Sodium in PDB 1jyv: E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Onpg
Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Onpg
All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Onpg:
3.2.1.23;
Protein crystallography data
The structure of E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Onpg, PDB code: 1jyv
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)
|
29.90 /
1.75
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
149.492,
167.455,
200.341,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
18 /
24
|
Other elements in 1jyv:
The structure of E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Onpg 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 Onpg
(pdb code 1jyv). 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 Onpg, PDB code: 1jyv:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 16 in 1jyv
Go back to
Sodium Binding Sites List in 1jyv
Sodium binding site 1 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Onpg
 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 Onpg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3101
b:17.1
occ:1.00
|
O
|
A:HOH8874
|
2.2
|
18.5
|
1.0
|
|
O6
|
A:1452001
|
2.3
|
16.3
|
1.0
|
|
OD1
|
A:ASN604
|
2.3
|
14.1
|
1.0
|
|
OD2
|
A:ASP201
|
2.3
|
13.3
|
1.0
|
|
O
|
A:PHE601
|
2.4
|
16.9
|
1.0
|
|
C6
|
A:1452001
|
3.2
|
17.8
|
1.0
|
|
CG
|
A:ASP201
|
3.3
|
17.3
|
1.0
|
|
CG
|
A:ASN604
|
3.3
|
15.3
|
1.0
|
|
C
|
A:PHE601
|
3.6
|
24.1
|
1.0
|
|
ND2
|
A:ASN604
|
3.6
|
13.9
|
1.0
|
|
OD1
|
A:ASP201
|
3.6
|
16.7
|
1.0
|
|
OH
|
A:TYR100
|
3.7
|
16.1
|
1.0
|
|
NE1
|
A:TRP568
|
4.1
|
14.0
|
1.0
|
|
CA
|
A:CYS602
|
4.2
|
14.2
|
1.0
|
|
O4
|
A:1452001
|
4.2
|
16.8
|
1.0
|
|
C5
|
A:1452001
|
4.3
|
16.6
|
1.0
|
|
N
|
A:CYS602
|
4.4
|
14.9
|
1.0
|
|
C4
|
A:1452001
|
4.4
|
18.7
|
1.0
|
|
O
|
A:HOH8653
|
4.4
|
16.2
|
1.0
|
|
CB
|
A:ASP201
|
4.5
|
14.7
|
1.0
|
|
CB
|
A:PHE601
|
4.6
|
12.1
|
1.0
|
|
O
|
A:ASP201
|
4.6
|
13.6
|
1.0
|
|
CA
|
A:PHE601
|
4.6
|
15.0
|
1.0
|
|
C
|
A:CYS602
|
4.7
|
14.7
|
1.0
|
|
NE2
|
A:HIS540
|
4.7
|
17.3
|
1.0
|
|
CZ2
|
A:TRP568
|
4.7
|
16.3
|
1.0
|
|
CB
|
A:ASN604
|
4.7
|
10.2
|
1.0
|
|
CE2
|
A:TRP568
|
4.7
|
14.5
|
1.0
|
|
CZ
|
A:TYR100
|
4.8
|
19.7
|
1.0
|
|
Sodium binding site 2 out
of 16 in 1jyv
Go back to
Sodium Binding Sites List in 1jyv
Sodium binding site 2 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Onpg
 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 Onpg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3102
b:15.3
occ:1.00
|
O
|
A:LEU562
|
2.3
|
12.7
|
1.0
|
|
O
|
A:PHE556
|
2.3
|
15.6
|
1.0
|
|
O
|
A:TYR559
|
2.3
|
16.4
|
1.0
|
|
O
|
A:HOH8998
|
2.4
|
25.8
|
1.0
|
|
O
|
A:HOH9213
|
2.5
|
23.5
|
1.0
|
|
O
|
A:PRO560
|
3.2
|
14.0
|
1.0
|
|
C
|
A:LEU562
|
3.3
|
13.4
|
1.0
|
|
C
|
A:TYR559
|
3.3
|
11.6
|
1.0
|
|
C
|
A:PHE556
|
3.5
|
16.6
|
1.0
|
|
C
|
A:PRO560
|
3.6
|
12.6
|
1.0
|
|
CA
|
A:PRO560
|
3.6
|
11.4
|
1.0
|
|
N
|
A:PRO560
|
3.9
|
14.3
|
1.0
|
|
N
|
A:LEU562
|
4.0
|
10.1
|
1.0
|
|
O
|
A:HOH8880
|
4.1
|
19.1
|
1.0
|
|
O
|
A:HOH9382
|
4.1
|
44.8
|
1.0
|
|
CA
|
A:PHE556
|
4.2
|
13.0
|
1.0
|
|
CA
|
A:LEU562
|
4.2
|
11.8
|
1.0
|
|
N
|
A:GLN563
|
4.2
|
9.3
|
1.0
|
|
CA
|
A:GLN563
|
4.3
|
10.7
|
1.0
|
|
CB
|
A:LEU562
|
4.4
|
11.4
|
1.0
|
|
N
|
A:TYR559
|
4.4
|
14.4
|
1.0
|
|
CA
|
A:TYR559
|
4.4
|
12.0
|
1.0
|
|
N
|
A:ARG561
|
4.5
|
11.2
|
1.0
|
|
N
|
A:ARG557
|
4.5
|
11.9
|
1.0
|
|
CG
|
A:GLN563
|
4.7
|
12.4
|
1.0
|
|
CA
|
A:ARG557
|
4.7
|
9.7
|
1.0
|
|
C
|
A:ARG557
|
4.7
|
12.0
|
1.0
|
|
O
|
A:ARG557
|
4.8
|
13.2
|
1.0
|
|
CB
|
A:PHE556
|
4.8
|
10.6
|
1.0
|
|
CD1
|
A:LEU350
|
4.8
|
13.6
|
1.0
|
|
C
|
A:ARG561
|
4.8
|
13.7
|
1.0
|
|
O
|
A:ALA555
|
4.9
|
13.4
|
1.0
|
|
CB
|
A:TYR559
|
5.0
|
9.2
|
1.0
|
|
Sodium binding site 3 out
of 16 in 1jyv
Go back to
Sodium Binding Sites List in 1jyv
Sodium binding site 3 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Onpg
 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 Onpg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3103
b:25.9
occ:1.00
|
O
|
A:PRO932
|
2.3
|
19.0
|
1.0
|
|
O
|
A:HOH9304
|
2.4
|
41.8
|
1.0
|
|
O
|
A:LEU967
|
2.5
|
22.6
|
1.0
|
|
O
|
A:HOH8804
|
2.7
|
19.0
|
1.0
|
|
O
|
A:THR970
|
2.7
|
22.9
|
1.0
|
|
CZ
|
A:PHE931
|
3.4
|
22.8
|
1.0
|
|
C
|
A:PRO932
|
3.4
|
14.9
|
1.0
|
|
O
|
A:HOH9134
|
3.6
|
29.8
|
1.0
|
|
CE1
|
A:PHE931
|
3.6
|
31.6
|
1.0
|
|
C
|
A:LEU967
|
3.7
|
21.9
|
1.0
|
|
CE2
|
A:PHE931
|
3.8
|
16.1
|
1.0
|
|
C
|
A:THR970
|
3.8
|
28.8
|
1.0
|
|
CB
|
A:PRO932
|
3.9
|
22.1
|
1.0
|
|
O
|
A:MET968
|
4.0
|
26.4
|
1.0
|
|
CA
|
A:MET968
|
4.0
|
14.6
|
1.0
|
|
CA
|
A:PRO932
|
4.0
|
15.1
|
1.0
|
|
C
|
A:MET968
|
4.1
|
24.9
|
1.0
|
|
N
|
A:PRO932
|
4.1
|
16.6
|
1.0
|
|
CD
|
A:PRO932
|
4.1
|
19.4
|
1.0
|
|
N
|
A:THR970
|
4.2
|
19.3
|
1.0
|
|
CD1
|
A:PHE931
|
4.3
|
16.6
|
1.0
|
|
N
|
A:MET968
|
4.4
|
16.0
|
1.0
|
|
CD2
|
A:PHE931
|
4.4
|
15.9
|
1.0
|
|
N
|
A:SER933
|
4.5
|
12.9
|
1.0
|
|
CG
|
A:PRO932
|
4.6
|
17.4
|
1.0
|
|
CA
|
A:THR970
|
4.6
|
21.9
|
1.0
|
|
CG
|
A:PHE931
|
4.6
|
16.1
|
1.0
|
|
CA
|
A:SER971
|
4.6
|
20.3
|
1.0
|
|
N
|
A:SER971
|
4.7
|
20.6
|
1.0
|
|
CA
|
A:SER933
|
4.7
|
15.4
|
1.0
|
|
N
|
A:GLU969
|
4.8
|
16.6
|
1.0
|
|
C
|
A:PHE931
|
4.8
|
23.5
|
1.0
|
|
CA
|
A:LEU967
|
4.8
|
17.9
|
1.0
|
|
O
|
A:HOH9330
|
4.9
|
41.7
|
1.0
|
|
Sodium binding site 4 out
of 16 in 1jyv
Go back to
Sodium Binding Sites List in 1jyv
Sodium binding site 4 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Onpg
 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 Onpg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3104
b:25.8
occ:1.00
|
O
|
A:DMS8425
|
2.1
|
41.3
|
1.0
|
|
O
|
A:LEU670
|
2.3
|
18.1
|
1.0
|
|
O
|
A:HOH9472
|
2.4
|
38.5
|
1.0
|
|
O
|
A:SER647
|
2.4
|
21.1
|
1.0
|
|
O
|
A:HOH9316
|
2.6
|
45.5
|
1.0
|
|
O
|
A:GLU650
|
2.6
|
23.1
|
1.0
|
|
S
|
A:DMS8425
|
3.3
|
42.6
|
1.0
|
|
C
|
A:LEU670
|
3.5
|
23.2
|
1.0
|
|
N
|
A:GLU650
|
3.5
|
16.1
|
1.0
|
|
C
|
A:SER647
|
3.6
|
21.0
|
1.0
|
|
C
|
A:GLU650
|
3.6
|
20.3
|
1.0
|
|
C2
|
A:DMS8425
|
3.7
|
28.4
|
1.0
|
|
N
|
A:LEU670
|
3.9
|
26.4
|
1.0
|
|
CA
|
A:GLU650
|
4.0
|
16.3
|
1.0
|
|
N
|
A:ASN649
|
4.1
|
18.0
|
1.0
|
|
CA
|
A:ASP648
|
4.1
|
25.1
|
1.0
|
|
CB
|
A:GLU650
|
4.1
|
14.1
|
1.0
|
|
C
|
A:ASP648
|
4.2
|
34.4
|
1.0
|
|
CA
|
A:LEU670
|
4.2
|
20.3
|
1.0
|
|
OG
|
A:SER647
|
4.2
|
17.4
|
1.0
|
|
CB
|
A:LEU670
|
4.2
|
28.3
|
1.0
|
|
N
|
A:ASP648
|
4.3
|
17.2
|
1.0
|
|
OD1
|
A:ASP671
|
4.5
|
74.1
|
1.0
|
|
N
|
A:ASP671
|
4.5
|
20.8
|
1.0
|
|
CB
|
A:SER647
|
4.6
|
18.8
|
1.0
|
|
C
|
A:ASN649
|
4.6
|
18.4
|
1.0
|
|
CA
|
A:ASP671
|
4.7
|
26.6
|
1.0
|
|
CA
|
A:SER647
|
4.7
|
15.8
|
1.0
|
|
O
|
A:ASP648
|
4.8
|
21.1
|
1.0
|
|
CA
|
A:ASN649
|
4.8
|
16.7
|
1.0
|
|
N
|
A:LEU651
|
4.8
|
18.3
|
1.0
|
|
OE1
|
A:GLU650
|
4.9
|
18.3
|
1.0
|
|
C1
|
A:DMS8425
|
4.9
|
32.8
|
1.0
|
|
C
|
A:PRO669
|
4.9
|
24.4
|
1.0
|
|
Sodium binding site 5 out
of 16 in 1jyv
Go back to
Sodium Binding Sites List in 1jyv
Sodium binding site 5 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Onpg
 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 Onpg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3101
b:16.6
occ:1.00
|
O6
|
B:1452001
|
2.3
|
16.2
|
1.0
|
|
O
|
B:HOH8891
|
2.3
|
16.0
|
1.0
|
|
OD2
|
B:ASP201
|
2.3
|
13.8
|
1.0
|
|
O
|
B:PHE601
|
2.3
|
15.0
|
1.0
|
|
OD1
|
B:ASN604
|
2.4
|
15.7
|
1.0
|
|
C6
|
B:1452001
|
3.2
|
15.3
|
1.0
|
|
CG
|
B:ASP201
|
3.3
|
17.0
|
1.0
|
|
CG
|
B:ASN604
|
3.3
|
14.8
|
1.0
|
|
C
|
B:PHE601
|
3.5
|
19.8
|
1.0
|
|
OD1
|
B:ASP201
|
3.6
|
15.3
|
1.0
|
|
OH
|
B:TYR100
|
3.6
|
17.8
|
1.0
|
|
ND2
|
B:ASN604
|
3.6
|
16.6
|
1.0
|
|
CA
|
B:CYS602
|
4.1
|
15.1
|
1.0
|
|
NE1
|
B:TRP568
|
4.2
|
15.0
|
1.0
|
|
O4
|
B:1452001
|
4.2
|
16.0
|
1.0
|
|
N
|
B:CYS602
|
4.3
|
15.6
|
1.0
|
|
C5
|
B:1452001
|
4.4
|
15.8
|
1.0
|
|
O
|
B:HOH8672
|
4.4
|
16.8
|
1.0
|
|
C4
|
B:1452001
|
4.5
|
11.7
|
1.0
|
|
CA
|
B:PHE601
|
4.5
|
18.8
|
1.0
|
|
CB
|
B:PHE601
|
4.5
|
17.1
|
1.0
|
|
CB
|
B:ASP201
|
4.6
|
13.0
|
1.0
|
|
NE2
|
B:HIS540
|
4.6
|
14.7
|
1.0
|
|
C
|
B:CYS602
|
4.7
|
15.2
|
1.0
|
|
CB
|
B:ASN604
|
4.7
|
12.4
|
1.0
|
|
CZ
|
B:TYR100
|
4.7
|
18.4
|
1.0
|
|
O
|
B:ASP201
|
4.7
|
15.3
|
1.0
|
|
CZ2
|
B:TRP568
|
4.9
|
18.7
|
1.0
|
|
CE2
|
B:TRP568
|
4.9
|
21.2
|
1.0
|
|
Sodium binding site 6 out
of 16 in 1jyv
Go back to
Sodium Binding Sites List in 1jyv
Sodium binding site 6 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Onpg
 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 Onpg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3102
b:16.5
occ:1.00
|
O
|
B:PHE556
|
2.3
|
13.4
|
1.0
|
|
O
|
B:TYR559
|
2.3
|
13.3
|
1.0
|
|
O
|
B:LEU562
|
2.3
|
13.5
|
1.0
|
|
O
|
B:HOH9223
|
2.3
|
30.1
|
1.0
|
|
O
|
B:HOH9010
|
2.5
|
25.4
|
1.0
|
|
O
|
B:PRO560
|
3.1
|
13.1
|
1.0
|
|
C
|
B:TYR559
|
3.3
|
16.2
|
1.0
|
|
C
|
B:LEU562
|
3.4
|
14.0
|
1.0
|
|
C
|
B:PHE556
|
3.4
|
15.3
|
1.0
|
|
C
|
B:PRO560
|
3.5
|
15.0
|
1.0
|
|
CA
|
B:PRO560
|
3.6
|
12.2
|
1.0
|
|
N
|
B:PRO560
|
3.9
|
14.5
|
1.0
|
|
N
|
B:LEU562
|
4.0
|
10.4
|
1.0
|
|
O
|
B:HOH8898
|
4.1
|
19.2
|
1.0
|
|
CA
|
B:PHE556
|
4.1
|
13.3
|
1.0
|
|
CA
|
B:LEU562
|
4.1
|
12.6
|
1.0
|
|
O
|
B:HOH9425
|
4.2
|
54.4
|
1.0
|
|
N
|
B:GLN563
|
4.3
|
12.3
|
1.0
|
|
O
|
B:HOH9390
|
4.3
|
48.8
|
1.0
|
|
CB
|
B:LEU562
|
4.3
|
9.3
|
1.0
|
|
CA
|
B:TYR559
|
4.4
|
9.7
|
1.0
|
|
N
|
B:TYR559
|
4.4
|
12.1
|
1.0
|
|
CA
|
B:GLN563
|
4.4
|
11.9
|
1.0
|
|
N
|
B:ARG557
|
4.5
|
10.3
|
1.0
|
|
N
|
B:ARG561
|
4.5
|
12.6
|
1.0
|
|
O
|
B:HOH9563
|
4.6
|
51.3
|
1.0
|
|
CA
|
B:ARG557
|
4.6
|
12.4
|
1.0
|
|
C
|
B:ARG557
|
4.7
|
14.7
|
1.0
|
|
CG
|
B:GLN563
|
4.7
|
9.9
|
1.0
|
|
CB
|
B:PHE556
|
4.7
|
13.3
|
1.0
|
|
O
|
B:ARG557
|
4.7
|
16.5
|
1.0
|
|
CD1
|
B:LEU350
|
4.8
|
12.2
|
1.0
|
|
C
|
B:ARG561
|
4.9
|
10.0
|
1.0
|
|
O
|
B:ALA555
|
4.9
|
11.7
|
1.0
|
|
CB
|
B:TYR559
|
4.9
|
12.0
|
1.0
|
|
Sodium binding site 7 out
of 16 in 1jyv
Go back to
Sodium Binding Sites List in 1jyv
Sodium binding site 7 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Onpg
 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 Onpg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3103
b:25.3
occ:1.00
|
O
|
B:PRO932
|
2.3
|
19.1
|
1.0
|
|
O
|
B:LEU967
|
2.4
|
22.6
|
1.0
|
|
O
|
B:HOH9314
|
2.5
|
46.1
|
1.0
|
|
O
|
B:THR970
|
2.6
|
26.1
|
1.0
|
|
O
|
B:HOH8822
|
2.8
|
19.8
|
1.0
|
|
C
|
B:PRO932
|
3.3
|
18.8
|
1.0
|
|
CZ
|
B:PHE931
|
3.4
|
20.8
|
1.0
|
|
C
|
B:LEU967
|
3.6
|
18.5
|
1.0
|
|
CE1
|
B:PHE931
|
3.7
|
20.4
|
1.0
|
|
O
|
B:HOH9145
|
3.7
|
30.7
|
1.0
|
|
C
|
B:THR970
|
3.8
|
24.9
|
1.0
|
|
CE2
|
B:PHE931
|
3.8
|
22.4
|
1.0
|
|
CA
|
B:MET968
|
4.0
|
12.7
|
1.0
|
|
CA
|
B:PRO932
|
4.0
|
19.3
|
1.0
|
|
CB
|
B:PRO932
|
4.0
|
23.4
|
1.0
|
|
N
|
B:PRO932
|
4.1
|
21.6
|
1.0
|
|
CD
|
B:PRO932
|
4.1
|
18.2
|
1.0
|
|
O
|
B:MET968
|
4.1
|
23.4
|
1.0
|
|
C
|
B:MET968
|
4.1
|
23.3
|
1.0
|
|
N
|
B:THR970
|
4.2
|
18.6
|
1.0
|
|
CD1
|
B:PHE931
|
4.3
|
17.4
|
1.0
|
|
N
|
B:SER933
|
4.3
|
16.1
|
1.0
|
|
N
|
B:MET968
|
4.4
|
14.7
|
1.0
|
|
CD2
|
B:PHE931
|
4.4
|
16.2
|
1.0
|
|
CG
|
B:PRO932
|
4.6
|
15.5
|
1.0
|
|
CA
|
B:THR970
|
4.6
|
24.1
|
1.0
|
|
CA
|
B:SER933
|
4.6
|
15.4
|
1.0
|
|
CG
|
B:PHE931
|
4.6
|
19.1
|
1.0
|
|
CA
|
B:SER971
|
4.7
|
17.4
|
1.0
|
|
N
|
B:SER971
|
4.7
|
22.3
|
1.0
|
|
CA
|
B:LEU967
|
4.8
|
16.7
|
1.0
|
|
C
|
B:PHE931
|
4.8
|
23.9
|
1.0
|
|
N
|
B:GLU969
|
4.8
|
20.1
|
1.0
|
|
Sodium binding site 8 out
of 16 in 1jyv
Go back to
Sodium Binding Sites List in 1jyv
Sodium binding site 8 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Onpg
 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 Onpg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3104
b:32.7
occ:1.00
|
O
|
B:DMS8425
|
2.2
|
35.7
|
1.0
|
|
O
|
B:LEU670
|
2.4
|
21.5
|
1.0
|
|
O
|
B:GLU650
|
2.5
|
23.9
|
1.0
|
|
O
|
B:SER647
|
2.5
|
21.8
|
1.0
|
|
O
|
B:HOH9326
|
2.9
|
35.1
|
1.0
|
|
S
|
B:DMS8425
|
3.3
|
43.6
|
1.0
|
|
N
|
B:GLU650
|
3.4
|
19.3
|
1.0
|
|
C
|
B:GLU650
|
3.5
|
27.3
|
1.0
|
|
C
|
B:LEU670
|
3.5
|
22.2
|
1.0
|
|
C
|
B:SER647
|
3.7
|
25.7
|
1.0
|
|
N
|
B:LEU670
|
3.8
|
23.9
|
1.0
|
|
C2
|
B:DMS8425
|
3.8
|
36.8
|
1.0
|
|
CA
|
B:GLU650
|
3.9
|
17.7
|
1.0
|
|
CB
|
B:LEU670
|
4.0
|
21.8
|
1.0
|
|
CA
|
B:ASP648
|
4.0
|
17.4
|
1.0
|
|
CB
|
B:GLU650
|
4.1
|
20.3
|
1.0
|
|
CA
|
B:LEU670
|
4.1
|
19.1
|
1.0
|
|
N
|
B:ASN649
|
4.1
|
21.2
|
1.0
|
|
C
|
B:ASP648
|
4.1
|
24.2
|
1.0
|
|
OG
|
B:SER647
|
4.2
|
18.1
|
1.0
|
|
N
|
B:ASP648
|
4.4
|
15.8
|
1.0
|
|
C
|
B:ASN649
|
4.6
|
27.4
|
1.0
|
|
CB
|
B:SER647
|
4.6
|
20.5
|
1.0
|
|
N
|
B:ASP671
|
4.6
|
22.4
|
1.0
|
|
N
|
B:LEU651
|
4.7
|
22.5
|
1.0
|
|
O
|
B:ASP648
|
4.7
|
23.6
|
1.0
|
|
CA
|
B:ASN649
|
4.8
|
15.7
|
1.0
|
|
OE1
|
B:GLU650
|
4.8
|
18.7
|
1.0
|
|
CA
|
B:ASP671
|
4.8
|
26.4
|
1.0
|
|
C1
|
B:DMS8425
|
4.8
|
29.4
|
1.0
|
|
CA
|
B:SER647
|
4.8
|
17.2
|
1.0
|
|
C
|
B:PRO669
|
4.9
|
27.1
|
1.0
|
|
O
|
B:HOH9440
|
5.0
|
35.6
|
1.0
|
|
Sodium binding site 9 out
of 16 in 1jyv
Go back to
Sodium Binding Sites List in 1jyv
Sodium binding site 9 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Onpg
 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 Onpg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na3101
b:15.5
occ:1.00
|
O6
|
C:1452001
|
2.2
|
16.8
|
1.0
|
|
OD1
|
C:ASN604
|
2.3
|
16.2
|
1.0
|
|
O
|
C:HOH8997
|
2.3
|
21.6
|
1.0
|
|
O
|
C:PHE601
|
2.4
|
17.9
|
1.0
|
|
OD2
|
C:ASP201
|
2.4
|
15.0
|
1.0
|
|
C6
|
C:1452001
|
3.2
|
14.2
|
1.0
|
|
CG
|
C:ASP201
|
3.3
|
17.3
|
1.0
|
|
CG
|
C:ASN604
|
3.3
|
14.0
|
1.0
|
|
C
|
C:PHE601
|
3.5
|
19.9
|
1.0
|
|
OD1
|
C:ASP201
|
3.6
|
16.1
|
1.0
|
|
ND2
|
C:ASN604
|
3.6
|
19.6
|
1.0
|
|
OH
|
C:TYR100
|
3.7
|
17.4
|
1.0
|
|
NE1
|
C:TRP568
|
4.2
|
16.5
|
1.0
|
|
CA
|
C:CYS602
|
4.2
|
19.3
|
1.0
|
|
O4
|
C:1452001
|
4.3
|
16.2
|
1.0
|
|
N
|
C:CYS602
|
4.3
|
17.9
|
1.0
|
|
C5
|
C:1452001
|
4.4
|
14.0
|
1.0
|
|
O
|
C:HOH8775
|
4.4
|
16.5
|
1.0
|
|
C4
|
C:1452001
|
4.4
|
13.0
|
1.0
|
|
CB
|
C:ASP201
|
4.5
|
17.1
|
1.0
|
|
CA
|
C:PHE601
|
4.6
|
14.7
|
1.0
|
|
CB
|
C:PHE601
|
4.6
|
13.1
|
1.0
|
|
NE2
|
C:HIS540
|
4.6
|
17.0
|
1.0
|
|
O
|
C:ASP201
|
4.7
|
14.2
|
1.0
|
|
CB
|
C:ASN604
|
4.7
|
13.9
|
1.0
|
|
C
|
C:CYS602
|
4.7
|
21.5
|
1.0
|
|
CZ
|
C:TYR100
|
4.8
|
16.4
|
1.0
|
|
CZ2
|
C:TRP568
|
4.8
|
14.8
|
1.0
|
|
CE2
|
C:TRP568
|
4.9
|
17.3
|
1.0
|
|
Sodium binding site 10 out
of 16 in 1jyv
Go back to
Sodium Binding Sites List in 1jyv
Sodium binding site 10 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Onpg
 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 Onpg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na3102
b:17.5
occ:1.00
|
O
|
C:PHE556
|
2.2
|
13.0
|
1.0
|
|
O
|
C:TYR559
|
2.3
|
13.7
|
1.0
|
|
O
|
C:LEU562
|
2.3
|
14.6
|
1.0
|
|
O
|
C:HOH9119
|
2.6
|
26.0
|
1.0
|
|
O
|
C:HOH9335
|
2.6
|
26.6
|
1.0
|
|
O
|
C:PRO560
|
3.1
|
15.5
|
1.0
|
|
C
|
C:TYR559
|
3.3
|
14.8
|
1.0
|
|
C
|
C:PHE556
|
3.4
|
17.2
|
1.0
|
|
C
|
C:LEU562
|
3.4
|
14.5
|
1.0
|
|
C
|
C:PRO560
|
3.5
|
16.9
|
1.0
|
|
CA
|
C:PRO560
|
3.6
|
11.6
|
1.0
|
|
N
|
C:PRO560
|
3.9
|
16.0
|
1.0
|
|
N
|
C:LEU562
|
3.9
|
11.1
|
1.0
|
|
CA
|
C:PHE556
|
4.1
|
13.4
|
1.0
|
|
O
|
C:HOH9004
|
4.1
|
20.4
|
1.0
|
|
CA
|
C:LEU562
|
4.2
|
8.8
|
1.0
|
|
CB
|
C:LEU562
|
4.3
|
10.6
|
1.0
|
|
N
|
C:GLN563
|
4.3
|
15.2
|
1.0
|
|
CA
|
C:GLN563
|
4.4
|
12.7
|
1.0
|
|
O
|
C:HOH9644
|
4.4
|
56.8
|
1.0
|
|
CA
|
C:TYR559
|
4.4
|
12.4
|
1.0
|
|
N
|
C:TYR559
|
4.4
|
14.2
|
1.0
|
|
N
|
C:ARG561
|
4.5
|
13.9
|
1.0
|
|
N
|
C:ARG557
|
4.5
|
11.4
|
1.0
|
|
CG
|
C:GLN563
|
4.6
|
11.0
|
1.0
|
|
CA
|
C:ARG557
|
4.7
|
11.7
|
1.0
|
|
O
|
C:ARG557
|
4.7
|
18.0
|
1.0
|
|
C
|
C:ARG557
|
4.7
|
18.3
|
1.0
|
|
CB
|
C:PHE556
|
4.8
|
13.9
|
1.0
|
|
O
|
C:ALA555
|
4.8
|
13.0
|
1.0
|
|
C
|
C:ARG561
|
4.8
|
13.7
|
1.0
|
|
O
|
C:HOH9514
|
4.9
|
38.8
|
1.0
|
|
CD1
|
C:LEU350
|
4.9
|
12.6
|
1.0
|
|
CB
|
C:TYR559
|
4.9
|
13.4
|
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 19:01:15 2024
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