Sodium in PDB 1jyn: E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose
Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose
All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose:
3.2.1.23;
Protein crystallography data
The structure of E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose, PDB code: 1jyn
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)
|
17.00 /
1.80
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
149.550,
168.630,
200.880,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
15.5 /
21.9
|
Other elements in 1jyn:
The structure of E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose also contains other interesting chemical elements:
Sodium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
15;
Binding sites:
The binding sites of Sodium atom in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose
(pdb code 1jyn). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 15 binding sites of Sodium where determined in the
E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose, PDB code: 1jyn:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 15 in 1jyn
Go back to
Sodium Binding Sites List in 1jyn
Sodium binding site 1 out
of 15 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose
 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 Lactose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3101
b:10.2
occ:1.00
|
O
|
A:HOH8781
|
2.2
|
12.6
|
1.0
|
|
O6
|
A:LAT2001
|
2.2
|
9.2
|
0.9
|
|
OD2
|
A:ASP201
|
2.3
|
9.4
|
1.0
|
|
OD1
|
A:ASN604
|
2.4
|
11.4
|
1.0
|
|
O
|
A:PHE601
|
2.4
|
10.3
|
1.0
|
|
C6
|
A:LAT2001
|
3.1
|
9.7
|
0.9
|
|
CG
|
A:ASP201
|
3.2
|
10.4
|
1.0
|
|
CG
|
A:ASN604
|
3.3
|
12.4
|
1.0
|
|
OD1
|
A:ASP201
|
3.6
|
11.1
|
1.0
|
|
C
|
A:PHE601
|
3.6
|
13.0
|
1.0
|
|
ND2
|
A:ASN604
|
3.6
|
10.5
|
1.0
|
|
OH
|
A:TYR100
|
3.6
|
10.9
|
1.0
|
|
NE1
|
A:TRP568
|
4.2
|
7.8
|
1.0
|
|
O4
|
A:LAT2001
|
4.2
|
9.8
|
0.9
|
|
CA
|
A:CYS602
|
4.3
|
7.7
|
1.0
|
|
C5
|
A:LAT2001
|
4.3
|
13.7
|
0.9
|
|
C4
|
A:LAT2001
|
4.3
|
13.7
|
0.9
|
|
N
|
A:CYS602
|
4.4
|
7.5
|
1.0
|
|
CB
|
A:ASP201
|
4.4
|
10.5
|
1.0
|
|
O
|
A:HOH8559
|
4.5
|
8.9
|
1.0
|
|
CB
|
A:PHE601
|
4.5
|
8.1
|
1.0
|
|
CA
|
A:PHE601
|
4.6
|
10.9
|
1.0
|
|
NE2
|
A:HIS540
|
4.6
|
10.3
|
1.0
|
|
O
|
A:ASP201
|
4.6
|
6.8
|
1.0
|
|
C
|
A:CYS602
|
4.7
|
9.8
|
1.0
|
|
CB
|
A:ASN604
|
4.7
|
3.8
|
1.0
|
|
CZ2
|
A:TRP568
|
4.8
|
11.0
|
1.0
|
|
CZ
|
A:TYR100
|
4.8
|
16.2
|
1.0
|
|
CE2
|
A:TRP568
|
4.8
|
5.5
|
1.0
|
|
Sodium binding site 2 out
of 15 in 1jyn
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Sodium Binding Sites List in 1jyn
Sodium binding site 2 out
of 15 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose
 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 Lactose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3102
b:12.3
occ:1.00
|
O
|
A:HOH9129
|
2.3
|
21.4
|
1.0
|
|
O
|
A:PHE556
|
2.3
|
11.4
|
1.0
|
|
O
|
A:TYR559
|
2.3
|
10.9
|
1.0
|
|
O
|
A:LEU562
|
2.3
|
7.6
|
1.0
|
|
O
|
A:HOH8908
|
2.5
|
20.9
|
1.0
|
|
O
|
A:PRO560
|
3.1
|
10.5
|
1.0
|
|
C
|
A:TYR559
|
3.4
|
12.9
|
1.0
|
|
C
|
A:LEU562
|
3.4
|
9.5
|
1.0
|
|
C
|
A:PHE556
|
3.5
|
10.8
|
1.0
|
|
C
|
A:PRO560
|
3.5
|
8.0
|
1.0
|
|
CA
|
A:PRO560
|
3.6
|
5.7
|
1.0
|
|
N
|
A:LEU562
|
3.9
|
5.6
|
1.0
|
|
N
|
A:PRO560
|
3.9
|
10.6
|
1.0
|
|
O
|
A:HOH8788
|
4.1
|
12.1
|
1.0
|
|
CA
|
A:PHE556
|
4.1
|
9.7
|
1.0
|
|
CA
|
A:LEU562
|
4.1
|
6.8
|
1.0
|
|
O
|
A:HOH9305
|
4.2
|
33.4
|
1.0
|
|
CB
|
A:LEU562
|
4.3
|
4.0
|
1.0
|
|
O
|
A:HOH9513
|
4.3
|
30.2
|
1.0
|
|
N
|
A:GLN563
|
4.3
|
6.8
|
1.0
|
|
N
|
A:TYR559
|
4.4
|
6.3
|
1.0
|
|
CA
|
A:GLN563
|
4.5
|
5.7
|
1.0
|
|
N
|
A:ARG561
|
4.5
|
7.8
|
1.0
|
|
CA
|
A:TYR559
|
4.5
|
4.1
|
1.0
|
|
N
|
A:ARG557
|
4.5
|
5.3
|
1.0
|
|
O
|
A:HOH9319
|
4.5
|
33.0
|
1.0
|
|
CA
|
A:ARG557
|
4.6
|
1.7
|
1.0
|
|
O
|
A:ARG557
|
4.7
|
7.5
|
1.0
|
|
C
|
A:ARG557
|
4.7
|
9.4
|
1.0
|
|
CG
|
A:GLN563
|
4.7
|
8.0
|
1.0
|
|
CB
|
A:PHE556
|
4.7
|
7.1
|
1.0
|
|
C
|
A:ARG561
|
4.8
|
8.4
|
1.0
|
|
O
|
A:ALA555
|
4.8
|
9.3
|
1.0
|
|
CD1
|
A:LEU350
|
4.9
|
6.1
|
1.0
|
|
Sodium binding site 3 out
of 15 in 1jyn
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Sodium Binding Sites List in 1jyn
Sodium binding site 3 out
of 15 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose
 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 Lactose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3103
b:21.8
occ:1.00
|
O
|
A:HOH9229
|
2.4
|
38.8
|
1.0
|
|
O
|
A:LEU967
|
2.5
|
14.6
|
1.0
|
|
O
|
A:PRO932
|
2.5
|
11.3
|
1.0
|
|
O
|
A:HOH8711
|
2.6
|
12.6
|
1.0
|
|
O
|
A:THR970
|
2.9
|
21.3
|
1.0
|
|
CZ
|
A:PHE931
|
3.4
|
18.3
|
1.0
|
|
C
|
A:PRO932
|
3.6
|
10.8
|
1.0
|
|
O
|
A:HOH9048
|
3.6
|
26.5
|
1.0
|
|
C
|
A:LEU967
|
3.6
|
11.8
|
1.0
|
|
CE2
|
A:PHE931
|
3.7
|
12.8
|
1.0
|
|
CE1
|
A:PHE931
|
3.8
|
22.8
|
1.0
|
|
O
|
A:MET968
|
3.9
|
19.1
|
1.0
|
|
CA
|
A:MET968
|
3.9
|
12.4
|
1.0
|
|
C
|
A:MET968
|
3.9
|
18.4
|
1.0
|
|
C
|
A:THR970
|
4.0
|
19.1
|
1.0
|
|
CB
|
A:PRO932
|
4.1
|
17.1
|
1.0
|
|
CA
|
A:PRO932
|
4.2
|
13.9
|
1.0
|
|
N
|
A:MET968
|
4.2
|
10.1
|
1.0
|
|
CD
|
A:PRO932
|
4.2
|
13.1
|
1.0
|
|
N
|
A:PRO932
|
4.3
|
12.6
|
1.0
|
|
N
|
A:THR970
|
4.3
|
10.8
|
1.0
|
|
CD2
|
A:PHE931
|
4.4
|
12.5
|
1.0
|
|
CD1
|
A:PHE931
|
4.4
|
11.9
|
1.0
|
|
N
|
A:SER933
|
4.6
|
6.7
|
1.0
|
|
CG
|
A:PRO932
|
4.6
|
30.0
|
1.0
|
|
N
|
A:GLU969
|
4.7
|
8.7
|
1.0
|
|
CG
|
A:PHE931
|
4.7
|
10.2
|
1.0
|
|
CA
|
A:THR970
|
4.7
|
13.5
|
1.0
|
|
CA
|
A:SER933
|
4.8
|
11.3
|
1.0
|
|
CA
|
A:LEU967
|
4.8
|
10.7
|
1.0
|
|
N
|
A:SER971
|
4.9
|
17.2
|
1.0
|
|
CA
|
A:SER971
|
4.9
|
19.3
|
1.0
|
|
C
|
A:PHE931
|
5.0
|
17.7
|
1.0
|
|
Sodium binding site 4 out
of 15 in 1jyn
Go back to
Sodium Binding Sites List in 1jyn
Sodium binding site 4 out
of 15 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose
 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 Lactose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3104
b:26.4
occ:1.00
|
O
|
A:DMS8425
|
2.1
|
35.6
|
1.0
|
|
O
|
A:LEU670
|
2.3
|
13.1
|
1.0
|
|
O
|
A:HOH9404
|
2.5
|
44.4
|
1.0
|
|
O
|
A:SER647
|
2.5
|
11.4
|
1.0
|
|
O
|
A:HOH9243
|
2.6
|
37.8
|
1.0
|
|
O
|
A:GLU650
|
2.6
|
14.2
|
1.0
|
|
S
|
A:DMS8425
|
3.2
|
40.7
|
1.0
|
|
C
|
A:LEU670
|
3.5
|
16.5
|
1.0
|
|
N
|
A:GLU650
|
3.5
|
7.8
|
1.0
|
|
C
|
A:GLU650
|
3.6
|
15.7
|
1.0
|
|
C2
|
A:DMS8425
|
3.6
|
37.0
|
1.0
|
|
C
|
A:SER647
|
3.7
|
16.2
|
1.0
|
|
N
|
A:LEU670
|
3.8
|
18.8
|
1.0
|
|
O
|
A:HOH9553
|
3.9
|
51.2
|
1.0
|
|
CA
|
A:GLU650
|
4.0
|
10.4
|
1.0
|
|
CA
|
A:LEU670
|
4.1
|
15.6
|
1.0
|
|
N
|
A:ASN649
|
4.1
|
13.1
|
1.0
|
|
CB
|
A:GLU650
|
4.1
|
8.1
|
1.0
|
|
C
|
A:ASP648
|
4.2
|
19.3
|
1.0
|
|
CA
|
A:ASP648
|
4.2
|
14.8
|
1.0
|
|
CB
|
A:LEU670
|
4.2
|
16.0
|
1.0
|
|
OG
|
A:SER647
|
4.3
|
13.8
|
1.0
|
|
N
|
A:ASP648
|
4.4
|
13.6
|
1.0
|
|
N
|
A:ASP671
|
4.6
|
16.2
|
1.0
|
|
C
|
A:ASN649
|
4.6
|
13.8
|
1.0
|
|
CB
|
A:SER647
|
4.6
|
15.7
|
1.0
|
|
C1
|
A:DMS8425
|
4.7
|
26.1
|
1.0
|
|
CA
|
A:ASN649
|
4.7
|
12.2
|
1.0
|
|
CA
|
A:ASP671
|
4.8
|
15.9
|
1.0
|
|
O
|
A:ASP648
|
4.8
|
13.7
|
1.0
|
|
C
|
A:PRO669
|
4.8
|
11.4
|
1.0
|
|
CA
|
A:SER647
|
4.8
|
8.1
|
1.0
|
|
N
|
A:LEU651
|
4.8
|
12.8
|
1.0
|
|
OE1
|
A:GLU650
|
4.9
|
12.5
|
1.0
|
|
Sodium binding site 5 out
of 15 in 1jyn
Go back to
Sodium Binding Sites List in 1jyn
Sodium binding site 5 out
of 15 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose
 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 Lactose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3101
b:11.7
occ:1.00
|
O
|
B:HOH8893
|
2.2
|
11.1
|
1.0
|
|
O6
|
B:LAT2001
|
2.3
|
10.1
|
0.9
|
|
OD2
|
B:ASP201
|
2.3
|
10.5
|
1.0
|
|
OD1
|
B:ASN604
|
2.4
|
7.6
|
1.0
|
|
O
|
B:PHE601
|
2.4
|
9.7
|
1.0
|
|
C6
|
B:LAT2001
|
3.2
|
4.7
|
0.9
|
|
CG
|
B:ASP201
|
3.3
|
17.2
|
1.0
|
|
CG
|
B:ASN604
|
3.4
|
16.5
|
1.0
|
|
C
|
B:PHE601
|
3.5
|
12.9
|
1.0
|
|
OD1
|
B:ASP201
|
3.6
|
8.9
|
1.0
|
|
OH
|
B:TYR100
|
3.7
|
10.9
|
1.0
|
|
ND2
|
B:ASN604
|
3.7
|
11.1
|
1.0
|
|
NE1
|
B:TRP568
|
4.1
|
7.6
|
1.0
|
|
O4
|
B:LAT2001
|
4.2
|
5.7
|
0.9
|
|
CA
|
B:CYS602
|
4.2
|
9.8
|
1.0
|
|
N
|
B:CYS602
|
4.3
|
9.3
|
1.0
|
|
C5
|
B:LAT2001
|
4.3
|
10.5
|
0.9
|
|
O
|
B:HOH8673
|
4.4
|
11.5
|
1.0
|
|
C4
|
B:LAT2001
|
4.4
|
5.7
|
0.9
|
|
CB
|
B:ASP201
|
4.5
|
4.6
|
1.0
|
|
CB
|
B:PHE601
|
4.5
|
9.9
|
1.0
|
|
CA
|
B:PHE601
|
4.5
|
8.1
|
1.0
|
|
NE2
|
B:HIS540
|
4.6
|
6.3
|
1.0
|
|
O
|
B:ASP201
|
4.7
|
9.2
|
1.0
|
|
C
|
B:CYS602
|
4.7
|
9.7
|
1.0
|
|
CB
|
B:ASN604
|
4.8
|
5.9
|
1.0
|
|
CZ
|
B:TYR100
|
4.8
|
14.2
|
1.0
|
|
CZ2
|
B:TRP568
|
4.8
|
9.2
|
1.0
|
|
CE2
|
B:TRP568
|
4.8
|
6.9
|
1.0
|
|
Sodium binding site 6 out
of 15 in 1jyn
Go back to
Sodium Binding Sites List in 1jyn
Sodium binding site 6 out
of 15 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose
 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 Lactose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3102
b:10.9
occ:1.00
|
O
|
B:LEU562
|
2.2
|
6.2
|
1.0
|
|
O
|
B:PHE556
|
2.3
|
8.5
|
1.0
|
|
O
|
B:TYR559
|
2.3
|
9.8
|
1.0
|
|
O
|
B:HOH9246
|
2.3
|
19.3
|
1.0
|
|
O
|
B:HOH9017
|
2.6
|
19.9
|
1.0
|
|
O
|
B:PRO560
|
3.2
|
9.3
|
1.0
|
|
C
|
B:TYR559
|
3.3
|
8.7
|
1.0
|
|
C
|
B:LEU562
|
3.3
|
9.1
|
1.0
|
|
C
|
B:PHE556
|
3.4
|
8.1
|
1.0
|
|
C
|
B:PRO560
|
3.6
|
12.0
|
1.0
|
|
CA
|
B:PRO560
|
3.6
|
6.3
|
1.0
|
|
N
|
B:PRO560
|
3.9
|
10.2
|
1.0
|
|
N
|
B:LEU562
|
3.9
|
3.8
|
1.0
|
|
CA
|
B:PHE556
|
4.0
|
5.4
|
1.0
|
|
CA
|
B:LEU562
|
4.1
|
4.4
|
1.0
|
|
CB
|
B:LEU562
|
4.2
|
2.4
|
1.0
|
|
O
|
B:HOH8900
|
4.2
|
10.8
|
1.0
|
|
N
|
B:GLN563
|
4.2
|
5.8
|
1.0
|
|
O
|
B:HOH9472
|
4.3
|
23.5
|
1.0
|
|
N
|
B:TYR559
|
4.4
|
7.4
|
1.0
|
|
CA
|
B:TYR559
|
4.4
|
8.1
|
1.0
|
|
CA
|
B:GLN563
|
4.4
|
4.6
|
1.0
|
|
N
|
B:ARG557
|
4.5
|
5.0
|
1.0
|
|
O
|
B:HOH9427
|
4.5
|
32.1
|
1.0
|
|
N
|
B:ARG561
|
4.5
|
8.7
|
1.0
|
|
CA
|
B:ARG557
|
4.6
|
7.4
|
1.0
|
|
CB
|
B:PHE556
|
4.7
|
3.4
|
1.0
|
|
C
|
B:ARG557
|
4.7
|
12.1
|
1.0
|
|
O
|
B:ARG557
|
4.7
|
13.6
|
1.0
|
|
CG
|
B:GLN563
|
4.7
|
8.3
|
1.0
|
|
C
|
B:ARG561
|
4.8
|
7.4
|
1.0
|
|
CD1
|
B:LEU350
|
4.8
|
8.7
|
1.0
|
|
O
|
B:ALA555
|
4.9
|
9.1
|
1.0
|
|
CB
|
B:TYR559
|
4.9
|
5.8
|
1.0
|
|
Sodium binding site 7 out
of 15 in 1jyn
Go back to
Sodium Binding Sites List in 1jyn
Sodium binding site 7 out
of 15 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose
 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 Lactose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3103
b:19.7
occ:1.00
|
O
|
B:PRO932
|
2.4
|
9.8
|
1.0
|
|
O
|
B:LEU967
|
2.5
|
15.5
|
1.0
|
|
O
|
B:HOH9339
|
2.6
|
37.0
|
1.0
|
|
O
|
B:THR970
|
2.7
|
24.2
|
1.0
|
|
O
|
B:HOH8824
|
2.7
|
12.5
|
1.0
|
|
CZ
|
B:PHE931
|
3.4
|
15.0
|
1.0
|
|
C
|
B:PRO932
|
3.5
|
10.6
|
1.0
|
|
C
|
B:LEU967
|
3.7
|
21.3
|
1.0
|
|
CE1
|
B:PHE931
|
3.7
|
13.5
|
1.0
|
|
O
|
B:HOH9161
|
3.7
|
24.1
|
1.0
|
|
CE2
|
B:PHE931
|
3.8
|
12.8
|
1.0
|
|
C
|
B:THR970
|
3.8
|
19.0
|
1.0
|
|
O
|
B:MET968
|
3.9
|
21.1
|
1.0
|
|
CA
|
B:MET968
|
3.9
|
9.4
|
1.0
|
|
C
|
B:MET968
|
4.0
|
24.2
|
1.0
|
|
CA
|
B:PRO932
|
4.1
|
12.3
|
1.0
|
|
CB
|
B:PRO932
|
4.1
|
12.6
|
1.0
|
|
CD
|
B:PRO932
|
4.2
|
15.8
|
1.0
|
|
N
|
B:PRO932
|
4.2
|
15.8
|
1.0
|
|
N
|
B:THR970
|
4.2
|
12.4
|
1.0
|
|
N
|
B:MET968
|
4.3
|
9.1
|
1.0
|
|
CD1
|
B:PHE931
|
4.3
|
12.3
|
1.0
|
|
CD2
|
B:PHE931
|
4.4
|
10.8
|
1.0
|
|
N
|
B:SER933
|
4.5
|
10.8
|
1.0
|
|
CG
|
B:PRO932
|
4.6
|
9.3
|
1.0
|
|
CA
|
B:THR970
|
4.6
|
14.8
|
1.0
|
|
CA
|
B:SER971
|
4.7
|
15.3
|
1.0
|
|
CA
|
B:SER933
|
4.7
|
5.3
|
1.0
|
|
CG
|
B:PHE931
|
4.7
|
10.8
|
1.0
|
|
N
|
B:SER971
|
4.7
|
16.2
|
1.0
|
|
N
|
B:GLU969
|
4.8
|
13.8
|
1.0
|
|
CA
|
B:LEU967
|
4.8
|
11.2
|
1.0
|
|
C
|
B:PHE931
|
4.9
|
14.2
|
1.0
|
|
O
|
B:HOH9368
|
5.0
|
27.4
|
1.0
|
|
Sodium binding site 8 out
of 15 in 1jyn
Go back to
Sodium Binding Sites List in 1jyn
Sodium binding site 8 out
of 15 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose
 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 Lactose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3104
b:27.2
occ:1.00
|
O
|
B:DMS8425
|
1.9
|
38.0
|
1.0
|
|
O
|
B:SER647
|
2.5
|
14.2
|
1.0
|
|
O
|
B:GLU650
|
2.6
|
15.0
|
1.0
|
|
O
|
B:LEU670
|
2.7
|
17.0
|
1.0
|
|
O
|
B:HOH9509
|
2.8
|
39.0
|
1.0
|
|
O
|
B:HOH9355
|
2.8
|
31.8
|
1.0
|
|
S
|
B:DMS8425
|
3.0
|
42.7
|
1.0
|
|
N
|
B:GLU650
|
3.2
|
12.1
|
1.0
|
|
C
|
B:GLU650
|
3.5
|
20.6
|
1.0
|
|
C2
|
B:DMS8425
|
3.5
|
26.4
|
1.0
|
|
C
|
B:SER647
|
3.6
|
26.0
|
1.0
|
|
N
|
B:ASN649
|
3.7
|
13.8
|
1.0
|
|
C
|
B:ASP648
|
3.8
|
20.4
|
1.0
|
|
C
|
B:LEU670
|
3.8
|
16.9
|
1.0
|
|
CA
|
B:ASP648
|
3.8
|
14.8
|
1.0
|
|
CA
|
B:GLU650
|
3.8
|
12.0
|
1.0
|
|
N
|
B:LEU670
|
4.0
|
17.6
|
1.0
|
|
CB
|
B:GLU650
|
4.1
|
11.2
|
1.0
|
|
N
|
B:ASP648
|
4.2
|
10.2
|
1.0
|
|
C
|
B:ASN649
|
4.3
|
24.4
|
1.0
|
|
CB
|
B:LEU670
|
4.3
|
19.1
|
1.0
|
|
CA
|
B:LEU670
|
4.3
|
14.1
|
1.0
|
|
O
|
B:ASP648
|
4.4
|
13.7
|
1.0
|
|
OG
|
B:SER647
|
4.4
|
11.8
|
1.0
|
|
CA
|
B:ASN649
|
4.4
|
5.8
|
1.0
|
|
C1
|
B:DMS8425
|
4.5
|
21.9
|
1.0
|
|
OE1
|
B:GLU650
|
4.6
|
10.7
|
1.0
|
|
N
|
B:LEU651
|
4.8
|
13.1
|
1.0
|
|
CB
|
B:SER647
|
4.8
|
12.4
|
1.0
|
|
CA
|
B:SER647
|
4.8
|
12.8
|
1.0
|
|
N
|
B:ASP671
|
4.9
|
11.0
|
1.0
|
|
C
|
B:PRO669
|
4.9
|
24.1
|
1.0
|
|
Sodium binding site 9 out
of 15 in 1jyn
Go back to
Sodium Binding Sites List in 1jyn
Sodium binding site 9 out
of 15 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose
 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 Lactose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na3101
b:9.6
occ:1.00
|
O
|
C:HOH8905
|
2.3
|
14.8
|
1.0
|
|
O6
|
C:LAT2001
|
2.3
|
7.6
|
0.9
|
|
OD2
|
C:ASP201
|
2.3
|
8.6
|
1.0
|
|
O
|
C:PHE601
|
2.4
|
11.2
|
1.0
|
|
OD1
|
C:ASN604
|
2.4
|
9.7
|
1.0
|
|
C6
|
C:LAT2001
|
3.2
|
5.4
|
0.9
|
|
CG
|
C:ASP201
|
3.3
|
11.4
|
1.0
|
|
CG
|
C:ASN604
|
3.4
|
12.9
|
1.0
|
|
C
|
C:PHE601
|
3.5
|
12.3
|
1.0
|
|
OD1
|
C:ASP201
|
3.6
|
10.0
|
1.0
|
|
OH
|
C:TYR100
|
3.6
|
8.4
|
1.0
|
|
ND2
|
C:ASN604
|
3.6
|
10.7
|
1.0
|
|
CA
|
C:CYS602
|
4.2
|
11.3
|
1.0
|
|
O4
|
C:LAT2001
|
4.2
|
7.6
|
0.9
|
|
NE1
|
C:TRP568
|
4.2
|
9.8
|
1.0
|
|
N
|
C:CYS602
|
4.3
|
8.8
|
1.0
|
|
C5
|
C:LAT2001
|
4.4
|
6.0
|
0.9
|
|
C4
|
C:LAT2001
|
4.4
|
4.0
|
0.9
|
|
O
|
C:HOH8682
|
4.4
|
10.0
|
1.0
|
|
CB
|
C:PHE601
|
4.5
|
7.1
|
1.0
|
|
CB
|
C:ASP201
|
4.5
|
5.5
|
1.0
|
|
CA
|
C:PHE601
|
4.5
|
9.4
|
1.0
|
|
O
|
C:ASP201
|
4.6
|
8.7
|
1.0
|
|
C
|
C:CYS602
|
4.7
|
17.9
|
1.0
|
|
CZ
|
C:TYR100
|
4.7
|
9.7
|
1.0
|
|
NE2
|
C:HIS540
|
4.7
|
7.4
|
1.0
|
|
CB
|
C:ASN604
|
4.8
|
5.1
|
1.0
|
|
CZ2
|
C:TRP568
|
4.8
|
10.3
|
1.0
|
|
CE2
|
C:TRP568
|
4.9
|
7.3
|
1.0
|
|
Sodium binding site 10 out
of 15 in 1jyn
Go back to
Sodium Binding Sites List in 1jyn
Sodium binding site 10 out
of 15 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose
 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 Lactose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na3102
b:11.6
occ:1.00
|
O
|
C:HOH9253
|
2.3
|
20.2
|
1.0
|
|
O
|
C:LEU562
|
2.3
|
7.7
|
1.0
|
|
O
|
C:PHE556
|
2.3
|
7.1
|
1.0
|
|
O
|
C:TYR559
|
2.4
|
10.4
|
1.0
|
|
O
|
C:HOH9030
|
2.5
|
20.7
|
1.0
|
|
O
|
C:PRO560
|
3.1
|
10.7
|
1.0
|
|
C
|
C:TYR559
|
3.3
|
7.1
|
1.0
|
|
C
|
C:LEU562
|
3.4
|
4.9
|
1.0
|
|
C
|
C:PHE556
|
3.5
|
11.5
|
1.0
|
|
C
|
C:PRO560
|
3.5
|
13.0
|
1.0
|
|
CA
|
C:PRO560
|
3.7
|
7.3
|
1.0
|
|
N
|
C:LEU562
|
3.9
|
9.0
|
1.0
|
|
N
|
C:PRO560
|
3.9
|
4.8
|
1.0
|
|
O
|
C:HOH8912
|
4.1
|
10.3
|
1.0
|
|
CA
|
C:PHE556
|
4.2
|
5.1
|
1.0
|
|
CA
|
C:LEU562
|
4.2
|
5.2
|
1.0
|
|
O
|
C:HOH9619
|
4.2
|
29.2
|
1.0
|
|
N
|
C:GLN563
|
4.3
|
6.8
|
1.0
|
|
CB
|
C:LEU562
|
4.3
|
5.0
|
1.0
|
|
O
|
C:HOH9696
|
4.4
|
29.3
|
1.0
|
|
CA
|
C:GLN563
|
4.4
|
8.8
|
1.0
|
|
CA
|
C:TYR559
|
4.4
|
8.5
|
1.0
|
|
N
|
C:TYR559
|
4.5
|
12.8
|
1.0
|
|
O
|
C:HOH9463
|
4.5
|
36.0
|
1.0
|
|
N
|
C:ARG557
|
4.5
|
9.6
|
1.0
|
|
N
|
C:ARG561
|
4.5
|
6.6
|
1.0
|
|
CA
|
C:ARG557
|
4.6
|
5.2
|
1.0
|
|
CG
|
C:GLN563
|
4.7
|
7.8
|
1.0
|
|
C
|
C:ARG557
|
4.7
|
13.0
|
1.0
|
|
O
|
C:ARG557
|
4.8
|
13.6
|
1.0
|
|
CB
|
C:PHE556
|
4.8
|
6.8
|
1.0
|
|
C
|
C:ARG561
|
4.8
|
9.4
|
1.0
|
|
CD1
|
C:LEU350
|
4.8
|
3.1
|
1.0
|
|
O
|
C:ALA555
|
4.9
|
9.4
|
1.0
|
|
CB
|
C:TYR559
|
4.9
|
6.7
|
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 19:00:03 2024
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