.10
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
149.701,
168.417,
200.709,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
18.2 /
22.1
|
Other elements in 3i3e:
The structure of E. Coli (Lacz) Beta-Galactosidase (M542A) 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 (M542A)
(pdb code 3i3e). 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 (M542A), PDB code: 3i3e:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 16 in 3i3e
Go back to
Sodium Binding Sites List in 3i3e
Sodium binding site 1 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (M542A)
 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 (M542A) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3101
b:36.5
occ:1.00
|
OD1
|
A:ASN604
|
2.2
|
20.7
|
1.0
|
|
O
|
A:PHE601
|
2.2
|
22.8
|
1.0
|
|
O
|
A:HOH4170
|
2.4
|
22.2
|
1.0
|
|
O
|
A:HOH4278
|
2.4
|
34.7
|
1.0
|
|
O
|
A:HOH7434
|
2.5
|
35.4
|
1.0
|
|
O
|
A:HOH7338
|
2.5
|
31.0
|
1.0
|
|
CG
|
A:ASN604
|
3.3
|
20.7
|
1.0
|
|
C
|
A:PHE601
|
3.4
|
23.9
|
1.0
|
|
OD2
|
A:ASP201
|
3.5
|
21.6
|
1.0
|
|
ND2
|
A:ASN604
|
3.7
|
22.6
|
1.0
|
|
NE2
|
A:HIS540
|
3.8
|
16.3
|
1.0
|
|
CA
|
A:PHE601
|
4.2
|
25.9
|
1.0
|
|
NE1
|
A:TRP568
|
4.2
|
12.3
|
1.0
|
|
CE1
|
A:HIS540
|
4.2
|
16.8
|
1.0
|
|
OH
|
A:TYR100
|
4.3
|
27.1
|
1.0
|
|
CB
|
A:PHE601
|
4.4
|
27.5
|
1.0
|
|
N
|
A:CYS602
|
4.4
|
21.3
|
1.0
|
|
CB
|
A:ASN604
|
4.5
|
20.0
|
1.0
|
|
O
|
A:HOH7309
|
4.5
|
40.7
|
1.0
|
|
CA
|
A:CYS602
|
4.6
|
20.3
|
1.0
|
|
O
|
A:HOH7435
|
4.6
|
38.8
|
1.0
|
|
CG
|
A:ASP201
|
4.6
|
20.9
|
1.0
|
|
O
|
A:HOH4052
|
4.7
|
17.9
|
1.0
|
|
C
|
A:CYS602
|
4.9
|
19.2
|
1.0
|
|
OD1
|
A:ASP201
|
4.9
|
21.0
|
1.0
|
|
O
|
A:HOH4300
|
5.0
|
43.1
|
1.0
|
|
N
|
A:MET603
|
5.0
|
18.3
|
1.0
|
|
Sodium binding site 2 out
of 16 in 3i3e
Go back to
Sodium Binding Sites List in 3i3e
Sodium binding site 2 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (M542A)
 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 (M542A) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3102
b:9.9
occ:1.00
|
O
|
A:PHE556
|
2.2
|
8.8
|
1.0
|
|
O
|
A:TYR559
|
2.3
|
13.3
|
1.0
|
|
O
|
A:LEU562
|
2.3
|
5.7
|
1.0
|
|
O
|
A:HOH4652
|
2.4
|
19.7
|
1.0
|
|
O
|
A:HOH4410
|
2.6
|
17.6
|
1.0
|
|
C
|
A:TYR559
|
3.3
|
8.9
|
1.0
|
|
O
|
A:PRO560
|
3.4
|
7.2
|
1.0
|
|
C
|
A:LEU562
|
3.4
|
7.0
|
1.0
|
|
C
|
A:PHE556
|
3.4
|
8.9
|
1.0
|
|
C
|
A:PRO560
|
3.7
|
7.2
|
1.0
|
|
CA
|
A:PRO560
|
3.8
|
6.9
|
1.0
|
|
N
|
A:LEU562
|
4.0
|
5.7
|
1.0
|
|
N
|
A:PRO560
|
4.0
|
7.6
|
1.0
|
|
O
|
A:HOH5118
|
4.0
|
47.9
|
1.0
|
|
O
|
A:HOH4286
|
4.1
|
18.8
|
1.0
|
|
CA
|
A:PHE556
|
4.1
|
7.3
|
1.0
|
|
CA
|
A:LEU562
|
4.2
|
6.7
|
1.0
|
|
N
|
A:GLN563
|
4.3
|
6.5
|
1.0
|
|
CA
|
A:GLN563
|
4.3
|
7.5
|
1.0
|
|
CB
|
A:LEU562
|
4.3
|
5.9
|
1.0
|
|
N
|
A:ARG557
|
4.4
|
7.7
|
1.0
|
|
CA
|
A:TYR559
|
4.4
|
8.4
|
1.0
|
|
N
|
A:TYR559
|
4.5
|
9.4
|
1.0
|
|
N
|
A:ARG561
|
4.6
|
6.7
|
1.0
|
|
CG
|
A:GLN563
|
4.6
|
7.6
|
1.0
|
|
CA
|
A:ARG557
|
4.6
|
8.3
|
1.0
|
|
C
|
A:ARG557
|
4.8
|
8.0
|
1.0
|
|
CB
|
A:PHE556
|
4.8
|
7.7
|
1.0
|
|
C
|
A:ARG561
|
4.9
|
7.2
|
1.0
|
|
O
|
A:ARG557
|
4.9
|
9.6
|
1.0
|
|
O
|
A:ALA555
|
4.9
|
6.8
|
1.0
|
|
CD1
|
A:LEU350
|
4.9
|
6.5
|
1.0
|
|
Sodium binding site 3 out
of 16 in 3i3e
Go back to
Sodium Binding Sites List in 3i3e
Sodium binding site 3 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (M542A)
 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 (M542A) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3103
b:29.4
occ:1.00
|
O
|
A:PRO932
|
2.7
|
13.6
|
1.0
|
|
O
|
A:THR970
|
2.8
|
21.8
|
1.0
|
|
O
|
A:LEU967
|
2.9
|
16.6
|
1.0
|
|
O
|
A:HOH4207
|
3.2
|
14.5
|
1.0
|
|
CZ
|
A:PHE931
|
3.6
|
28.2
|
1.0
|
|
C
|
A:PRO932
|
3.6
|
14.8
|
1.0
|
|
CE1
|
A:PHE931
|
3.8
|
28.5
|
1.0
|
|
O
|
A:HOH7324
|
3.8
|
34.4
|
1.0
|
|
CB
|
A:PRO932
|
3.8
|
16.7
|
1.0
|
|
C
|
A:THR970
|
3.9
|
23.3
|
1.0
|
|
CE2
|
A:PHE931
|
3.9
|
27.3
|
1.0
|
|
O
|
A:MET968
|
4.0
|
20.3
|
1.0
|
|
CA
|
A:PRO932
|
4.1
|
16.6
|
1.0
|
|
CD
|
A:PRO932
|
4.1
|
15.5
|
1.0
|
|
C
|
A:LEU967
|
4.1
|
16.3
|
1.0
|
|
N
|
A:PRO932
|
4.1
|
17.5
|
1.0
|
|
C
|
A:MET968
|
4.2
|
21.3
|
1.0
|
|
CD1
|
A:PHE931
|
4.3
|
26.4
|
1.0
|
|
CA
|
A:MET968
|
4.4
|
20.0
|
1.0
|
|
CD2
|
A:PHE931
|
4.4
|
25.7
|
1.0
|
|
CG
|
A:PRO932
|
4.5
|
16.9
|
1.0
|
|
N
|
A:THR970
|
4.5
|
23.4
|
1.0
|
|
CG
|
A:PHE931
|
4.6
|
23.8
|
1.0
|
|
CA
|
A:SER971
|
4.7
|
22.8
|
1.0
|
|
N
|
A:SER971
|
4.7
|
22.5
|
1.0
|
|
N
|
A:MET968
|
4.7
|
17.2
|
1.0
|
|
N
|
A:SER933
|
4.7
|
13.5
|
1.0
|
|
C
|
A:PHE931
|
4.8
|
18.6
|
1.0
|
|
CA
|
A:THR970
|
4.8
|
23.1
|
1.0
|
|
N
|
A:GLU969
|
4.9
|
20.7
|
1.0
|
|
Sodium binding site 4 out
of 16 in 3i3e
Go back to
Sodium Binding Sites List in 3i3e
Sodium binding site 4 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (M542A)
 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 (M542A) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3104
b:28.2
occ:1.00
|
O
|
A:DMS8425
|
2.3
|
45.5
|
1.0
|
|
O
|
A:LEU670
|
2.4
|
20.6
|
1.0
|
|
O
|
A:GLU650
|
2.5
|
18.7
|
1.0
|
|
O
|
A:SER647
|
2.6
|
15.4
|
1.0
|
|
O
|
A:HOH6122
|
2.9
|
35.5
|
1.0
|
|
S
|
A:DMS8425
|
3.4
|
46.3
|
1.0
|
|
C
|
A:LEU670
|
3.5
|
21.6
|
1.0
|
|
N
|
A:GLU650
|
3.5
|
16.6
|
1.0
|
|
C
|
A:GLU650
|
3.5
|
18.6
|
1.0
|
|
N
|
A:LEU670
|
3.8
|
20.9
|
1.0
|
|
C
|
A:SER647
|
3.8
|
17.0
|
1.0
|
|
CA
|
A:GLU650
|
4.0
|
17.0
|
1.0
|
|
CA
|
A:LEU670
|
4.0
|
21.2
|
1.0
|
|
C1
|
A:DMS8425
|
4.1
|
46.5
|
1.0
|
|
N
|
A:ASN649
|
4.2
|
18.2
|
1.0
|
|
C
|
A:ASP648
|
4.2
|
18.5
|
1.0
|
|
CB
|
A:LEU670
|
4.2
|
22.2
|
1.0
|
|
CA
|
A:ASP648
|
4.3
|
19.5
|
1.0
|
|
OG
|
A:SER647
|
4.3
|
12.8
|
1.0
|
|
CB
|
A:GLU650
|
4.4
|
15.8
|
1.0
|
|
N
|
A:ASP648
|
4.5
|
17.9
|
1.0
|
|
N
|
A:ASP671
|
4.6
|
23.1
|
1.0
|
|
C
|
A:ASN649
|
4.6
|
17.4
|
1.0
|
|
O
|
A:ASP648
|
4.7
|
18.5
|
1.0
|
|
N
|
A:LEU651
|
4.7
|
18.8
|
1.0
|
|
C
|
A:PRO669
|
4.7
|
20.8
|
1.0
|
|
CA
|
A:ASN649
|
4.7
|
16.7
|
1.0
|
|
CB
|
A:SER647
|
4.8
|
15.5
|
1.0
|
|
CA
|
A:SER647
|
4.9
|
15.5
|
1.0
|
|
C2
|
A:DMS8425
|
4.9
|
45.5
|
1.0
|
|
CA
|
A:ASP671
|
5.0
|
25.3
|
1.0
|
|
OE1
|
A:GLU650
|
5.0
|
13.2
|
1.0
|
|
Sodium binding site 5 out
of 16 in 3i3e
Go back to
Sodium Binding Sites List in 3i3e
Sodium binding site 5 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (M542A)
 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 (M542A) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3101
b:26.2
occ:1.00
|
O
|
B:PHE601
|
2.1
|
17.6
|
1.0
|
|
OD1
|
B:ASN604
|
2.3
|
17.4
|
1.0
|
|
O
|
B:HOH4170
|
2.3
|
15.6
|
1.0
|
|
O
|
B:HOH4278
|
2.4
|
31.6
|
1.0
|
|
O
|
B:HOH7211
|
2.4
|
25.2
|
1.0
|
|
O
|
B:HOH7216
|
2.4
|
31.0
|
1.0
|
|
CG
|
B:ASN604
|
3.2
|
18.7
|
1.0
|
|
C
|
B:PHE601
|
3.3
|
18.7
|
1.0
|
|
OD2
|
B:ASP201
|
3.6
|
19.7
|
1.0
|
|
ND2
|
B:ASN604
|
3.7
|
20.6
|
1.0
|
|
NE2
|
B:HIS540
|
3.8
|
13.1
|
1.0
|
|
CA
|
B:PHE601
|
4.0
|
21.2
|
1.0
|
|
CB
|
B:PHE601
|
4.1
|
23.4
|
1.0
|
|
CE1
|
B:HIS540
|
4.2
|
13.2
|
1.0
|
|
OH
|
B:TYR100
|
4.2
|
19.4
|
1.0
|
|
N
|
B:CYS602
|
4.3
|
18.5
|
1.0
|
|
O
|
B:HOH7279
|
4.4
|
42.7
|
1.0
|
|
NE1
|
B:TRP568
|
4.5
|
9.0
|
1.0
|
|
CA
|
B:CYS602
|
4.5
|
18.2
|
1.0
|
|
CB
|
B:ASN604
|
4.5
|
18.4
|
1.0
|
|
CG
|
B:ASP201
|
4.6
|
18.8
|
1.0
|
|
O
|
B:HOH7191
|
4.6
|
25.9
|
1.0
|
|
O
|
B:HOH4052
|
4.8
|
14.0
|
1.0
|
|
C
|
B:CYS602
|
4.8
|
17.9
|
1.0
|
|
OD1
|
B:ASP201
|
4.8
|
19.9
|
1.0
|
|
N
|
B:MET603
|
4.9
|
15.3
|
1.0
|
|
Sodium binding site 6 out
of 16 in 3i3e
Go back to
Sodium Binding Sites List in 3i3e
Sodium binding site 6 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (M542A)
 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 (M542A) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3102
b:12.4
occ:1.00
|
O
|
B:PHE556
|
2.2
|
4.5
|
1.0
|
|
O
|
B:TYR559
|
2.2
|
12.7
|
1.0
|
|
O
|
B:LEU562
|
2.3
|
8.8
|
1.0
|
|
O
|
B:HOH4652
|
2.4
|
19.7
|
1.0
|
|
O
|
B:HOH4410
|
2.6
|
20.1
|
1.0
|
|
C
|
B:TYR559
|
3.3
|
10.3
|
1.0
|
|
C
|
B:LEU562
|
3.3
|
7.3
|
1.0
|
|
O
|
B:PRO560
|
3.3
|
7.3
|
1.0
|
|
C
|
B:PHE556
|
3.4
|
7.2
|
1.0
|
|
C
|
B:PRO560
|
3.6
|
8.6
|
1.0
|
|
CA
|
B:PRO560
|
3.7
|
8.1
|
1.0
|
|
N
|
B:PRO560
|
3.9
|
10.4
|
1.0
|
|
N
|
B:LEU562
|
3.9
|
4.2
|
1.0
|
|
O
|
B:HOH4286
|
3.9
|
16.6
|
1.0
|
|
CA
|
B:PHE556
|
4.1
|
5.5
|
1.0
|
|
CA
|
B:LEU562
|
4.1
|
6.4
|
1.0
|
|
N
|
B:GLN563
|
4.2
|
6.6
|
1.0
|
|
O
|
B:HOH5118
|
4.3
|
56.2
|
1.0
|
|
CB
|
B:LEU562
|
4.3
|
5.5
|
1.0
|
|
CA
|
B:GLN563
|
4.3
|
6.6
|
1.0
|
|
CA
|
B:TYR559
|
4.4
|
10.4
|
1.0
|
|
N
|
B:ARG557
|
4.4
|
6.7
|
1.0
|
|
N
|
B:ARG561
|
4.5
|
5.8
|
1.0
|
|
N
|
B:TYR559
|
4.5
|
10.1
|
1.0
|
|
CA
|
B:ARG557
|
4.7
|
9.5
|
1.0
|
|
CD1
|
B:LEU350
|
4.7
|
6.0
|
1.0
|
|
CG
|
B:GLN563
|
4.7
|
5.5
|
1.0
|
|
CB
|
B:PHE556
|
4.7
|
5.7
|
1.0
|
|
C
|
B:ARG557
|
4.8
|
9.7
|
1.0
|
|
C
|
B:ARG561
|
4.8
|
6.5
|
1.0
|
|
O
|
B:ARG557
|
4.9
|
11.2
|
1.0
|
|
O
|
B:ALA555
|
4.9
|
7.5
|
1.0
|
|
CB
|
B:TYR559
|
5.0
|
10.2
|
1.0
|
|
Sodium binding site 7 out
of 16 in 3i3e
Go back to
Sodium Binding Sites List in 3i3e
Sodium binding site 7 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (M542A)
 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 (M542A) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3103
b:30.8
occ:1.00
|
O
|
B:THR970
|
2.5
|
21.8
|
1.0
|
|
O
|
B:LEU967
|
2.6
|
16.9
|
1.0
|
|
O
|
B:PRO932
|
2.7
|
15.1
|
1.0
|
|
O
|
B:HOH4558
|
3.1
|
34.7
|
1.0
|
|
O
|
B:HOH4207
|
3.2
|
15.4
|
1.0
|
|
O
|
B:HOH4763
|
3.3
|
33.5
|
1.0
|
|
C
|
B:PRO932
|
3.6
|
15.9
|
1.0
|
|
C
|
B:THR970
|
3.7
|
22.8
|
1.0
|
|
CZ
|
B:PHE931
|
3.7
|
29.3
|
1.0
|
|
C
|
B:LEU967
|
3.8
|
16.7
|
1.0
|
|
O
|
B:MET968
|
3.8
|
21.9
|
1.0
|
|
CB
|
B:PRO932
|
3.9
|
16.6
|
1.0
|
|
CE2
|
B:PHE931
|
4.0
|
28.8
|
1.0
|
|
CE1
|
B:PHE931
|
4.0
|
27.4
|
1.0
|
|
C
|
B:MET968
|
4.0
|
22.9
|
1.0
|
|
CA
|
B:PRO932
|
4.1
|
16.2
|
1.0
|
|
CD
|
B:PRO932
|
4.1
|
17.3
|
1.0
|
|
N
|
B:PRO932
|
4.1
|
17.9
|
1.0
|
|
CA
|
B:MET968
|
4.1
|
21.3
|
1.0
|
|
N
|
B:THR970
|
4.2
|
22.4
|
1.0
|
|
N
|
B:MET968
|
4.4
|
18.2
|
1.0
|
|
CD2
|
B:PHE931
|
4.5
|
26.4
|
1.0
|
|
CD1
|
B:PHE931
|
4.5
|
25.6
|
1.0
|
|
CG
|
B:PRO932
|
4.5
|
15.0
|
1.0
|
|
CA
|
B:THR970
|
4.5
|
22.7
|
1.0
|
|
N
|
B:SER971
|
4.6
|
21.5
|
1.0
|
|
CA
|
B:SER971
|
4.6
|
21.1
|
1.0
|
|
N
|
B:SER933
|
4.7
|
15.2
|
1.0
|
|
CG
|
B:PHE931
|
4.7
|
24.4
|
1.0
|
|
N
|
B:GLU969
|
4.8
|
21.5
|
1.0
|
|
C
|
B:PHE931
|
4.8
|
17.1
|
1.0
|
|
CA
|
B:LEU967
|
5.0
|
15.6
|
1.0
|
|
Sodium binding site 8 out
of 16 in 3i3e
Go back to
Sodium Binding Sites List in 3i3e
Sodium binding site 8 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (M542A)
 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 (M542A) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3104
b:28.7
occ:1.00
|
O
|
B:DMS8425
|
2.2
|
49.1
|
1.0
|
|
O
|
B:SER647
|
2.4
|
16.3
|
1.0
|
|
O
|
B:HOH7217
|
2.6
|
43.2
|
1.0
|
|
O
|
B:GLU650
|
2.8
|
17.4
|
1.0
|
|
O
|
B:LEU670
|
2.9
|
23.4
|
1.0
|
|
N
|
B:GLU650
|
3.1
|
14.6
|
1.0
|
|
O
|
B:HOH5010
|
3.3
|
45.5
|
1.0
|
|
N
|
B:ASN649
|
3.4
|
16.9
|
1.0
|
|
S
|
B:DMS8425
|
3.4
|
49.7
|
1.0
|
|
C
|
B:SER647
|
3.4
|
17.1
|
1.0
|
|
C
|
B:ASP648
|
3.5
|
18.5
|
1.0
|
|
CA
|
B:ASP648
|
3.6
|
18.6
|
1.0
|
|
C
|
B:GLU650
|
3.6
|
17.4
|
1.0
|
|
C1
|
B:DMS8425
|
3.7
|
49.1
|
1.0
|
|
CA
|
B:GLU650
|
3.8
|
15.2
|
1.0
|
|
N
|
B:ASP648
|
3.9
|
16.4
|
1.0
|
|
C
|
B:LEU670
|
4.0
|
22.7
|
1.0
|
|
C
|
B:ASN649
|
4.1
|
15.3
|
1.0
|
|
CA
|
B:ASN649
|
4.1
|
15.3
|
1.0
|
|
O
|
B:ASP648
|
4.1
|
18.9
|
1.0
|
|
CB
|
B:GLU650
|
4.2
|
14.8
|
1.0
|
|
N
|
B:LEU670
|
4.4
|
23.5
|
1.0
|
|
OE1
|
B:GLU650
|
4.5
|
14.1
|
1.0
|
|
OG
|
B:SER647
|
4.5
|
15.8
|
1.0
|
|
O
|
B:HOH5124
|
4.6
|
37.0
|
1.0
|
|
CA
|
B:LEU670
|
4.6
|
23.4
|
1.0
|
|
C2
|
B:DMS8425
|
4.6
|
48.2
|
1.0
|
|
CA
|
B:SER647
|
4.7
|
16.9
|
1.0
|
|
CB
|
B:LEU670
|
4.7
|
23.5
|
1.0
|
|
CB
|
B:SER647
|
4.7
|
17.4
|
1.0
|
|
N
|
B:LEU651
|
4.9
|
18.7
|
1.0
|
|
Sodium binding site 9 out
of 16 in 3i3e
Go back to
Sodium Binding Sites List in 3i3e
Sodium binding site 9 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (M542A)
 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 (M542A) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na3101
b:35.1
occ:1.00
|
O
|
C:PHE601
|
2.2
|
17.9
|
1.0
|
|
OD1
|
C:ASN604
|
2.2
|
20.5
|
1.0
|
|
O
|
C:HOH4278
|
2.3
|
32.7
|
1.0
|
|
O
|
C:HOH4170
|
2.3
|
23.0
|
1.0
|
|
O
|
C:HOH7268
|
2.4
|
35.3
|
1.0
|
|
O
|
C:HOH7262
|
2.5
|
26.6
|
1.0
|
|
CG
|
C:ASN604
|
3.0
|
18.5
|
1.0
|
|
ND2
|
C:ASN604
|
3.3
|
20.6
|
1.0
|
|
C
|
C:PHE601
|
3.4
|
19.0
|
1.0
|
|
OD2
|
C:ASP201
|
3.5
|
17.4
|
1.0
|
|
NE2
|
C:HIS540
|
3.8
|
17.1
|
1.0
|
|
CA
|
C:PHE601
|
4.2
|
20.9
|
1.0
|
|
CE1
|
C:HIS540
|
4.2
|
14.8
|
1.0
|
|
NE1
|
C:TRP568
|
4.2
|
9.3
|
1.0
|
|
CB
|
C:PHE601
|
4.2
|
23.6
|
1.0
|
|
OH
|
C:TYR100
|
4.3
|
20.8
|
1.0
|
|
CB
|
C:ASN604
|
4.4
|
19.0
|
1.0
|
|
O
|
C:HOH7252
|
4.4
|
32.4
|
1.0
|
|
N
|
C:CYS602
|
4.4
|
18.4
|
1.0
|
|
CA
|
C:CYS602
|
4.5
|
18.6
|
1.0
|
|
O
|
C:HOH7263
|
4.6
|
43.8
|
1.0
|
|
O
|
C:HOH4052
|
4.6
|
15.7
|
1.0
|
|
CG
|
C:ASP201
|
4.6
|
16.6
|
1.0
|
|
C
|
C:CYS602
|
4.9
|
18.5
|
1.0
|
|
OD1
|
C:ASP201
|
4.9
|
19.3
|
1.0
|
|
N
|
C:MET603
|
5.0
|
17.3
|
1.0
|
|
CD1
|
C:TRP568
|
5.0
|
11.3
|
1.0
|
|
Sodium binding site 10 out
of 16 in 3i3e
Go back to
Sodium Binding Sites List in 3i3e
Sodium binding site 10 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (M542A)
 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 (M542A) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na3102
b:9.7
occ:1.00
|
O
|
C:TYR559
|
2.3
|
10.7
|
1.0
|
|
O
|
C:PHE556
|
2.3
|
7.2
|
1.0
|
|
O
|
C:LEU562
|
2.3
|
5.4
|
1.0
|
|
O
|
C:HOH4410
|
2.6
|
15.0
|
1.0
|
|
O
|
C:HOH4652
|
2.7
|
18.3
|
1.0
|
|
O
|
C:PRO560
|
3.2
|
7.8
|
1.0
|
|
C
|
C:TYR559
|
3.3
|
9.2
|
1.0
|
|
C
|
C:LEU562
|
3.3
|
6.0
|
1.0
|
|
C
|
C:PHE556
|
3.5
|
8.1
|
1.0
|
|
C
|
C:PRO560
|
3.6
|
8.8
|
1.0
|
|
CA
|
C:PRO560
|
3.7
|
8.3
|
1.0
|
|
N
|
C:PRO560
|
3.9
|
8.1
|
1.0
|
|
N
|
C:LEU562
|
3.9
|
5.7
|
1.0
|
|
O
|
C:HOH4286
|
4.0
|
15.8
|
1.0
|
|
CA
|
C:LEU562
|
4.2
|
5.2
|
1.0
|
|
CA
|
C:PHE556
|
4.2
|
7.4
|
1.0
|
|
N
|
C:GLN563
|
4.2
|
6.1
|
1.0
|
|
O
|
C:HOH4580
|
4.3
|
45.2
|
1.0
|
|
CA
|
C:GLN563
|
4.3
|
5.7
|
1.0
|
|
CB
|
C:LEU562
|
4.3
|
4.9
|
1.0
|
|
CA
|
C:TYR559
|
4.4
|
10.0
|
1.0
|
|
N
|
C:ARG561
|
4.5
|
7.0
|
1.0
|
|
N
|
C:ARG557
|
4.5
|
8.7
|
1.0
|
|
N
|
C:TYR559
|
4.5
|
10.3
|
1.0
|
|
CG
|
C:GLN563
|
4.6
|
8.2
|
1.0
|
|
CA
|
C:ARG557
|
4.7
|
9.6
|
1.0
|
|
C
|
C:ARG557
|
4.8
|
9.4
|
1.0
|
|
CB
|
C:PHE556
|
4.8
|
7.0
|
1.0
|
|
C
|
C:ARG561
|
4.8
|
7.1
|
1.0
|
|
CD1
|
C:LEU350
|
4.9
|
6.1
|
1.0
|
|
O
|
C:ARG557
|
4.9
|
9.9
|
1.0
|
|
O
|
C:ALA555
|
4.9
|
8.2
|
1.0
|
|
CB
|
C:TYR559
|
5.0
|
10.4
|
1.0
|
|
Reference:
M.L.Dugdale,
D.L.Dymianiw,
B.K.Minhas,
I.D'angelo,
R.E.Huber.
Role of Met-542 As A Guide For the Conformational Changes of Phe-601 That Occur During the Reaction of β-Galactosidase (Escherichia Coli). Biochem.Cell Biol. V. 88 861 2010.
ISSN: ISSN 0829-8211
PubMed: 20921997
DOI: 10.1139/O10-009
Page generated: Tue Dec 15 06:14:05 2020
|
