Sodium in PDB 1jz3: E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate
Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate
All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate:
3.2.1.23;
Protein crystallography data
The structure of E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate, PDB code: 1jz3
was solved by
D.H.Juers,
B.W.Matthews,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
16.00 /
1.75
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
149.560,
168.190,
200.690,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
15.8 /
22.2
|
Other elements in 1jz3:
The structure of E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate 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-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate
(pdb code 1jz3). 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-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate, PDB code: 1jz3:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 16 in 1jz3
Go back to
Sodium Binding Sites List in 1jz3
Sodium binding site 1 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate
 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-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3101
b:17.0
occ:1.00
|
O
|
A:HOH8875
|
2.3
|
16.4
|
1.0
|
|
OD2
|
A:ASP201
|
2.3
|
12.4
|
1.0
|
|
OD1
|
A:ASN604
|
2.5
|
14.5
|
1.0
|
|
O6
|
A:2DG2001
|
2.5
|
13.3
|
1.0
|
|
O
|
A:PHE601
|
2.5
|
13.0
|
1.0
|
|
CD2
|
A:PHE601
|
3.0
|
38.6
|
1.0
|
|
CE2
|
A:PHE601
|
3.0
|
14.0
|
1.0
|
|
CG
|
A:ASP201
|
3.2
|
14.7
|
1.0
|
|
CG
|
A:ASN604
|
3.5
|
12.4
|
1.0
|
|
OD1
|
A:ASP201
|
3.5
|
15.6
|
1.0
|
|
C
|
A:PHE601
|
3.7
|
24.3
|
1.0
|
|
C6
|
A:2DG2001
|
3.8
|
11.0
|
1.0
|
|
ND2
|
A:ASN604
|
3.8
|
13.8
|
1.0
|
|
CG
|
A:PHE601
|
3.8
|
45.6
|
1.0
|
|
OH
|
A:TYR100
|
3.9
|
17.9
|
1.0
|
|
CZ
|
A:PHE601
|
3.9
|
33.5
|
1.0
|
|
C4
|
A:2DG2001
|
4.0
|
9.5
|
1.0
|
|
O4
|
A:2DG2001
|
4.1
|
13.9
|
1.0
|
|
NE1
|
A:TRP568
|
4.1
|
15.1
|
1.0
|
|
C5
|
A:2DG2001
|
4.4
|
10.6
|
1.0
|
|
CB
|
A:ASP201
|
4.4
|
13.5
|
1.0
|
|
CA
|
A:CYS602
|
4.4
|
12.6
|
1.0
|
|
NE2
|
A:HIS540
|
4.5
|
13.3
|
1.0
|
|
N
|
A:CYS602
|
4.5
|
13.3
|
1.0
|
|
CB
|
A:PHE601
|
4.5
|
12.8
|
1.0
|
|
CD1
|
A:PHE601
|
4.6
|
18.1
|
1.0
|
|
CE1
|
A:PHE601
|
4.6
|
33.6
|
1.0
|
|
CA
|
A:PHE601
|
4.6
|
16.1
|
1.0
|
|
O
|
A:HOH8652
|
4.7
|
15.1
|
1.0
|
|
O
|
A:ASP201
|
4.8
|
12.3
|
1.0
|
|
CB
|
A:ASN604
|
4.9
|
8.6
|
1.0
|
|
CE2
|
A:TRP568
|
4.9
|
14.9
|
1.0
|
|
CD1
|
A:TRP568
|
5.0
|
13.4
|
1.0
|
|
Sodium binding site 2 out
of 16 in 1jz3
Go back to
Sodium Binding Sites List in 1jz3
Sodium binding site 2 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate
 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-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3102
b:14.6
occ:1.00
|
O
|
A:PHE556
|
2.3
|
17.6
|
1.0
|
|
O
|
A:LEU562
|
2.3
|
12.7
|
1.0
|
|
O
|
A:TYR559
|
2.4
|
14.8
|
1.0
|
|
O
|
A:HOH9229
|
2.4
|
22.4
|
1.0
|
|
O
|
A:HOH8999
|
2.4
|
21.5
|
1.0
|
|
O
|
A:PRO560
|
3.2
|
16.0
|
1.0
|
|
C
|
A:LEU562
|
3.4
|
16.6
|
1.0
|
|
C
|
A:TYR559
|
3.4
|
16.5
|
1.0
|
|
C
|
A:PHE556
|
3.5
|
14.2
|
1.0
|
|
C
|
A:PRO560
|
3.6
|
13.1
|
1.0
|
|
CA
|
A:PRO560
|
3.7
|
12.2
|
1.0
|
|
N
|
A:LEU562
|
3.9
|
9.3
|
1.0
|
|
O
|
A:HOH8882
|
3.9
|
19.6
|
1.0
|
|
N
|
A:PRO560
|
4.0
|
16.6
|
1.0
|
|
O
|
A:HOH9407
|
4.1
|
37.9
|
1.0
|
|
CA
|
A:PHE556
|
4.2
|
11.7
|
1.0
|
|
CA
|
A:LEU562
|
4.2
|
12.3
|
1.0
|
|
N
|
A:GLN563
|
4.3
|
11.3
|
1.0
|
|
CB
|
A:LEU562
|
4.4
|
12.4
|
1.0
|
|
CA
|
A:GLN563
|
4.4
|
12.4
|
1.0
|
|
N
|
A:ARG561
|
4.5
|
11.7
|
1.0
|
|
N
|
A:ARG557
|
4.5
|
9.5
|
1.0
|
|
N
|
A:TYR559
|
4.6
|
12.2
|
1.0
|
|
CA
|
A:TYR559
|
4.6
|
9.6
|
1.0
|
|
CA
|
A:ARG557
|
4.7
|
5.0
|
1.0
|
|
O
|
A:ARG557
|
4.7
|
16.2
|
1.0
|
|
CG
|
A:GLN563
|
4.7
|
8.3
|
1.0
|
|
C
|
A:ARG557
|
4.7
|
11.8
|
1.0
|
|
CB
|
A:PHE556
|
4.8
|
12.1
|
1.0
|
|
C
|
A:ARG561
|
4.8
|
12.1
|
1.0
|
|
CD1
|
A:LEU350
|
4.9
|
12.6
|
1.0
|
|
O
|
A:ALA555
|
4.9
|
13.6
|
1.0
|
|
Sodium binding site 3 out
of 16 in 1jz3
Go back to
Sodium Binding Sites List in 1jz3
Sodium binding site 3 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate
 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-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3103
b:28.1
occ:1.00
|
O
|
A:HOH9324
|
2.2
|
42.5
|
1.0
|
|
O
|
A:PRO932
|
2.5
|
18.2
|
1.0
|
|
O
|
A:LEU967
|
2.5
|
18.7
|
1.0
|
|
O
|
A:THR970
|
2.7
|
27.0
|
1.0
|
|
O
|
A:HOH8805
|
2.8
|
19.1
|
1.0
|
|
CZ
|
A:PHE931
|
3.5
|
22.3
|
1.0
|
|
C
|
A:PRO932
|
3.5
|
19.5
|
1.0
|
|
O
|
A:HOH9142
|
3.6
|
33.1
|
1.0
|
|
C
|
A:LEU967
|
3.7
|
17.4
|
1.0
|
|
CE2
|
A:PHE931
|
3.8
|
22.1
|
1.0
|
|
C
|
A:THR970
|
3.8
|
24.5
|
1.0
|
|
CE1
|
A:PHE931
|
3.8
|
22.0
|
1.0
|
|
CB
|
A:PRO932
|
3.9
|
16.1
|
1.0
|
|
O
|
A:MET968
|
4.0
|
26.4
|
1.0
|
|
CA
|
A:MET968
|
4.0
|
16.4
|
1.0
|
|
C
|
A:MET968
|
4.0
|
26.0
|
1.0
|
|
CD
|
A:PRO932
|
4.1
|
14.7
|
1.0
|
|
CA
|
A:PRO932
|
4.1
|
16.6
|
1.0
|
|
N
|
A:PRO932
|
4.2
|
16.7
|
1.0
|
|
N
|
A:THR970
|
4.3
|
19.3
|
1.0
|
|
N
|
A:MET968
|
4.3
|
17.6
|
1.0
|
|
CD2
|
A:PHE931
|
4.4
|
17.8
|
1.0
|
|
CD1
|
A:PHE931
|
4.4
|
19.9
|
1.0
|
|
CG
|
A:PRO932
|
4.4
|
24.3
|
1.0
|
|
N
|
A:SER933
|
4.6
|
10.8
|
1.0
|
|
CA
|
A:THR970
|
4.6
|
20.4
|
1.0
|
|
CG
|
A:PHE931
|
4.7
|
15.2
|
1.0
|
|
N
|
A:SER971
|
4.7
|
24.0
|
1.0
|
|
CA
|
A:SER971
|
4.8
|
28.4
|
1.0
|
|
N
|
A:GLU969
|
4.8
|
16.5
|
1.0
|
|
CA
|
A:SER933
|
4.8
|
15.1
|
1.0
|
|
C
|
A:PHE931
|
4.9
|
23.1
|
1.0
|
|
CA
|
A:LEU967
|
4.9
|
18.4
|
1.0
|
|
Sodium binding site 4 out
of 16 in 1jz3
Go back to
Sodium Binding Sites List in 1jz3
Sodium binding site 4 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate
 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-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3104
b:25.1
occ:1.00
|
O
|
A:DMS8425
|
2.1
|
42.9
|
1.0
|
|
O
|
A:LEU670
|
2.4
|
15.8
|
1.0
|
|
O
|
A:SER647
|
2.4
|
14.4
|
1.0
|
|
O
|
A:GLU650
|
2.6
|
20.4
|
1.0
|
|
O
|
A:HOH9338
|
2.6
|
46.5
|
1.0
|
|
O
|
A:HOH9515
|
2.6
|
44.4
|
1.0
|
|
S
|
A:DMS8425
|
3.1
|
43.7
|
1.0
|
|
N
|
A:GLU650
|
3.4
|
15.4
|
1.0
|
|
C
|
A:LEU670
|
3.5
|
22.0
|
1.0
|
|
C
|
A:GLU650
|
3.6
|
18.0
|
1.0
|
|
C2
|
A:DMS8425
|
3.6
|
38.8
|
1.0
|
|
C
|
A:SER647
|
3.6
|
18.6
|
1.0
|
|
N
|
A:LEU670
|
3.9
|
18.6
|
1.0
|
|
CA
|
A:GLU650
|
4.0
|
14.1
|
1.0
|
|
N
|
A:ASN649
|
4.0
|
19.7
|
1.0
|
|
C
|
A:ASP648
|
4.1
|
24.6
|
1.0
|
|
CA
|
A:ASP648
|
4.1
|
17.8
|
1.0
|
|
CB
|
A:GLU650
|
4.1
|
12.4
|
1.0
|
|
CA
|
A:LEU670
|
4.2
|
19.7
|
1.0
|
|
OG
|
A:SER647
|
4.2
|
18.1
|
1.0
|
|
CB
|
A:LEU670
|
4.3
|
28.7
|
1.0
|
|
N
|
A:ASP648
|
4.3
|
17.6
|
1.0
|
|
C
|
A:ASN649
|
4.5
|
17.3
|
1.0
|
|
CB
|
A:SER647
|
4.5
|
17.6
|
1.0
|
|
N
|
A:ASP671
|
4.6
|
24.5
|
1.0
|
|
C1
|
A:DMS8425
|
4.7
|
31.2
|
1.0
|
|
CA
|
A:ASN649
|
4.7
|
16.9
|
1.0
|
|
O
|
A:ASP648
|
4.7
|
18.4
|
1.0
|
|
CA
|
A:SER647
|
4.8
|
17.5
|
1.0
|
|
N
|
A:LEU651
|
4.8
|
13.1
|
1.0
|
|
OE1
|
A:GLU650
|
4.8
|
19.4
|
1.0
|
|
CA
|
A:ASP671
|
4.8
|
24.3
|
1.0
|
|
C
|
A:PRO669
|
4.9
|
19.3
|
1.0
|
|
Sodium binding site 5 out
of 16 in 1jz3
Go back to
Sodium Binding Sites List in 1jz3
Sodium binding site 5 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate
 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-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3101
b:15.7
occ:1.00
|
O
|
B:HOH8894
|
2.3
|
13.4
|
1.0
|
|
OD1
|
B:ASN604
|
2.4
|
12.8
|
1.0
|
|
O
|
B:PHE601
|
2.5
|
14.2
|
1.0
|
|
OD2
|
B:ASP201
|
2.5
|
17.5
|
1.0
|
|
O6
|
B:2DG2001
|
2.5
|
13.3
|
0.9
|
|
CE2
|
B:PHE601
|
3.0
|
1.0
|
0.6
|
|
CD2
|
B:PHE601
|
3.0
|
15.7
|
0.6
|
|
CG
|
B:ASP201
|
3.4
|
19.3
|
1.0
|
|
CG
|
B:ASN604
|
3.4
|
19.3
|
1.0
|
|
OD1
|
B:ASP201
|
3.6
|
15.5
|
1.0
|
|
C
|
B:PHE601
|
3.6
|
12.4
|
1.0
|
|
ND2
|
B:ASN604
|
3.7
|
14.1
|
1.0
|
|
C6
|
B:2DG2001
|
3.8
|
9.3
|
0.9
|
|
CZ
|
B:PHE601
|
3.8
|
13.1
|
0.6
|
|
CG
|
B:PHE601
|
3.8
|
15.4
|
0.6
|
|
OH
|
B:TYR100
|
3.9
|
15.9
|
1.0
|
|
NE1
|
B:TRP568
|
4.1
|
11.9
|
1.0
|
|
C4
|
B:2DG2001
|
4.1
|
10.7
|
0.9
|
|
O4
|
B:2DG2001
|
4.1
|
9.7
|
0.9
|
|
CA
|
B:CYS602
|
4.4
|
13.5
|
1.0
|
|
N
|
B:CYS602
|
4.4
|
17.2
|
1.0
|
|
NE2
|
B:HIS540
|
4.4
|
12.2
|
1.0
|
|
CE1
|
B:PHE601
|
4.5
|
21.3
|
0.6
|
|
CD1
|
B:PHE601
|
4.5
|
10.0
|
0.6
|
|
C5
|
B:2DG2001
|
4.5
|
5.8
|
0.9
|
|
CB
|
B:ASP201
|
4.5
|
12.3
|
1.0
|
|
O
|
B:HOH8673
|
4.6
|
13.5
|
1.0
|
|
CA
|
B:PHE601
|
4.6
|
13.6
|
1.0
|
|
CB
|
B:PHE601
|
4.6
|
15.0
|
1.0
|
|
CB
|
B:ASN604
|
4.8
|
10.4
|
1.0
|
|
O
|
B:ASP201
|
4.9
|
14.6
|
1.0
|
|
CE2
|
B:TRP568
|
4.9
|
16.9
|
1.0
|
|
CD1
|
B:TRP568
|
5.0
|
9.4
|
1.0
|
|
C
|
B:CYS602
|
5.0
|
15.8
|
1.0
|
|
CE1
|
B:HIS540
|
5.0
|
12.9
|
1.0
|
|
Sodium binding site 6 out
of 16 in 1jz3
Go back to
Sodium Binding Sites List in 1jz3
Sodium binding site 6 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate
 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-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3102
b:16.1
occ:1.00
|
O
|
B:LEU562
|
2.3
|
11.5
|
1.0
|
|
O
|
B:PHE556
|
2.3
|
12.7
|
1.0
|
|
O
|
B:TYR559
|
2.3
|
15.3
|
1.0
|
|
O
|
B:HOH9015
|
2.6
|
23.9
|
1.0
|
|
O
|
B:HOH9660
|
2.7
|
54.4
|
1.0
|
|
O
|
B:HOH9239
|
2.8
|
28.2
|
1.0
|
|
O
|
B:PRO560
|
3.2
|
14.0
|
1.0
|
|
C
|
B:TYR559
|
3.3
|
17.6
|
1.0
|
|
C
|
B:LEU562
|
3.4
|
13.2
|
1.0
|
|
C
|
B:PHE556
|
3.4
|
14.0
|
1.0
|
|
C
|
B:PRO560
|
3.6
|
16.6
|
1.0
|
|
CA
|
B:PRO560
|
3.7
|
12.6
|
1.0
|
|
N
|
B:PRO560
|
3.9
|
14.0
|
1.0
|
|
N
|
B:LEU562
|
4.0
|
10.9
|
1.0
|
|
O
|
B:HOH8901
|
4.1
|
17.2
|
1.0
|
|
CA
|
B:PHE556
|
4.1
|
11.8
|
1.0
|
|
CA
|
B:LEU562
|
4.2
|
12.7
|
1.0
|
|
N
|
B:GLN563
|
4.3
|
11.0
|
1.0
|
|
CB
|
B:LEU562
|
4.3
|
8.8
|
1.0
|
|
CA
|
B:GLN563
|
4.4
|
8.5
|
1.0
|
|
CA
|
B:TYR559
|
4.4
|
11.2
|
1.0
|
|
N
|
B:TYR559
|
4.4
|
13.4
|
1.0
|
|
N
|
B:ARG557
|
4.5
|
9.0
|
1.0
|
|
N
|
B:ARG561
|
4.6
|
10.4
|
1.0
|
|
CA
|
B:ARG557
|
4.6
|
11.9
|
1.0
|
|
CB
|
B:PHE556
|
4.7
|
10.9
|
1.0
|
|
C
|
B:ARG557
|
4.7
|
17.3
|
1.0
|
|
CG
|
B:GLN563
|
4.7
|
14.3
|
1.0
|
|
O
|
B:ARG557
|
4.7
|
16.8
|
1.0
|
|
CD1
|
B:LEU350
|
4.8
|
11.4
|
1.0
|
|
O
|
B:ALA555
|
4.9
|
11.4
|
1.0
|
|
C
|
B:ARG561
|
4.9
|
10.2
|
1.0
|
|
CB
|
B:TYR559
|
4.9
|
10.5
|
1.0
|
|
Sodium binding site 7 out
of 16 in 1jz3
Go back to
Sodium Binding Sites List in 1jz3
Sodium binding site 7 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate
 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-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3103
b:23.5
occ:1.00
|
O
|
B:PRO932
|
2.4
|
18.4
|
1.0
|
|
O
|
B:LEU967
|
2.5
|
17.7
|
1.0
|
|
O
|
B:HOH8824
|
2.7
|
21.6
|
1.0
|
|
O
|
B:THR970
|
2.8
|
27.8
|
1.0
|
|
O
|
B:HOH9338
|
3.1
|
47.7
|
1.0
|
|
CZ
|
B:PHE931
|
3.4
|
19.5
|
1.0
|
|
C
|
B:PRO932
|
3.4
|
16.9
|
1.0
|
|
C
|
B:LEU967
|
3.7
|
22.9
|
1.0
|
|
O
|
B:HOH9156
|
3.7
|
28.8
|
1.0
|
|
CE2
|
B:PHE931
|
3.7
|
21.7
|
1.0
|
|
CE1
|
B:PHE931
|
3.8
|
23.4
|
1.0
|
|
C
|
B:THR970
|
3.9
|
29.4
|
1.0
|
|
CA
|
B:MET968
|
4.0
|
15.6
|
1.0
|
|
O
|
B:MET968
|
4.0
|
22.0
|
1.0
|
|
C
|
B:MET968
|
4.1
|
22.0
|
1.0
|
|
CA
|
B:PRO932
|
4.1
|
15.8
|
1.0
|
|
CB
|
B:PRO932
|
4.2
|
14.6
|
1.0
|
|
N
|
B:PRO932
|
4.2
|
17.1
|
1.0
|
|
CD
|
B:PRO932
|
4.2
|
21.8
|
1.0
|
|
N
|
B:MET968
|
4.4
|
15.8
|
1.0
|
|
CD2
|
B:PHE931
|
4.4
|
15.2
|
1.0
|
|
N
|
B:THR970
|
4.4
|
14.5
|
1.0
|
|
N
|
B:SER933
|
4.4
|
14.2
|
1.0
|
|
CD1
|
B:PHE931
|
4.4
|
23.0
|
1.0
|
|
CA
|
B:SER933
|
4.6
|
12.3
|
1.0
|
|
CG
|
B:PRO932
|
4.6
|
18.4
|
1.0
|
|
CG
|
B:PHE931
|
4.7
|
21.5
|
1.0
|
|
CA
|
B:THR970
|
4.7
|
19.9
|
1.0
|
|
N
|
B:SER971
|
4.8
|
23.1
|
1.0
|
|
CA
|
B:LEU967
|
4.8
|
20.4
|
1.0
|
|
CA
|
B:SER971
|
4.9
|
24.5
|
1.0
|
|
N
|
B:GLU969
|
4.9
|
22.2
|
1.0
|
|
C
|
B:PHE931
|
4.9
|
20.9
|
1.0
|
|
O
|
B:HOH9368
|
5.0
|
38.4
|
1.0
|
|
Sodium binding site 8 out
of 16 in 1jz3
Go back to
Sodium Binding Sites List in 1jz3
Sodium binding site 8 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate
 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-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3104
b:33.5
occ:1.00
|
O
|
B:DMS8425
|
2.2
|
44.7
|
1.0
|
|
O
|
B:LEU670
|
2.4
|
18.5
|
1.0
|
|
O
|
B:GLU650
|
2.5
|
23.6
|
1.0
|
|
O
|
B:SER647
|
2.5
|
17.4
|
1.0
|
|
O
|
B:HOH9354
|
2.8
|
33.2
|
1.0
|
|
S
|
B:DMS8425
|
3.4
|
50.2
|
1.0
|
|
N
|
B:GLU650
|
3.4
|
16.1
|
1.0
|
|
C
|
B:GLU650
|
3.5
|
24.3
|
1.0
|
|
C
|
B:LEU670
|
3.5
|
22.0
|
1.0
|
|
N
|
B:LEU670
|
3.7
|
24.9
|
1.0
|
|
C
|
B:SER647
|
3.7
|
22.7
|
1.0
|
|
C2
|
B:DMS8425
|
3.9
|
34.4
|
1.0
|
|
CA
|
B:GLU650
|
3.9
|
15.5
|
1.0
|
|
CA
|
B:LEU670
|
4.0
|
20.1
|
1.0
|
|
CB
|
B:LEU670
|
4.0
|
22.9
|
1.0
|
|
N
|
B:ASN649
|
4.1
|
19.5
|
1.0
|
|
CA
|
B:ASP648
|
4.1
|
14.9
|
1.0
|
|
CB
|
B:GLU650
|
4.1
|
17.3
|
1.0
|
|
C
|
B:ASP648
|
4.2
|
18.3
|
1.0
|
|
OG
|
B:SER647
|
4.2
|
17.4
|
1.0
|
|
N
|
B:ASP648
|
4.4
|
17.1
|
1.0
|
|
C
|
B:ASN649
|
4.6
|
35.9
|
1.0
|
|
CB
|
B:SER647
|
4.6
|
17.8
|
1.0
|
|
N
|
B:ASP671
|
4.6
|
19.4
|
1.0
|
|
C
|
B:PRO669
|
4.6
|
26.5
|
1.0
|
|
N
|
B:LEU651
|
4.7
|
15.7
|
1.0
|
|
CA
|
B:ASN649
|
4.8
|
15.0
|
1.0
|
|
CA
|
B:ASP671
|
4.8
|
17.3
|
1.0
|
|
O
|
B:ASP648
|
4.8
|
19.5
|
1.0
|
|
C1
|
B:DMS8425
|
4.8
|
23.3
|
1.0
|
|
CA
|
B:SER647
|
4.8
|
16.0
|
1.0
|
|
CB
|
B:PRO669
|
4.8
|
54.8
|
1.0
|
|
OE1
|
B:GLU650
|
4.9
|
16.5
|
1.0
|
|
CA
|
B:PRO669
|
5.0
|
27.4
|
1.0
|
|
Sodium binding site 9 out
of 16 in 1jz3
Go back to
Sodium Binding Sites List in 1jz3
Sodium binding site 9 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate
 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-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na3101
b:15.0
occ:1.00
|
OD1
|
C:ASN604
|
2.3
|
13.6
|
1.0
|
|
O
|
C:HOH8895
|
2.4
|
20.7
|
1.0
|
|
O6
|
C:2DG2001
|
2.4
|
18.4
|
1.0
|
|
OD2
|
C:ASP201
|
2.4
|
14.0
|
1.0
|
|
O
|
C:PHE601
|
2.5
|
15.3
|
1.0
|
|
CE2
|
C:PHE601
|
3.0
|
19.1
|
1.0
|
|
CD2
|
C:PHE601
|
3.0
|
31.6
|
1.0
|
|
CG
|
C:ASP201
|
3.4
|
20.0
|
1.0
|
|
CG
|
C:ASN604
|
3.4
|
17.1
|
1.0
|
|
C
|
C:PHE601
|
3.7
|
15.1
|
1.0
|
|
OD1
|
C:ASP201
|
3.7
|
15.0
|
1.0
|
|
ND2
|
C:ASN604
|
3.7
|
15.0
|
1.0
|
|
C6
|
C:2DG2001
|
3.7
|
15.2
|
1.0
|
|
CZ
|
C:PHE601
|
3.8
|
28.7
|
1.0
|
|
CG
|
C:PHE601
|
3.9
|
41.2
|
1.0
|
|
OH
|
C:TYR100
|
3.9
|
16.7
|
1.0
|
|
C4
|
C:2DG2001
|
4.0
|
16.3
|
1.0
|
|
O4
|
C:2DG2001
|
4.1
|
14.5
|
1.0
|
|
NE1
|
C:TRP568
|
4.1
|
14.4
|
1.0
|
|
NE2
|
C:HIS540
|
4.4
|
13.1
|
1.0
|
|
CA
|
C:CYS602
|
4.4
|
19.3
|
1.0
|
|
C5
|
C:2DG2001
|
4.5
|
16.9
|
1.0
|
|
N
|
C:CYS602
|
4.5
|
12.5
|
1.0
|
|
CB
|
C:ASP201
|
4.5
|
13.8
|
1.0
|
|
O
|
C:HOH8673
|
4.5
|
13.2
|
1.0
|
|
CE1
|
C:PHE601
|
4.6
|
0.0
|
1.0
|
|
CB
|
C:PHE601
|
4.6
|
17.7
|
1.0
|
|
CD1
|
C:PHE601
|
4.6
|
19.6
|
1.0
|
|
CA
|
C:PHE601
|
4.6
|
13.6
|
1.0
|
|
CB
|
C:ASN604
|
4.8
|
9.5
|
1.0
|
|
O
|
C:ASP201
|
4.9
|
13.1
|
1.0
|
|
CE2
|
C:TRP568
|
4.9
|
15.2
|
1.0
|
|
CE1
|
C:HIS540
|
4.9
|
11.0
|
1.0
|
|
Sodium binding site 10 out
of 16 in 1jz3
Go back to
Sodium Binding Sites List in 1jz3
Sodium binding site 10 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate
 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-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na3102
b:17.5
occ:1.00
|
O
|
C:PHE556
|
2.3
|
11.8
|
1.0
|
|
O
|
C:LEU562
|
2.3
|
11.6
|
1.0
|
|
O
|
C:TYR559
|
2.4
|
16.9
|
1.0
|
|
O
|
C:HOH9020
|
2.6
|
24.3
|
1.0
|
|
O
|
C:HOH9244
|
2.6
|
26.8
|
1.0
|
|
O
|
C:PRO560
|
3.1
|
16.2
|
1.0
|
|
C
|
C:TYR559
|
3.4
|
10.7
|
1.0
|
|
C
|
C:LEU562
|
3.4
|
11.5
|
1.0
|
|
C
|
C:PHE556
|
3.4
|
15.9
|
1.0
|
|
C
|
C:PRO560
|
3.5
|
19.3
|
1.0
|
|
CA
|
C:PRO560
|
3.7
|
13.4
|
1.0
|
|
N
|
C:PRO560
|
4.0
|
14.5
|
1.0
|
|
N
|
C:LEU562
|
4.0
|
13.6
|
1.0
|
|
O
|
C:HOH8902
|
4.1
|
19.7
|
1.0
|
|
CA
|
C:PHE556
|
4.1
|
13.3
|
1.0
|
|
CA
|
C:LEU562
|
4.2
|
7.7
|
1.0
|
|
N
|
C:GLN563
|
4.3
|
15.1
|
1.0
|
|
CB
|
C:LEU562
|
4.3
|
9.0
|
1.0
|
|
CA
|
C:GLN563
|
4.4
|
16.6
|
1.0
|
|
N
|
C:TYR559
|
4.5
|
13.2
|
1.0
|
|
CA
|
C:TYR559
|
4.5
|
11.0
|
1.0
|
|
N
|
C:ARG557
|
4.5
|
12.9
|
1.0
|
|
N
|
C:ARG561
|
4.5
|
12.5
|
1.0
|
|
CA
|
C:ARG557
|
4.6
|
13.0
|
1.0
|
|
CG
|
C:GLN563
|
4.7
|
13.3
|
1.0
|
|
CB
|
C:PHE556
|
4.7
|
15.0
|
1.0
|
|
C
|
C:ARG557
|
4.7
|
27.2
|
1.0
|
|
O
|
C:ARG557
|
4.8
|
18.8
|
1.0
|
|
CD1
|
C:LEU350
|
4.8
|
12.2
|
1.0
|
|
C
|
C:ARG561
|
4.9
|
12.9
|
1.0
|
|
O
|
C:ALA555
|
4.9
|
13.5
|
1.0
|
|
CB
|
C:TYR559
|
5.0
|
14.4
|
1.0
|
|
Reference:
D.H.Juers,
T.D.Heightman,
A.Vasella,
J.D.Mccarter,
L.Mackenzie,
S.G.Withers,
B.W.Matthews.
A Structural View of the Action of Escherichia Coli (Lacz) Beta-Galactosidase Biochemistry V. 40 14781 2001.
ISSN: ISSN 0006-2960
PubMed: 11732897
DOI: 10.1021/BI011727I
Page generated: Sun Oct 6 19:03:31 2024
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