Sodium in PDB 1jyx: E. Coli (Lacz) Beta-Galactosidase in Complex with Iptg
Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase in Complex with Iptg
All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase in Complex with Iptg:
3.2.1.23;
Protein crystallography data
The structure of E. Coli (Lacz) Beta-Galactosidase in Complex with Iptg, PDB code: 1jyx
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)
|
27.00 /
1.75
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
151.770,
161.190,
202.910,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
16.8 /
24.4
|
Other elements in 1jyx:
The structure of E. Coli (Lacz) Beta-Galactosidase in Complex with Iptg also contains other interesting chemical elements:
Sodium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
14;
Binding sites:
The binding sites of Sodium atom in the E. Coli (Lacz) Beta-Galactosidase in Complex with Iptg
(pdb code 1jyx). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 14 binding sites of Sodium where determined in the
E. Coli (Lacz) Beta-Galactosidase in Complex with Iptg, PDB code: 1jyx:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 14 in 1jyx
Go back to
Sodium Binding Sites List in 1jyx
Sodium binding site 1 out
of 14 in the E. Coli (Lacz) Beta-Galactosidase in Complex with Iptg
 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 in Complex with Iptg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3101
b:18.7
occ:1.00
|
OD1
|
A:ASN604
|
2.3
|
19.0
|
1.0
|
|
O
|
A:PHE601
|
2.3
|
20.9
|
1.0
|
|
O
|
A:HOH8876
|
2.4
|
27.4
|
1.0
|
|
O6
|
A:IPT2001
|
2.4
|
18.6
|
0.9
|
|
OD2
|
A:ASP201
|
2.4
|
21.7
|
1.0
|
|
C6
|
A:IPT2001
|
3.1
|
16.3
|
0.9
|
|
CG
|
A:ASN604
|
3.2
|
18.6
|
1.0
|
|
CG
|
A:ASP201
|
3.4
|
22.0
|
1.0
|
|
ND2
|
A:ASN604
|
3.5
|
21.1
|
1.0
|
|
C
|
A:PHE601
|
3.5
|
24.7
|
1.0
|
|
OD1
|
A:ASP201
|
3.6
|
20.7
|
1.0
|
|
OH
|
A:TYR100
|
3.8
|
17.7
|
1.0
|
|
NE1
|
A:TRP568
|
4.0
|
18.0
|
1.0
|
|
O4
|
A:IPT2001
|
4.2
|
17.1
|
0.9
|
|
CA
|
A:CYS602
|
4.2
|
14.7
|
1.0
|
|
N
|
A:CYS602
|
4.2
|
17.1
|
1.0
|
|
C5
|
A:IPT2001
|
4.3
|
18.3
|
0.9
|
|
C4
|
A:IPT2001
|
4.5
|
19.1
|
0.9
|
|
NE2
|
A:HIS540
|
4.5
|
17.6
|
1.0
|
|
O
|
A:HOH8654
|
4.5
|
16.8
|
1.0
|
|
CA
|
A:PHE601
|
4.5
|
18.3
|
1.0
|
|
CB
|
A:PHE601
|
4.5
|
15.4
|
1.0
|
|
CB
|
A:ASP201
|
4.6
|
16.0
|
1.0
|
|
CB
|
A:ASN604
|
4.6
|
17.9
|
1.0
|
|
C
|
A:CYS602
|
4.7
|
13.2
|
1.0
|
|
O
|
A:ASP201
|
4.7
|
19.2
|
1.0
|
|
CE2
|
A:TRP568
|
4.8
|
15.7
|
1.0
|
|
CZ2
|
A:TRP568
|
4.9
|
17.5
|
1.0
|
|
CZ
|
A:TYR100
|
4.9
|
27.5
|
1.0
|
|
Sodium binding site 2 out
of 14 in 1jyx
Go back to
Sodium Binding Sites List in 1jyx
Sodium binding site 2 out
of 14 in the E. Coli (Lacz) Beta-Galactosidase in Complex with Iptg
 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 in Complex with Iptg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3102
b:16.1
occ:1.00
|
O
|
A:LEU562
|
2.3
|
14.6
|
1.0
|
|
O
|
A:TYR559
|
2.3
|
18.2
|
1.0
|
|
O
|
A:PHE556
|
2.3
|
13.3
|
1.0
|
|
O
|
A:HOH8995
|
2.4
|
21.6
|
1.0
|
|
O
|
A:HOH9181
|
2.5
|
21.4
|
1.0
|
|
O
|
A:PRO560
|
3.2
|
15.5
|
1.0
|
|
C
|
A:TYR559
|
3.3
|
12.8
|
1.0
|
|
C
|
A:LEU562
|
3.4
|
18.1
|
1.0
|
|
C
|
A:PHE556
|
3.4
|
13.5
|
1.0
|
|
C
|
A:PRO560
|
3.6
|
16.0
|
1.0
|
|
CA
|
A:PRO560
|
3.7
|
17.8
|
1.0
|
|
O
|
A:HOH8882
|
3.9
|
22.6
|
1.0
|
|
O
|
A:HOH9296
|
3.9
|
47.5
|
1.0
|
|
N
|
A:PRO560
|
3.9
|
20.7
|
1.0
|
|
N
|
A:LEU562
|
4.0
|
12.9
|
1.0
|
|
CA
|
A:PHE556
|
4.2
|
12.3
|
1.0
|
|
CA
|
A:LEU562
|
4.2
|
12.1
|
1.0
|
|
N
|
A:GLN563
|
4.3
|
14.4
|
1.0
|
|
CA
|
A:GLN563
|
4.4
|
12.7
|
1.0
|
|
CA
|
A:TYR559
|
4.5
|
10.1
|
1.0
|
|
N
|
A:ARG557
|
4.5
|
11.6
|
1.0
|
|
CB
|
A:LEU562
|
4.5
|
12.0
|
1.0
|
|
N
|
A:TYR559
|
4.6
|
10.4
|
1.0
|
|
N
|
A:ARG561
|
4.6
|
12.2
|
1.0
|
|
CA
|
A:ARG557
|
4.6
|
15.4
|
1.0
|
|
CG
|
A:GLN563
|
4.7
|
14.6
|
1.0
|
|
C
|
A:ARG557
|
4.7
|
17.6
|
1.0
|
|
CD1
|
A:LEU350
|
4.8
|
12.6
|
1.0
|
|
O
|
A:ARG557
|
4.8
|
14.3
|
1.0
|
|
CB
|
A:PHE556
|
4.8
|
13.9
|
1.0
|
|
C
|
A:ARG561
|
4.9
|
17.8
|
1.0
|
|
O
|
A:ALA555
|
5.0
|
17.3
|
1.0
|
|
Sodium binding site 3 out
of 14 in 1jyx
Go back to
Sodium Binding Sites List in 1jyx
Sodium binding site 3 out
of 14 in the E. Coli (Lacz) Beta-Galactosidase in Complex with Iptg
 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 in Complex with Iptg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3103
b:29.5
occ:1.00
|
O
|
A:HOH9246
|
2.3
|
34.0
|
1.0
|
|
O
|
A:PRO932
|
2.4
|
20.2
|
1.0
|
|
O
|
A:HOH8807
|
2.6
|
23.9
|
1.0
|
|
O
|
A:LEU967
|
2.6
|
22.1
|
1.0
|
|
O
|
A:THR970
|
2.8
|
30.4
|
1.0
|
|
O
|
A:HOH9116
|
3.4
|
39.1
|
1.0
|
|
CZ
|
A:PHE931
|
3.4
|
33.8
|
1.0
|
|
C
|
A:PRO932
|
3.5
|
14.3
|
1.0
|
|
CE1
|
A:PHE931
|
3.7
|
22.6
|
1.0
|
|
C
|
A:LEU967
|
3.7
|
17.9
|
1.0
|
|
O
|
A:MET968
|
3.9
|
31.9
|
1.0
|
|
CE2
|
A:PHE931
|
3.9
|
20.4
|
1.0
|
|
CA
|
A:MET968
|
3.9
|
23.9
|
1.0
|
|
C
|
A:MET968
|
4.0
|
43.6
|
1.0
|
|
C
|
A:THR970
|
4.0
|
31.4
|
1.0
|
|
CA
|
A:PRO932
|
4.2
|
20.8
|
1.0
|
|
N
|
A:PRO932
|
4.2
|
24.8
|
1.0
|
|
CB
|
A:PRO932
|
4.3
|
27.8
|
1.0
|
|
CD1
|
A:PHE931
|
4.3
|
23.6
|
1.0
|
|
CD
|
A:PRO932
|
4.3
|
21.6
|
1.0
|
|
N
|
A:MET968
|
4.3
|
17.4
|
1.0
|
|
N
|
A:THR970
|
4.4
|
22.3
|
1.0
|
|
O
|
A:HOH9404
|
4.5
|
50.7
|
1.0
|
|
N
|
A:SER933
|
4.5
|
17.1
|
1.0
|
|
CD2
|
A:PHE931
|
4.5
|
19.8
|
1.0
|
|
CG
|
A:PRO932
|
4.7
|
20.7
|
1.0
|
|
N
|
A:GLU969
|
4.7
|
20.5
|
1.0
|
|
CG
|
A:PHE931
|
4.7
|
18.8
|
1.0
|
|
CA
|
A:SER933
|
4.7
|
17.4
|
1.0
|
|
CA
|
A:THR970
|
4.8
|
17.7
|
1.0
|
|
CA
|
A:SER971
|
4.8
|
23.7
|
1.0
|
|
N
|
A:SER971
|
4.9
|
32.7
|
1.0
|
|
CA
|
A:LEU967
|
4.9
|
26.6
|
1.0
|
|
C
|
A:PHE931
|
5.0
|
27.7
|
1.0
|
|
Sodium binding site 4 out
of 14 in 1jyx
Go back to
Sodium Binding Sites List in 1jyx
Sodium binding site 4 out
of 14 in the E. Coli (Lacz) Beta-Galactosidase in Complex with Iptg
 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 in Complex with Iptg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3101
b:17.2
occ:1.00
|
O
|
B:HOH8786
|
2.3
|
16.1
|
1.0
|
|
OD2
|
B:ASP201
|
2.3
|
16.5
|
1.0
|
|
OD1
|
B:ASN604
|
2.4
|
15.7
|
1.0
|
|
O6
|
B:IPT2001
|
2.4
|
16.0
|
1.0
|
|
O
|
B:PHE601
|
2.5
|
17.7
|
1.0
|
|
CG
|
B:ASP201
|
3.2
|
17.5
|
1.0
|
|
C6
|
B:IPT2001
|
3.3
|
10.7
|
1.0
|
|
CG
|
B:ASN604
|
3.4
|
16.1
|
1.0
|
|
OD1
|
B:ASP201
|
3.5
|
15.5
|
1.0
|
|
C
|
B:PHE601
|
3.6
|
30.1
|
1.0
|
|
OH
|
B:TYR100
|
3.7
|
16.9
|
1.0
|
|
ND2
|
B:ASN604
|
3.7
|
11.6
|
1.0
|
|
NE1
|
B:TRP568
|
4.0
|
15.2
|
1.0
|
|
O4
|
B:IPT2001
|
4.1
|
16.1
|
1.0
|
|
CA
|
B:CYS602
|
4.2
|
15.8
|
1.0
|
|
O
|
B:HOH8567
|
4.2
|
23.2
|
1.0
|
|
C5
|
B:IPT2001
|
4.3
|
15.9
|
1.0
|
|
N
|
B:CYS602
|
4.3
|
23.3
|
1.0
|
|
C4
|
B:IPT2001
|
4.4
|
19.6
|
1.0
|
|
CB
|
B:ASP201
|
4.4
|
18.1
|
1.0
|
|
O
|
B:ASP201
|
4.5
|
14.0
|
1.0
|
|
CA
|
B:PHE601
|
4.7
|
16.5
|
1.0
|
|
CB
|
B:PHE601
|
4.7
|
13.3
|
1.0
|
|
C
|
B:CYS602
|
4.7
|
16.1
|
1.0
|
|
NE2
|
B:HIS540
|
4.7
|
16.6
|
1.0
|
|
CB
|
B:ASN604
|
4.7
|
14.3
|
1.0
|
|
CE2
|
B:TRP568
|
4.8
|
13.2
|
1.0
|
|
CZ
|
B:TYR100
|
4.8
|
15.4
|
1.0
|
|
CZ2
|
B:TRP568
|
4.9
|
13.4
|
1.0
|
|
Sodium binding site 5 out
of 14 in 1jyx
Go back to
Sodium Binding Sites List in 1jyx
Sodium binding site 5 out
of 14 in the E. Coli (Lacz) Beta-Galactosidase in Complex with Iptg
 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 in Complex with Iptg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3102
b:17.0
occ:1.00
|
O
|
B:LEU562
|
2.2
|
14.7
|
1.0
|
|
O
|
B:PHE556
|
2.3
|
13.6
|
1.0
|
|
O
|
B:TYR559
|
2.3
|
13.2
|
1.0
|
|
O
|
B:HOH9095
|
2.4
|
30.3
|
1.0
|
|
O
|
B:HOH8908
|
2.5
|
33.6
|
1.0
|
|
O
|
B:PRO560
|
3.3
|
16.1
|
1.0
|
|
C
|
B:LEU562
|
3.3
|
20.1
|
1.0
|
|
C
|
B:TYR559
|
3.3
|
23.8
|
1.0
|
|
C
|
B:PHE556
|
3.5
|
14.3
|
1.0
|
|
C
|
B:PRO560
|
3.6
|
16.2
|
1.0
|
|
CA
|
B:PRO560
|
3.6
|
14.4
|
1.0
|
|
N
|
B:PRO560
|
3.9
|
17.5
|
1.0
|
|
N
|
B:LEU562
|
3.9
|
12.6
|
1.0
|
|
O
|
B:HOH8793
|
4.0
|
19.2
|
1.0
|
|
CA
|
B:LEU562
|
4.2
|
13.1
|
1.0
|
|
CA
|
B:PHE556
|
4.2
|
10.1
|
1.0
|
|
N
|
B:GLN563
|
4.2
|
12.4
|
1.0
|
|
CA
|
B:GLN563
|
4.4
|
13.5
|
1.0
|
|
CB
|
B:LEU562
|
4.4
|
9.1
|
1.0
|
|
N
|
B:ARG561
|
4.5
|
13.9
|
1.0
|
|
CA
|
B:TYR559
|
4.5
|
13.2
|
1.0
|
|
O
|
B:HOH9255
|
4.5
|
43.0
|
1.0
|
|
O
|
B:HOH9226
|
4.5
|
42.6
|
1.0
|
|
N
|
B:TYR559
|
4.5
|
11.9
|
1.0
|
|
N
|
B:ARG557
|
4.6
|
13.9
|
1.0
|
|
CD1
|
B:LEU350
|
4.6
|
20.4
|
1.0
|
|
CG
|
B:GLN563
|
4.7
|
12.0
|
1.0
|
|
O
|
B:ARG557
|
4.7
|
15.1
|
1.0
|
|
CA
|
B:ARG557
|
4.7
|
12.7
|
1.0
|
|
CB
|
B:PHE556
|
4.7
|
15.8
|
1.0
|
|
C
|
B:ARG557
|
4.7
|
20.6
|
1.0
|
|
C
|
B:ARG561
|
4.8
|
15.2
|
1.0
|
|
CB
|
B:TYR559
|
4.9
|
12.4
|
1.0
|
|
O
|
B:ALA555
|
5.0
|
15.0
|
1.0
|
|
Sodium binding site 6 out
of 14 in 1jyx
Go back to
Sodium Binding Sites List in 1jyx
Sodium binding site 6 out
of 14 in the E. Coli (Lacz) Beta-Galactosidase in Complex with Iptg
 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 in Complex with Iptg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3103
b:35.2
occ:1.00
|
O
|
B:PRO932
|
2.3
|
20.0
|
1.0
|
|
O
|
B:LEU967
|
2.5
|
22.9
|
1.0
|
|
O
|
B:HOH8719
|
2.7
|
23.4
|
1.0
|
|
O
|
B:THR970
|
2.8
|
34.2
|
1.0
|
|
CZ
|
B:PHE931
|
3.3
|
23.7
|
1.0
|
|
C
|
B:PRO932
|
3.3
|
14.2
|
1.0
|
|
CE1
|
B:PHE931
|
3.6
|
23.5
|
1.0
|
|
C
|
B:LEU967
|
3.6
|
23.4
|
1.0
|
|
CE2
|
B:PHE931
|
3.7
|
19.2
|
1.0
|
|
O
|
B:HOH9166
|
3.8
|
48.3
|
1.0
|
|
C
|
B:THR970
|
3.9
|
34.1
|
1.0
|
|
O
|
B:HOH9034
|
3.9
|
37.7
|
1.0
|
|
CA
|
B:MET968
|
3.9
|
19.6
|
1.0
|
|
O
|
B:MET968
|
4.0
|
26.7
|
1.0
|
|
CA
|
B:PRO932
|
4.1
|
17.7
|
1.0
|
|
C
|
B:MET968
|
4.1
|
21.7
|
1.0
|
|
N
|
B:PRO932
|
4.2
|
22.2
|
1.0
|
|
CB
|
B:PRO932
|
4.2
|
36.1
|
1.0
|
|
CD
|
B:PRO932
|
4.2
|
27.7
|
1.0
|
|
N
|
B:SER933
|
4.3
|
21.9
|
1.0
|
|
N
|
B:MET968
|
4.3
|
21.9
|
1.0
|
|
CD1
|
B:PHE931
|
4.4
|
17.7
|
1.0
|
|
N
|
B:THR970
|
4.4
|
18.3
|
1.0
|
|
CD2
|
B:PHE931
|
4.4
|
17.7
|
1.0
|
|
CG
|
B:PRO932
|
4.5
|
35.9
|
1.0
|
|
CA
|
B:SER933
|
4.5
|
23.0
|
1.0
|
|
CG
|
B:PHE931
|
4.7
|
19.3
|
1.0
|
|
CA
|
B:THR970
|
4.7
|
17.9
|
1.0
|
|
N
|
B:SER971
|
4.8
|
27.1
|
1.0
|
|
CA
|
B:LEU967
|
4.8
|
21.7
|
1.0
|
|
CA
|
B:SER971
|
4.8
|
31.4
|
1.0
|
|
C
|
B:PHE931
|
4.8
|
23.5
|
1.0
|
|
N
|
B:GLU969
|
4.9
|
24.7
|
1.0
|
|
Sodium binding site 7 out
of 14 in 1jyx
Go back to
Sodium Binding Sites List in 1jyx
Sodium binding site 7 out
of 14 in the E. Coli (Lacz) Beta-Galactosidase in Complex with Iptg
 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 in Complex with Iptg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3104
b:28.2
occ:1.00
|
O
|
B:DMS8425
|
2.2
|
64.8
|
1.0
|
|
O
|
B:SER647
|
2.4
|
19.9
|
1.0
|
|
O
|
B:GLU650
|
2.4
|
22.5
|
1.0
|
|
O
|
B:LEU670
|
2.7
|
24.8
|
1.0
|
|
O
|
B:HOH9280
|
2.8
|
39.4
|
1.0
|
|
O
|
B:HOH9175
|
3.2
|
46.4
|
1.0
|
|
S
|
B:DMS8425
|
3.3
|
54.8
|
1.0
|
|
N
|
B:GLU650
|
3.3
|
17.7
|
1.0
|
|
C
|
B:GLU650
|
3.4
|
23.8
|
1.0
|
|
C
|
B:SER647
|
3.6
|
25.0
|
1.0
|
|
CA
|
B:GLU650
|
3.7
|
22.8
|
1.0
|
|
C
|
B:LEU670
|
3.8
|
25.8
|
1.0
|
|
N
|
B:ASN649
|
3.9
|
17.5
|
1.0
|
|
CA
|
B:ASP648
|
3.9
|
21.8
|
1.0
|
|
CB
|
B:GLU650
|
3.9
|
16.1
|
1.0
|
|
C
|
B:ASP648
|
3.9
|
20.8
|
1.0
|
|
N
|
B:LEU670
|
4.0
|
28.0
|
1.0
|
|
C2
|
B:DMS8425
|
4.1
|
43.0
|
1.0
|
|
OG
|
B:SER647
|
4.1
|
20.3
|
1.0
|
|
N
|
B:ASP648
|
4.2
|
21.4
|
1.0
|
|
CA
|
B:LEU670
|
4.3
|
23.2
|
1.0
|
|
C
|
B:ASN649
|
4.4
|
19.0
|
1.0
|
|
CB
|
B:LEU670
|
4.4
|
24.0
|
1.0
|
|
CB
|
B:SER647
|
4.5
|
26.1
|
1.0
|
|
CA
|
B:ASN649
|
4.6
|
19.2
|
1.0
|
|
N
|
B:LEU651
|
4.6
|
19.3
|
1.0
|
|
O
|
B:ASP648
|
4.6
|
21.2
|
1.0
|
|
OE2
|
B:GLU650
|
4.7
|
15.3
|
1.0
|
|
C1
|
B:DMS8425
|
4.7
|
0.0
|
1.0
|
|
CA
|
B:SER647
|
4.8
|
17.1
|
1.0
|
|
N
|
B:ASP671
|
4.9
|
21.8
|
1.0
|
|
Sodium binding site 8 out
of 14 in 1jyx
Go back to
Sodium Binding Sites List in 1jyx
Sodium binding site 8 out
of 14 in the E. Coli (Lacz) Beta-Galactosidase in Complex with Iptg
 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 in Complex with Iptg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na3101
b:17.4
occ:1.00
|
O6
|
C:IPT2001
|
2.2
|
18.1
|
1.0
|
|
OD1
|
C:ASN604
|
2.3
|
17.0
|
1.0
|
|
O
|
C:HOH8799
|
2.3
|
20.7
|
1.0
|
|
OD2
|
C:ASP201
|
2.4
|
17.1
|
1.0
|
|
O
|
C:PHE601
|
2.4
|
16.4
|
1.0
|
|
C6
|
C:IPT2001
|
3.2
|
20.3
|
1.0
|
|
CG
|
C:ASN604
|
3.3
|
15.3
|
1.0
|
|
CG
|
C:ASP201
|
3.3
|
28.1
|
1.0
|
|
ND2
|
C:ASN604
|
3.6
|
16.2
|
1.0
|
|
OD1
|
C:ASP201
|
3.6
|
19.5
|
1.0
|
|
C
|
C:PHE601
|
3.6
|
19.1
|
1.0
|
|
OH
|
C:TYR100
|
3.8
|
13.8
|
1.0
|
|
NE1
|
C:TRP568
|
4.0
|
16.6
|
1.0
|
|
O4
|
C:IPT2001
|
4.1
|
17.5
|
1.0
|
|
CA
|
C:CYS602
|
4.2
|
19.1
|
1.0
|
|
C5
|
C:IPT2001
|
4.3
|
19.1
|
1.0
|
|
C4
|
C:IPT2001
|
4.3
|
16.1
|
1.0
|
|
O
|
C:HOH8578
|
4.4
|
16.6
|
1.0
|
|
N
|
C:CYS602
|
4.4
|
13.5
|
1.0
|
|
CB
|
C:ASP201
|
4.5
|
10.6
|
1.0
|
|
CB
|
C:PHE601
|
4.5
|
10.6
|
1.0
|
|
CA
|
C:PHE601
|
4.6
|
11.9
|
1.0
|
|
NE2
|
C:HIS540
|
4.6
|
17.2
|
1.0
|
|
CB
|
C:ASN604
|
4.7
|
13.6
|
1.0
|
|
O
|
C:ASP201
|
4.7
|
18.7
|
1.0
|
|
C
|
C:CYS602
|
4.7
|
21.9
|
1.0
|
|
CE2
|
C:TRP568
|
4.7
|
13.7
|
1.0
|
|
CZ2
|
C:TRP568
|
4.8
|
14.4
|
1.0
|
|
CZ
|
C:TYR100
|
4.9
|
23.7
|
1.0
|
|
CD1
|
C:TRP568
|
5.0
|
14.3
|
1.0
|
|
Sodium binding site 9 out
of 14 in 1jyx
Go back to
Sodium Binding Sites List in 1jyx
Sodium binding site 9 out
of 14 in the E. Coli (Lacz) Beta-Galactosidase in Complex with Iptg
 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 in Complex with Iptg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na3102
b:16.7
occ:1.00
|
O
|
C:LEU562
|
2.2
|
14.1
|
1.0
|
|
O
|
C:TYR559
|
2.3
|
15.2
|
1.0
|
|
O
|
C:PHE556
|
2.4
|
14.1
|
1.0
|
|
O
|
C:HOH9123
|
2.5
|
34.2
|
1.0
|
|
O
|
C:HOH8924
|
2.6
|
26.9
|
1.0
|
|
O
|
C:PRO560
|
3.2
|
14.3
|
1.0
|
|
C
|
C:LEU562
|
3.3
|
16.8
|
1.0
|
|
C
|
C:TYR559
|
3.4
|
16.5
|
1.0
|
|
C
|
C:PHE556
|
3.5
|
16.3
|
1.0
|
|
C
|
C:PRO560
|
3.6
|
15.3
|
1.0
|
|
CA
|
C:PRO560
|
3.7
|
16.6
|
1.0
|
|
N
|
C:LEU562
|
3.9
|
11.2
|
1.0
|
|
N
|
C:PRO560
|
4.0
|
16.4
|
1.0
|
|
CA
|
C:LEU562
|
4.1
|
12.8
|
1.0
|
|
O
|
C:HOH8806
|
4.1
|
17.1
|
1.0
|
|
CA
|
C:PHE556
|
4.2
|
10.7
|
1.0
|
|
N
|
C:GLN563
|
4.2
|
12.6
|
1.0
|
|
CB
|
C:LEU562
|
4.3
|
9.2
|
1.0
|
|
CA
|
C:GLN563
|
4.3
|
14.1
|
1.0
|
|
CA
|
C:TYR559
|
4.5
|
10.2
|
1.0
|
|
N
|
C:TYR559
|
4.5
|
14.1
|
1.0
|
|
N
|
C:ARG561
|
4.5
|
9.6
|
1.0
|
|
O
|
C:HOH9370
|
4.5
|
60.1
|
1.0
|
|
N
|
C:ARG557
|
4.6
|
13.8
|
1.0
|
|
CG
|
C:GLN563
|
4.7
|
13.7
|
1.0
|
|
CB
|
C:PHE556
|
4.7
|
14.4
|
1.0
|
|
O
|
C:ARG557
|
4.8
|
14.0
|
1.0
|
|
C
|
C:ARG561
|
4.8
|
12.3
|
1.0
|
|
C
|
C:ARG557
|
4.8
|
15.1
|
1.0
|
|
CA
|
C:ARG557
|
4.8
|
18.4
|
1.0
|
|
CD1
|
C:LEU350
|
4.8
|
16.1
|
1.0
|
|
O
|
C:ALA555
|
4.9
|
14.8
|
1.0
|
|
CB
|
C:TYR559
|
4.9
|
12.7
|
1.0
|
|
Sodium binding site 10 out
of 14 in 1jyx
Go back to
Sodium Binding Sites List in 1jyx
Sodium binding site 10 out
of 14 in the E. Coli (Lacz) Beta-Galactosidase in Complex with Iptg
 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 in Complex with Iptg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na3103
b:30.2
occ:1.00
|
O
|
C:LEU967
|
2.5
|
19.7
|
1.0
|
|
O
|
C:PRO932
|
2.5
|
16.9
|
1.0
|
|
O
|
C:HOH8730
|
2.7
|
19.3
|
1.0
|
|
O
|
C:THR970
|
2.8
|
26.7
|
1.0
|
|
O
|
C:HOH9205
|
2.9
|
41.4
|
1.0
|
|
CZ
|
C:PHE931
|
3.4
|
24.2
|
1.0
|
|
C
|
C:PRO932
|
3.5
|
18.7
|
1.0
|
|
C
|
C:LEU967
|
3.6
|
19.4
|
1.0
|
|
CE1
|
C:PHE931
|
3.7
|
22.0
|
1.0
|
|
O
|
C:HOH9052
|
3.7
|
42.0
|
1.0
|
|
C
|
C:THR970
|
3.8
|
24.0
|
1.0
|
|
CA
|
C:MET968
|
3.8
|
18.3
|
1.0
|
|
CE2
|
C:PHE931
|
3.9
|
14.3
|
1.0
|
|
O
|
C:MET968
|
4.0
|
28.1
|
1.0
|
|
C
|
C:MET968
|
4.0
|
32.3
|
1.0
|
|
CA
|
C:PRO932
|
4.1
|
22.4
|
1.0
|
|
N
|
C:THR970
|
4.2
|
19.7
|
1.0
|
|
N
|
C:MET968
|
4.2
|
14.9
|
1.0
|
|
CB
|
C:PRO932
|
4.2
|
22.5
|
1.0
|
|
N
|
C:PRO932
|
4.2
|
20.1
|
1.0
|
|
CD
|
C:PRO932
|
4.3
|
22.1
|
1.0
|
|
CD1
|
C:PHE931
|
4.3
|
18.4
|
1.0
|
|
N
|
C:SER933
|
4.5
|
19.5
|
1.0
|
|
CD2
|
C:PHE931
|
4.6
|
17.8
|
1.0
|
|
CA
|
C:THR970
|
4.6
|
13.3
|
1.0
|
|
N
|
C:SER971
|
4.7
|
23.0
|
1.0
|
|
CA
|
C:SER971
|
4.7
|
32.7
|
1.0
|
|
CG
|
C:PHE931
|
4.7
|
18.7
|
1.0
|
|
N
|
C:GLU969
|
4.8
|
18.5
|
1.0
|
|
CA
|
C:SER933
|
4.8
|
19.4
|
1.0
|
|
CA
|
C:LEU967
|
4.8
|
17.6
|
1.0
|
|
CG
|
C:PRO932
|
4.8
|
17.4
|
1.0
|
|
C
|
C:PHE931
|
5.0
|
22.6
|
1.0
|
|
Reference:
D.H.Juers,
T.D.Heightman,
A.Vasella,
J.D.Mccarter,
L.Mackenzie,
S.G.Withers,
B.W.Matthews.
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ISSN: ISSN 0006-2960
PubMed: 11732897
DOI: 10.1021/BI011727I
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