Sodium in PDB 1jyw: E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Pnpg
Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Pnpg
All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Pnpg:
3.2.1.23;
Protein crystallography data
The structure of E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Pnpg, PDB code: 1jyw
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)
|
28.80 /
1.55
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
149.680,
168.600,
201.090,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
18 /
22.9
|
Other elements in 1jyw:
The structure of E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Pnpg 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 (E537Q) in Complex with Pnpg
(pdb code 1jyw). 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 (E537Q) in Complex with Pnpg, PDB code: 1jyw:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 16 in 1jyw
Go back to
Sodium Binding Sites List in 1jyw
Sodium binding site 1 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Pnpg
 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 (E537Q) in Complex with Pnpg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3101
b:13.0
occ:1.00
|
O
|
A:HOH8870
|
2.2
|
17.8
|
1.0
|
|
O6
|
A:1472001
|
2.3
|
11.4
|
1.0
|
|
OD2
|
A:ASP201
|
2.3
|
12.4
|
1.0
|
|
OD1
|
A:ASN604
|
2.4
|
12.3
|
1.0
|
|
O
|
A:PHE601
|
2.4
|
11.4
|
1.0
|
|
C6
|
A:1472001
|
3.2
|
10.6
|
1.0
|
|
CG
|
A:ASP201
|
3.3
|
11.2
|
1.0
|
|
CG
|
A:ASN604
|
3.3
|
12.9
|
1.0
|
|
C
|
A:PHE601
|
3.6
|
13.2
|
1.0
|
|
OH
|
A:TYR100
|
3.6
|
14.4
|
1.0
|
|
OD1
|
A:ASP201
|
3.6
|
13.4
|
1.0
|
|
ND2
|
A:ASN604
|
3.7
|
11.0
|
1.0
|
|
O4
|
A:1472001
|
4.2
|
11.6
|
1.0
|
|
NE1
|
A:TRP568
|
4.2
|
10.2
|
1.0
|
|
CA
|
A:CYS602
|
4.2
|
13.8
|
1.0
|
|
C5
|
A:1472001
|
4.3
|
12.6
|
1.0
|
|
C4
|
A:1472001
|
4.3
|
13.5
|
1.0
|
|
N
|
A:CYS602
|
4.3
|
12.6
|
1.0
|
|
CB
|
A:PHE601
|
4.5
|
11.4
|
1.0
|
|
O
|
A:HOH8652
|
4.5
|
13.9
|
1.0
|
|
CB
|
A:ASP201
|
4.5
|
9.9
|
1.0
|
|
CA
|
A:PHE601
|
4.5
|
12.8
|
1.0
|
|
NE2
|
A:HIS540
|
4.6
|
11.5
|
1.0
|
|
C
|
A:CYS602
|
4.7
|
16.1
|
1.0
|
|
O
|
A:ASP201
|
4.7
|
11.7
|
1.0
|
|
CB
|
A:ASN604
|
4.7
|
8.9
|
1.0
|
|
CZ
|
A:TYR100
|
4.8
|
18.1
|
1.0
|
|
CZ2
|
A:TRP568
|
4.8
|
14.3
|
1.0
|
|
CE2
|
A:TRP568
|
4.9
|
11.1
|
1.0
|
|
Sodium binding site 2 out
of 16 in 1jyw
Go back to
Sodium Binding Sites List in 1jyw
Sodium binding site 2 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Pnpg
 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 (E537Q) in Complex with Pnpg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3102
b:12.9
occ:1.00
|
O
|
A:PHE556
|
2.2
|
12.1
|
1.0
|
|
O
|
A:TYR559
|
2.3
|
11.0
|
1.0
|
|
O
|
A:LEU562
|
2.3
|
9.3
|
1.0
|
|
O
|
A:HOH8995
|
2.5
|
20.7
|
1.0
|
|
O
|
A:HOH9220
|
2.6
|
24.5
|
1.0
|
|
O
|
A:PRO560
|
3.2
|
10.7
|
1.0
|
|
C
|
A:TYR559
|
3.3
|
11.5
|
1.0
|
|
C
|
A:LEU562
|
3.4
|
9.7
|
1.0
|
|
C
|
A:PHE556
|
3.4
|
12.1
|
1.0
|
|
C
|
A:PRO560
|
3.5
|
8.2
|
1.0
|
|
CA
|
A:PRO560
|
3.6
|
9.6
|
1.0
|
|
N
|
A:PRO560
|
3.9
|
11.6
|
1.0
|
|
N
|
A:LEU562
|
4.0
|
7.0
|
1.0
|
|
O
|
A:HOH8877
|
4.1
|
14.9
|
1.0
|
|
CA
|
A:PHE556
|
4.1
|
9.0
|
1.0
|
|
CA
|
A:LEU562
|
4.2
|
8.9
|
1.0
|
|
O
|
A:HOH9390
|
4.3
|
34.2
|
1.0
|
|
CB
|
A:LEU562
|
4.3
|
8.2
|
1.0
|
|
N
|
A:GLN563
|
4.4
|
8.3
|
1.0
|
|
N
|
A:TYR559
|
4.4
|
9.1
|
1.0
|
|
CA
|
A:GLN563
|
4.4
|
8.2
|
1.0
|
|
CA
|
A:TYR559
|
4.4
|
7.9
|
1.0
|
|
N
|
A:ARG557
|
4.5
|
9.2
|
1.0
|
|
N
|
A:ARG561
|
4.5
|
7.7
|
1.0
|
|
CA
|
A:ARG557
|
4.6
|
7.6
|
1.0
|
|
C
|
A:ARG557
|
4.7
|
10.8
|
1.0
|
|
O
|
A:ARG557
|
4.7
|
11.2
|
1.0
|
|
CG
|
A:GLN563
|
4.7
|
8.9
|
1.0
|
|
CB
|
A:PHE556
|
4.8
|
9.2
|
1.0
|
|
C
|
A:ARG561
|
4.8
|
10.1
|
1.0
|
|
O
|
A:ALA555
|
4.9
|
10.4
|
1.0
|
|
CD1
|
A:LEU350
|
4.9
|
9.3
|
1.0
|
|
Sodium binding site 3 out
of 16 in 1jyw
Go back to
Sodium Binding Sites List in 1jyw
Sodium binding site 3 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Pnpg
 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 (E537Q) in Complex with Pnpg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3103
b:23.9
occ:1.00
|
O
|
A:HOH9311
|
2.4
|
38.6
|
1.0
|
|
O
|
A:PRO932
|
2.4
|
14.4
|
1.0
|
|
O
|
A:LEU967
|
2.4
|
17.5
|
1.0
|
|
O
|
A:HOH8802
|
2.6
|
16.1
|
1.0
|
|
O
|
A:THR970
|
2.7
|
23.6
|
1.0
|
|
C
|
A:PRO932
|
3.5
|
15.7
|
1.0
|
|
CZ
|
A:PHE931
|
3.5
|
16.4
|
1.0
|
|
C
|
A:LEU967
|
3.6
|
18.1
|
1.0
|
|
O
|
A:MET968
|
3.8
|
24.2
|
1.0
|
|
CE1
|
A:PHE931
|
3.8
|
18.5
|
1.0
|
|
CE2
|
A:PHE931
|
3.8
|
13.6
|
1.0
|
|
C
|
A:THR970
|
3.9
|
26.4
|
1.0
|
|
CA
|
A:MET968
|
3.9
|
14.0
|
1.0
|
|
O
|
A:HOH9137
|
3.9
|
28.9
|
1.0
|
|
C
|
A:MET968
|
3.9
|
23.2
|
1.0
|
|
CB
|
A:PRO932
|
4.0
|
13.4
|
1.0
|
|
CA
|
A:PRO932
|
4.2
|
12.4
|
1.0
|
|
N
|
A:MET968
|
4.2
|
14.1
|
1.0
|
|
CD
|
A:PRO932
|
4.2
|
12.3
|
1.0
|
|
N
|
A:PRO932
|
4.2
|
13.7
|
1.0
|
|
N
|
A:THR970
|
4.3
|
16.4
|
1.0
|
|
CD1
|
A:PHE931
|
4.5
|
13.3
|
1.0
|
|
CD2
|
A:PHE931
|
4.5
|
15.1
|
1.0
|
|
N
|
A:SER933
|
4.5
|
11.2
|
1.0
|
|
CA
|
A:SER971
|
4.6
|
21.1
|
1.0
|
|
CG
|
A:PRO932
|
4.6
|
16.4
|
1.0
|
|
N
|
A:SER971
|
4.7
|
20.5
|
1.0
|
|
CA
|
A:THR970
|
4.7
|
15.6
|
1.0
|
|
CA
|
A:SER933
|
4.7
|
13.2
|
1.0
|
|
N
|
A:GLU969
|
4.8
|
13.5
|
1.0
|
|
CG
|
A:PHE931
|
4.8
|
13.9
|
1.0
|
|
CA
|
A:LEU967
|
4.8
|
16.8
|
1.0
|
|
C
|
A:PHE931
|
4.9
|
17.0
|
1.0
|
|
Sodium binding site 4 out
of 16 in 1jyw
Go back to
Sodium Binding Sites List in 1jyw
Sodium binding site 4 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Pnpg
 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 (E537Q) in Complex with Pnpg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3104
b:23.3
occ:1.00
|
O
|
A:DMS8425
|
2.1
|
33.6
|
1.0
|
|
O
|
A:LEU670
|
2.3
|
16.7
|
1.0
|
|
O
|
A:HOH9325
|
2.4
|
37.1
|
1.0
|
|
O
|
A:SER647
|
2.5
|
17.5
|
1.0
|
|
O
|
A:GLU650
|
2.5
|
15.7
|
1.0
|
|
O
|
A:HOH9481
|
2.5
|
32.9
|
1.0
|
|
S
|
A:DMS8425
|
3.2
|
38.4
|
1.0
|
|
C
|
A:LEU670
|
3.4
|
15.4
|
1.0
|
|
C
|
A:GLU650
|
3.6
|
14.5
|
1.0
|
|
N
|
A:GLU650
|
3.6
|
12.3
|
1.0
|
|
C
|
A:SER647
|
3.7
|
17.0
|
1.0
|
|
C2
|
A:DMS8425
|
3.7
|
44.4
|
1.0
|
|
N
|
A:LEU670
|
3.8
|
18.0
|
1.0
|
|
CA
|
A:GLU650
|
4.0
|
14.3
|
1.0
|
|
CA
|
A:LEU670
|
4.1
|
17.0
|
1.0
|
|
CA
|
A:ASP648
|
4.1
|
17.8
|
1.0
|
|
CB
|
A:LEU670
|
4.2
|
22.9
|
1.0
|
|
N
|
A:ASN649
|
4.2
|
16.4
|
1.0
|
|
C
|
A:ASP648
|
4.2
|
19.8
|
1.0
|
|
CB
|
A:GLU650
|
4.2
|
14.5
|
1.0
|
|
OG
|
A:SER647
|
4.2
|
15.8
|
1.0
|
|
N
|
A:ASP648
|
4.4
|
15.7
|
1.0
|
|
N
|
A:ASP671
|
4.5
|
16.8
|
1.0
|
|
CB
|
A:SER647
|
4.6
|
16.4
|
1.0
|
|
C
|
A:ASN649
|
4.7
|
17.5
|
1.0
|
|
N
|
A:LEU651
|
4.8
|
13.8
|
1.0
|
|
O
|
A:ASP648
|
4.8
|
18.6
|
1.0
|
|
CA
|
A:ASP671
|
4.8
|
20.9
|
1.0
|
|
CA
|
A:SER647
|
4.8
|
11.8
|
1.0
|
|
C1
|
A:DMS8425
|
4.9
|
38.0
|
1.0
|
|
C
|
A:PRO669
|
4.9
|
17.7
|
1.0
|
|
CA
|
A:ASN649
|
4.9
|
15.0
|
1.0
|
|
OE1
|
A:GLU650
|
5.0
|
17.2
|
1.0
|
|
Sodium binding site 5 out
of 16 in 1jyw
Go back to
Sodium Binding Sites List in 1jyw
Sodium binding site 5 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Pnpg
 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 (E537Q) in Complex with Pnpg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3101
b:12.1
occ:1.00
|
O6
|
B:1472001
|
2.3
|
11.4
|
1.0
|
|
O
|
B:HOH8894
|
2.3
|
13.9
|
1.0
|
|
OD2
|
B:ASP201
|
2.3
|
11.2
|
1.0
|
|
OD1
|
B:ASN604
|
2.4
|
11.7
|
1.0
|
|
O
|
B:PHE601
|
2.4
|
11.6
|
1.0
|
|
C6
|
B:1472001
|
3.3
|
10.9
|
1.0
|
|
CG
|
B:ASP201
|
3.3
|
17.2
|
1.0
|
|
CG
|
B:ASN604
|
3.4
|
13.6
|
1.0
|
|
C
|
B:PHE601
|
3.5
|
11.3
|
1.0
|
|
OD1
|
B:ASP201
|
3.6
|
12.6
|
1.0
|
|
ND2
|
B:ASN604
|
3.7
|
11.3
|
1.0
|
|
OH
|
B:TYR100
|
3.7
|
12.3
|
1.0
|
|
O4
|
B:1472001
|
4.1
|
10.7
|
1.0
|
|
CA
|
B:CYS602
|
4.2
|
11.8
|
1.0
|
|
NE1
|
B:TRP568
|
4.2
|
10.4
|
1.0
|
|
N
|
B:CYS602
|
4.3
|
9.6
|
1.0
|
|
C5
|
B:1472001
|
4.3
|
10.7
|
1.0
|
|
C4
|
B:1472001
|
4.4
|
10.3
|
1.0
|
|
CB
|
B:ASP201
|
4.5
|
9.2
|
1.0
|
|
O
|
B:HOH8675
|
4.5
|
12.8
|
1.0
|
|
CA
|
B:PHE601
|
4.5
|
11.4
|
1.0
|
|
CB
|
B:PHE601
|
4.5
|
12.0
|
1.0
|
|
NE2
|
B:HIS540
|
4.6
|
10.6
|
1.0
|
|
O
|
B:ASP201
|
4.7
|
11.6
|
1.0
|
|
CB
|
B:ASN604
|
4.8
|
11.4
|
1.0
|
|
C
|
B:CYS602
|
4.8
|
10.7
|
1.0
|
|
CZ2
|
B:TRP568
|
4.8
|
9.9
|
1.0
|
|
CZ
|
B:TYR100
|
4.8
|
12.9
|
1.0
|
|
CE2
|
B:TRP568
|
4.9
|
12.2
|
1.0
|
|
Sodium binding site 6 out
of 16 in 1jyw
Go back to
Sodium Binding Sites List in 1jyw
Sodium binding site 6 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Pnpg
 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 (E537Q) in Complex with Pnpg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3102
b:11.7
occ:1.00
|
O
|
B:HOH9236
|
2.2
|
25.4
|
1.0
|
|
O
|
B:LEU562
|
2.2
|
10.0
|
1.0
|
|
O
|
B:TYR559
|
2.3
|
11.5
|
1.0
|
|
O
|
B:PHE556
|
2.3
|
9.4
|
1.0
|
|
O
|
B:HOH9019
|
2.6
|
18.0
|
1.0
|
|
O
|
B:PRO560
|
3.2
|
10.0
|
1.0
|
|
C
|
B:TYR559
|
3.3
|
11.5
|
1.0
|
|
C
|
B:LEU562
|
3.3
|
11.2
|
1.0
|
|
C
|
B:PHE556
|
3.4
|
9.4
|
1.0
|
|
C
|
B:PRO560
|
3.6
|
9.7
|
1.0
|
|
CA
|
B:PRO560
|
3.6
|
9.0
|
1.0
|
|
N
|
B:PRO560
|
3.9
|
10.6
|
1.0
|
|
N
|
B:LEU562
|
4.0
|
7.0
|
1.0
|
|
CA
|
B:PHE556
|
4.1
|
8.9
|
1.0
|
|
CA
|
B:LEU562
|
4.2
|
8.1
|
1.0
|
|
O
|
B:HOH8901
|
4.2
|
15.2
|
1.0
|
|
CB
|
B:LEU562
|
4.3
|
8.1
|
1.0
|
|
N
|
B:GLN563
|
4.3
|
7.4
|
1.0
|
|
CA
|
B:TYR559
|
4.4
|
9.3
|
1.0
|
|
N
|
B:TYR559
|
4.4
|
9.6
|
1.0
|
|
O
|
B:HOH9459
|
4.4
|
22.8
|
1.0
|
|
CA
|
B:GLN563
|
4.4
|
5.7
|
1.0
|
|
N
|
B:ARG557
|
4.5
|
7.8
|
1.0
|
|
O
|
B:HOH9414
|
4.5
|
38.3
|
1.0
|
|
N
|
B:ARG561
|
4.5
|
9.3
|
1.0
|
|
CA
|
B:ARG557
|
4.6
|
8.1
|
1.0
|
|
C
|
B:ARG557
|
4.7
|
11.0
|
1.0
|
|
O
|
B:ARG557
|
4.7
|
12.6
|
1.0
|
|
CG
|
B:GLN563
|
4.7
|
7.2
|
1.0
|
|
CB
|
B:PHE556
|
4.8
|
8.0
|
1.0
|
|
O
|
B:HOH9659
|
4.8
|
50.8
|
1.0
|
|
C
|
B:ARG561
|
4.8
|
8.5
|
1.0
|
|
CD1
|
B:LEU350
|
4.9
|
10.2
|
1.0
|
|
O
|
B:ALA555
|
4.9
|
10.0
|
1.0
|
|
CB
|
B:TYR559
|
4.9
|
8.6
|
1.0
|
|
Sodium binding site 7 out
of 16 in 1jyw
Go back to
Sodium Binding Sites List in 1jyw
Sodium binding site 7 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Pnpg
 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 (E537Q) in Complex with Pnpg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3103
b:20.0
occ:1.00
|
O
|
B:HOH9332
|
2.2
|
48.7
|
1.0
|
|
O
|
B:PRO932
|
2.4
|
13.3
|
1.0
|
|
O
|
B:LEU967
|
2.4
|
14.7
|
1.0
|
|
O
|
B:THR970
|
2.6
|
27.8
|
1.0
|
|
O
|
B:HOH8824
|
2.6
|
17.2
|
1.0
|
|
C
|
B:PRO932
|
3.4
|
12.9
|
1.0
|
|
CZ
|
B:PHE931
|
3.5
|
13.5
|
1.0
|
|
C
|
B:LEU967
|
3.6
|
13.9
|
1.0
|
|
O
|
B:HOH9155
|
3.7
|
25.6
|
1.0
|
|
C
|
B:THR970
|
3.7
|
23.3
|
1.0
|
|
O
|
B:MET968
|
3.7
|
21.2
|
1.0
|
|
CE1
|
B:PHE931
|
3.8
|
13.2
|
1.0
|
|
CE2
|
B:PHE931
|
3.9
|
14.5
|
1.0
|
|
CA
|
B:MET968
|
3.9
|
13.5
|
1.0
|
|
C
|
B:MET968
|
3.9
|
26.4
|
1.0
|
|
CB
|
B:PRO932
|
4.1
|
14.4
|
1.0
|
|
CA
|
B:PRO932
|
4.2
|
12.1
|
1.0
|
|
N
|
B:THR970
|
4.2
|
16.1
|
1.0
|
|
N
|
B:PRO932
|
4.2
|
14.6
|
1.0
|
|
N
|
B:MET968
|
4.3
|
12.0
|
1.0
|
|
CD
|
B:PRO932
|
4.3
|
13.7
|
1.0
|
|
CD1
|
B:PHE931
|
4.4
|
13.9
|
1.0
|
|
N
|
B:SER933
|
4.4
|
11.7
|
1.0
|
|
CD2
|
B:PHE931
|
4.5
|
11.0
|
1.0
|
|
CA
|
B:THR970
|
4.6
|
17.4
|
1.0
|
|
CA
|
B:SER971
|
4.6
|
16.0
|
1.0
|
|
N
|
B:SER971
|
4.6
|
18.1
|
1.0
|
|
CA
|
B:SER933
|
4.6
|
10.2
|
1.0
|
|
CG
|
B:PRO932
|
4.7
|
11.1
|
1.0
|
|
CA
|
B:LEU967
|
4.7
|
13.8
|
1.0
|
|
N
|
B:GLU969
|
4.7
|
16.6
|
1.0
|
|
CG
|
B:PHE931
|
4.7
|
11.4
|
1.0
|
|
C
|
B:PHE931
|
4.9
|
16.8
|
1.0
|
|
O
|
B:HOH9360
|
4.9
|
30.2
|
1.0
|
|
Sodium binding site 8 out
of 16 in 1jyw
Go back to
Sodium Binding Sites List in 1jyw
Sodium binding site 8 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Pnpg
 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 (E537Q) in Complex with Pnpg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3104
b:20.8
occ:1.00
|
O
|
B:DMS8425
|
2.1
|
26.0
|
1.0
|
|
O
|
B:LEU670
|
2.3
|
19.5
|
1.0
|
|
O
|
B:SER647
|
2.4
|
16.8
|
1.0
|
|
O
|
B:HOH9490
|
2.4
|
23.5
|
1.0
|
|
O
|
B:HOH9347
|
2.5
|
21.5
|
1.0
|
|
O
|
B:GLU650
|
2.6
|
20.0
|
1.0
|
|
S
|
B:DMS8425
|
3.3
|
29.5
|
1.0
|
|
C
|
B:LEU670
|
3.4
|
14.5
|
1.0
|
|
N
|
B:GLU650
|
3.6
|
15.4
|
1.0
|
|
C
|
B:GLU650
|
3.6
|
19.2
|
1.0
|
|
C
|
B:SER647
|
3.6
|
20.2
|
1.0
|
|
C2
|
B:DMS8425
|
3.8
|
27.1
|
1.0
|
|
N
|
B:LEU670
|
3.9
|
20.9
|
1.0
|
|
CA
|
B:LEU670
|
4.1
|
19.1
|
1.0
|
|
CA
|
B:ASP648
|
4.1
|
19.6
|
1.0
|
|
CB
|
B:LEU670
|
4.1
|
17.9
|
1.0
|
|
O
|
B:HOH9631
|
4.1
|
51.9
|
1.0
|
|
CA
|
B:GLU650
|
4.1
|
11.7
|
1.0
|
|
C
|
B:ASP648
|
4.2
|
21.4
|
1.0
|
|
OG
|
B:SER647
|
4.2
|
15.1
|
1.0
|
|
N
|
B:ASN649
|
4.2
|
17.2
|
1.0
|
|
CB
|
B:GLU650
|
4.2
|
15.5
|
1.0
|
|
N
|
B:ASP648
|
4.3
|
15.3
|
1.0
|
|
O
|
B:HOH9473
|
4.4
|
25.2
|
1.0
|
|
N
|
B:ASP671
|
4.5
|
15.5
|
1.0
|
|
O
|
B:HOH9707
|
4.6
|
33.8
|
1.0
|
|
CB
|
B:SER647
|
4.7
|
15.4
|
1.0
|
|
CA
|
B:ASP671
|
4.7
|
19.0
|
1.0
|
|
C1
|
B:DMS8425
|
4.7
|
19.8
|
1.0
|
|
C
|
B:ASN649
|
4.7
|
18.3
|
1.0
|
|
CA
|
B:SER647
|
4.8
|
12.1
|
1.0
|
|
N
|
B:LEU651
|
4.8
|
15.7
|
1.0
|
|
O
|
B:ASP648
|
4.8
|
18.0
|
1.0
|
|
CA
|
B:ASN649
|
4.9
|
13.5
|
1.0
|
|
C
|
B:PRO669
|
5.0
|
17.7
|
1.0
|
|
OE1
|
B:GLU650
|
5.0
|
14.5
|
1.0
|
|
Sodium binding site 9 out
of 16 in 1jyw
Go back to
Sodium Binding Sites List in 1jyw
Sodium binding site 9 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Pnpg
 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 (E537Q) in Complex with Pnpg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na3101
b:11.2
occ:1.00
|
O6
|
C:1472001
|
2.3
|
12.2
|
1.0
|
|
O
|
C:HOH8904
|
2.3
|
16.0
|
1.0
|
|
OD1
|
C:ASN604
|
2.3
|
11.3
|
1.0
|
|
OD2
|
C:ASP201
|
2.4
|
11.2
|
1.0
|
|
O
|
C:PHE601
|
2.4
|
13.3
|
1.0
|
|
C6
|
C:1472001
|
3.2
|
10.5
|
1.0
|
|
CG
|
C:ASP201
|
3.3
|
10.5
|
1.0
|
|
CG
|
C:ASN604
|
3.3
|
11.4
|
1.0
|
|
C
|
C:PHE601
|
3.5
|
13.3
|
1.0
|
|
ND2
|
C:ASN604
|
3.6
|
11.9
|
1.0
|
|
OD1
|
C:ASP201
|
3.6
|
12.3
|
1.0
|
|
OH
|
C:TYR100
|
3.7
|
12.5
|
1.0
|
|
O4
|
C:1472001
|
4.1
|
12.2
|
1.0
|
|
CA
|
C:CYS602
|
4.2
|
13.4
|
1.0
|
|
NE1
|
C:TRP568
|
4.2
|
11.8
|
1.0
|
|
N
|
C:CYS602
|
4.3
|
10.8
|
1.0
|
|
C4
|
C:1472001
|
4.4
|
10.6
|
1.0
|
|
C5
|
C:1472001
|
4.4
|
10.4
|
1.0
|
|
CB
|
C:PHE601
|
4.4
|
13.6
|
1.0
|
|
O
|
C:HOH8682
|
4.5
|
12.6
|
1.0
|
|
CB
|
C:ASP201
|
4.5
|
10.8
|
1.0
|
|
CA
|
C:PHE601
|
4.5
|
12.9
|
1.0
|
|
NE2
|
C:HIS540
|
4.6
|
10.7
|
1.0
|
|
O
|
C:ASP201
|
4.7
|
10.5
|
1.0
|
|
C
|
C:CYS602
|
4.7
|
13.9
|
1.0
|
|
CB
|
C:ASN604
|
4.7
|
9.3
|
1.0
|
|
CZ
|
C:TYR100
|
4.8
|
11.7
|
1.0
|
|
CZ2
|
C:TRP568
|
4.8
|
12.8
|
1.0
|
|
CE2
|
C:TRP568
|
4.9
|
12.9
|
1.0
|
|
Sodium binding site 10 out
of 16 in 1jyw
Go back to
Sodium Binding Sites List in 1jyw
Sodium binding site 10 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Pnpg
 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 (E537Q) in Complex with Pnpg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na3102
b:12.8
occ:1.00
|
O
|
C:PHE556
|
2.3
|
10.2
|
1.0
|
|
O
|
C:LEU562
|
2.3
|
10.7
|
1.0
|
|
O
|
C:HOH9251
|
2.3
|
28.2
|
1.0
|
|
O
|
C:TYR559
|
2.4
|
12.4
|
1.0
|
|
O
|
C:HOH9029
|
2.5
|
22.2
|
1.0
|
|
O
|
C:PRO560
|
3.1
|
12.1
|
1.0
|
|
C
|
C:TYR559
|
3.4
|
10.3
|
1.0
|
|
C
|
C:LEU562
|
3.4
|
10.2
|
1.0
|
|
C
|
C:PHE556
|
3.4
|
9.3
|
1.0
|
|
C
|
C:PRO560
|
3.6
|
12.4
|
1.0
|
|
CA
|
C:PRO560
|
3.7
|
11.1
|
1.0
|
|
N
|
C:PRO560
|
3.9
|
11.1
|
1.0
|
|
N
|
C:LEU562
|
4.0
|
8.3
|
1.0
|
|
CA
|
C:PHE556
|
4.1
|
8.3
|
1.0
|
|
O
|
C:HOH8911
|
4.1
|
17.2
|
1.0
|
|
CA
|
C:LEU562
|
4.2
|
7.7
|
1.0
|
|
N
|
C:GLN563
|
4.3
|
8.9
|
1.0
|
|
CB
|
C:LEU562
|
4.3
|
8.3
|
1.0
|
|
O
|
C:HOH9641
|
4.3
|
34.3
|
1.0
|
|
CA
|
C:GLN563
|
4.4
|
8.1
|
1.0
|
|
CA
|
C:TYR559
|
4.4
|
9.5
|
1.0
|
|
N
|
C:TYR559
|
4.4
|
10.9
|
1.0
|
|
N
|
C:ARG557
|
4.5
|
9.5
|
1.0
|
|
O
|
C:HOH9449
|
4.5
|
43.4
|
1.0
|
|
N
|
C:ARG561
|
4.5
|
9.4
|
1.0
|
|
CA
|
C:ARG557
|
4.6
|
7.7
|
1.0
|
|
CG
|
C:GLN563
|
4.7
|
9.7
|
1.0
|
|
C
|
C:ARG557
|
4.7
|
11.3
|
1.0
|
|
O
|
C:HOH9684
|
4.7
|
53.2
|
1.0
|
|
CB
|
C:PHE556
|
4.7
|
10.2
|
1.0
|
|
O
|
C:ARG557
|
4.8
|
14.1
|
1.0
|
|
CD1
|
C:LEU350
|
4.8
|
9.7
|
1.0
|
|
C
|
C:ARG561
|
4.9
|
8.8
|
1.0
|
|
O
|
C:ALA555
|
4.9
|
11.3
|
1.0
|
|
CB
|
C:TYR559
|
5.0
|
9.4
|
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 19:01:54 2024
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