Sodium in PDB 1jz5: E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on
Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on
All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on:
3.2.1.23;
Protein crystallography data
The structure of E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on, PDB code: 1jz5
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 (°)
|
149.690,
168.020,
201.040,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
16 /
23.1
|
Other elements in 1jz5:
The structure of E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on 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 in Complex with D-Galctopyranosyl-1- on
(pdb code 1jz5). 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 in Complex with D-Galctopyranosyl-1- on, PDB code: 1jz5:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 16 in 1jz5
Go back to
Sodium Binding Sites List in 1jz5
Sodium binding site 1 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on
 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 D-Galctopyranosyl-1- on within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3101
b:23.0
occ:1.00
|
O
|
A:HOH8869
|
2.4
|
20.3
|
1.0
|
|
OD1
|
A:ASN604
|
2.4
|
20.9
|
1.0
|
|
O
|
A:PHE601
|
2.4
|
20.1
|
1.0
|
|
OD2
|
A:ASP201
|
2.5
|
19.1
|
1.0
|
|
O6
|
A:1492001
|
2.5
|
21.3
|
1.0
|
|
CD2
|
A:PHE601
|
3.2
|
24.7
|
1.0
|
|
CE2
|
A:PHE601
|
3.2
|
29.5
|
1.0
|
|
CG
|
A:ASP201
|
3.3
|
25.7
|
1.0
|
|
CG
|
A:ASN604
|
3.4
|
21.9
|
1.0
|
|
C
|
A:PHE601
|
3.6
|
28.1
|
1.0
|
|
ND2
|
A:ASN604
|
3.6
|
16.7
|
1.0
|
|
OD1
|
A:ASP201
|
3.7
|
22.7
|
1.0
|
|
C6
|
A:1492001
|
3.7
|
19.6
|
1.0
|
|
OH
|
A:TYR100
|
3.9
|
23.6
|
1.0
|
|
CG
|
A:PHE601
|
3.9
|
25.1
|
1.0
|
|
CZ
|
A:PHE601
|
4.0
|
27.1
|
1.0
|
|
O4
|
A:1492001
|
4.1
|
16.4
|
1.0
|
|
C4
|
A:1492001
|
4.1
|
17.3
|
1.0
|
|
NE1
|
A:TRP568
|
4.2
|
20.9
|
1.0
|
|
CA
|
A:CYS602
|
4.3
|
19.8
|
1.0
|
|
N
|
A:CYS602
|
4.4
|
19.6
|
1.0
|
|
C5
|
A:1492001
|
4.5
|
17.6
|
1.0
|
|
NE2
|
A:HIS540
|
4.5
|
24.1
|
1.0
|
|
O
|
A:HOH8652
|
4.5
|
23.9
|
1.0
|
|
CB
|
A:ASP201
|
4.5
|
22.2
|
1.0
|
|
CD1
|
A:PHE601
|
4.6
|
22.1
|
1.0
|
|
CA
|
A:PHE601
|
4.6
|
19.9
|
1.0
|
|
CE1
|
A:PHE601
|
4.6
|
23.9
|
1.0
|
|
CB
|
A:PHE601
|
4.7
|
20.1
|
1.0
|
|
CB
|
A:ASN604
|
4.8
|
14.1
|
1.0
|
|
C
|
A:CYS602
|
4.8
|
24.8
|
1.0
|
|
O
|
A:ASP201
|
4.8
|
16.6
|
1.0
|
|
CE2
|
A:TRP568
|
4.9
|
22.6
|
1.0
|
|
Sodium binding site 2 out
of 16 in 1jz5
Go back to
Sodium Binding Sites List in 1jz5
Sodium binding site 2 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on
 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 D-Galctopyranosyl-1- on within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3102
b:17.1
occ:1.00
|
O
|
A:TYR559
|
2.3
|
18.8
|
1.0
|
|
O
|
A:PHE556
|
2.4
|
19.3
|
1.0
|
|
O
|
A:LEU562
|
2.4
|
17.3
|
1.0
|
|
O
|
A:HOH8992
|
2.5
|
25.4
|
1.0
|
|
O
|
A:HOH9188
|
2.6
|
24.3
|
1.0
|
|
O
|
A:PRO560
|
3.1
|
17.1
|
1.0
|
|
C
|
A:TYR559
|
3.3
|
20.8
|
1.0
|
|
C
|
A:LEU562
|
3.5
|
17.9
|
1.0
|
|
C
|
A:PHE556
|
3.5
|
21.2
|
1.0
|
|
C
|
A:PRO560
|
3.6
|
14.8
|
1.0
|
|
CA
|
A:PRO560
|
3.6
|
11.0
|
1.0
|
|
N
|
A:PRO560
|
3.9
|
18.2
|
1.0
|
|
N
|
A:LEU562
|
3.9
|
14.2
|
1.0
|
|
O
|
A:HOH9334
|
4.0
|
62.2
|
1.0
|
|
O
|
A:HOH8876
|
4.0
|
23.0
|
1.0
|
|
CA
|
A:PHE556
|
4.2
|
11.2
|
1.0
|
|
CA
|
A:LEU562
|
4.2
|
15.3
|
1.0
|
|
N
|
A:GLN563
|
4.4
|
15.2
|
1.0
|
|
CB
|
A:LEU562
|
4.4
|
12.6
|
1.0
|
|
CA
|
A:GLN563
|
4.4
|
15.1
|
1.0
|
|
N
|
A:TYR559
|
4.4
|
12.6
|
1.0
|
|
CA
|
A:TYR559
|
4.4
|
12.9
|
1.0
|
|
N
|
A:ARG561
|
4.5
|
13.3
|
1.0
|
|
N
|
A:ARG557
|
4.5
|
16.6
|
1.0
|
|
CG
|
A:GLN563
|
4.6
|
14.2
|
1.0
|
|
CA
|
A:ARG557
|
4.7
|
9.1
|
1.0
|
|
C
|
A:ARG557
|
4.7
|
13.7
|
1.0
|
|
O
|
A:ARG557
|
4.8
|
18.0
|
1.0
|
|
CB
|
A:PHE556
|
4.8
|
11.5
|
1.0
|
|
C
|
A:ARG561
|
4.9
|
16.4
|
1.0
|
|
O
|
A:ALA555
|
4.9
|
16.2
|
1.0
|
|
CD1
|
A:LEU350
|
4.9
|
14.3
|
1.0
|
|
Sodium binding site 3 out
of 16 in 1jz5
Go back to
Sodium Binding Sites List in 1jz5
Sodium binding site 3 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on
 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 D-Galctopyranosyl-1- on within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3103
b:34.7
occ:1.00
|
O
|
A:HOH9273
|
2.2
|
38.9
|
1.0
|
|
O
|
A:LEU967
|
2.6
|
24.6
|
1.0
|
|
O
|
A:PRO932
|
2.6
|
25.8
|
1.0
|
|
O
|
A:THR970
|
2.7
|
34.4
|
1.0
|
|
O
|
A:HOH8803
|
3.0
|
24.8
|
1.0
|
|
O
|
A:HOH9113
|
3.4
|
38.5
|
1.0
|
|
CZ
|
A:PHE931
|
3.5
|
35.3
|
1.0
|
|
C
|
A:PRO932
|
3.6
|
28.7
|
1.0
|
|
C
|
A:LEU967
|
3.7
|
23.6
|
1.0
|
|
O
|
A:MET968
|
3.8
|
27.6
|
1.0
|
|
CE1
|
A:PHE931
|
3.8
|
33.1
|
1.0
|
|
C
|
A:THR970
|
3.9
|
44.0
|
1.0
|
|
C
|
A:MET968
|
3.9
|
37.7
|
1.0
|
|
CE2
|
A:PHE931
|
3.9
|
32.6
|
1.0
|
|
CB
|
A:PRO932
|
4.0
|
26.3
|
1.0
|
|
CA
|
A:MET968
|
4.0
|
22.3
|
1.0
|
|
CD
|
A:PRO932
|
4.2
|
19.4
|
1.0
|
|
CA
|
A:PRO932
|
4.2
|
25.4
|
1.0
|
|
N
|
A:PRO932
|
4.3
|
24.8
|
1.0
|
|
N
|
A:THR970
|
4.3
|
20.5
|
1.0
|
|
N
|
A:MET968
|
4.3
|
22.6
|
1.0
|
|
CD1
|
A:PHE931
|
4.5
|
26.3
|
1.0
|
|
CG
|
A:PRO932
|
4.5
|
32.9
|
1.0
|
|
CD2
|
A:PHE931
|
4.5
|
24.8
|
1.0
|
|
N
|
A:SER933
|
4.7
|
17.3
|
1.0
|
|
CA
|
A:THR970
|
4.7
|
23.4
|
1.0
|
|
N
|
A:SER971
|
4.7
|
34.4
|
1.0
|
|
N
|
A:GLU969
|
4.7
|
24.0
|
1.0
|
|
CA
|
A:SER971
|
4.8
|
35.4
|
1.0
|
|
CG
|
A:PHE931
|
4.8
|
20.7
|
1.0
|
|
CA
|
A:LEU967
|
4.9
|
18.4
|
1.0
|
|
C
|
A:GLU969
|
4.9
|
31.1
|
1.0
|
|
C
|
A:PHE931
|
4.9
|
29.4
|
1.0
|
|
CA
|
A:SER933
|
5.0
|
17.4
|
1.0
|
|
Sodium binding site 4 out
of 16 in 1jz5
Go back to
Sodium Binding Sites List in 1jz5
Sodium binding site 4 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on
 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 D-Galctopyranosyl-1- on within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3104
b:30.6
occ:1.00
|
O
|
A:DMS8425
|
2.2
|
43.7
|
1.0
|
|
O
|
A:LEU670
|
2.4
|
21.8
|
1.0
|
|
O
|
A:SER647
|
2.4
|
19.9
|
1.0
|
|
O
|
A:GLU650
|
2.5
|
24.2
|
1.0
|
|
O
|
A:HOH9284
|
2.6
|
48.0
|
1.0
|
|
S
|
A:DMS8425
|
3.1
|
49.1
|
1.0
|
|
N
|
A:GLU650
|
3.4
|
18.7
|
1.0
|
|
C
|
A:GLU650
|
3.5
|
26.1
|
1.0
|
|
C
|
A:LEU670
|
3.6
|
28.3
|
1.0
|
|
C
|
A:SER647
|
3.6
|
23.6
|
1.0
|
|
C2
|
A:DMS8425
|
3.9
|
89.5
|
1.0
|
|
CA
|
A:GLU650
|
3.9
|
20.3
|
1.0
|
|
N
|
A:LEU670
|
4.0
|
23.6
|
1.0
|
|
N
|
A:ASN649
|
4.0
|
23.1
|
1.0
|
|
C
|
A:ASP648
|
4.1
|
27.7
|
1.0
|
|
CA
|
A:ASP648
|
4.1
|
22.3
|
1.0
|
|
CB
|
A:GLU650
|
4.1
|
20.4
|
1.0
|
|
CA
|
A:LEU670
|
4.2
|
28.8
|
1.0
|
|
OG
|
A:SER647
|
4.3
|
21.4
|
1.0
|
|
CB
|
A:LEU670
|
4.3
|
30.0
|
1.0
|
|
N
|
A:ASP648
|
4.4
|
21.9
|
1.0
|
|
OD1
|
A:ASP671
|
4.4
|
0.0
|
1.0
|
|
C
|
A:ASN649
|
4.5
|
26.1
|
1.0
|
|
CA
|
A:ASN649
|
4.6
|
22.2
|
1.0
|
|
O
|
A:ASP648
|
4.6
|
22.1
|
1.0
|
|
CB
|
A:SER647
|
4.6
|
19.0
|
1.0
|
|
N
|
A:ASP671
|
4.7
|
23.8
|
1.0
|
|
N
|
A:LEU651
|
4.7
|
23.7
|
1.0
|
|
C1
|
A:DMS8425
|
4.8
|
35.0
|
1.0
|
|
CA
|
A:SER647
|
4.8
|
19.8
|
1.0
|
|
OE1
|
A:GLU650
|
4.8
|
20.6
|
1.0
|
|
CA
|
A:ASP671
|
4.9
|
29.6
|
1.0
|
|
C
|
A:PRO669
|
5.0
|
23.7
|
1.0
|
|
Sodium binding site 5 out
of 16 in 1jz5
Go back to
Sodium Binding Sites List in 1jz5
Sodium binding site 5 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on
 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 D-Galctopyranosyl-1- on within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3101
b:21.7
occ:1.00
|
O
|
B:HOH8887
|
2.2
|
19.2
|
1.0
|
|
O
|
B:PHE601
|
2.4
|
17.3
|
1.0
|
|
OD2
|
B:ASP201
|
2.4
|
18.8
|
1.0
|
|
O6
|
B:1492001
|
2.5
|
21.1
|
1.0
|
|
OD1
|
B:ASN604
|
2.5
|
17.5
|
1.0
|
|
CD2
|
B:PHE601
|
3.1
|
29.5
|
1.0
|
|
CE2
|
B:PHE601
|
3.2
|
21.6
|
1.0
|
|
CG
|
B:ASP201
|
3.3
|
25.5
|
1.0
|
|
CG
|
B:ASN604
|
3.4
|
24.0
|
1.0
|
|
C
|
B:PHE601
|
3.5
|
23.3
|
1.0
|
|
C6
|
B:1492001
|
3.6
|
24.7
|
1.0
|
|
OD1
|
B:ASP201
|
3.6
|
20.6
|
1.0
|
|
ND2
|
B:ASN604
|
3.7
|
19.3
|
1.0
|
|
OH
|
B:TYR100
|
3.8
|
19.0
|
1.0
|
|
CG
|
B:PHE601
|
3.9
|
26.1
|
1.0
|
|
CZ
|
B:PHE601
|
4.0
|
32.5
|
1.0
|
|
O4
|
B:1492001
|
4.1
|
18.6
|
1.0
|
|
C4
|
B:1492001
|
4.2
|
33.1
|
1.0
|
|
CA
|
B:CYS602
|
4.2
|
19.8
|
1.0
|
|
N
|
B:CYS602
|
4.3
|
17.4
|
1.0
|
|
NE1
|
B:TRP568
|
4.3
|
16.0
|
1.0
|
|
C5
|
B:1492001
|
4.4
|
20.2
|
1.0
|
|
NE2
|
B:HIS540
|
4.5
|
15.8
|
1.0
|
|
CB
|
B:ASP201
|
4.5
|
17.0
|
1.0
|
|
CA
|
B:PHE601
|
4.5
|
20.7
|
1.0
|
|
O
|
B:HOH8665
|
4.5
|
17.7
|
1.0
|
|
CD1
|
B:PHE601
|
4.6
|
24.9
|
1.0
|
|
CB
|
B:PHE601
|
4.7
|
23.6
|
1.0
|
|
CE1
|
B:PHE601
|
4.7
|
26.9
|
1.0
|
|
O
|
B:ASP201
|
4.7
|
19.4
|
1.0
|
|
C
|
B:CYS602
|
4.9
|
23.2
|
1.0
|
|
CB
|
B:ASN604
|
4.9
|
15.3
|
1.0
|
|
CZ
|
B:TYR100
|
4.9
|
24.7
|
1.0
|
|
Sodium binding site 6 out
of 16 in 1jz5
Go back to
Sodium Binding Sites List in 1jz5
Sodium binding site 6 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on
 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 D-Galctopyranosyl-1- on within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3102
b:20.4
occ:1.00
|
O
|
B:PHE556
|
2.2
|
12.6
|
1.0
|
|
O
|
B:LEU562
|
2.2
|
16.9
|
1.0
|
|
O
|
B:TYR559
|
2.3
|
19.1
|
1.0
|
|
O
|
B:HOH9007
|
2.6
|
28.1
|
1.0
|
|
O
|
B:HOH9201
|
2.7
|
29.8
|
1.0
|
|
O
|
B:PRO560
|
3.2
|
16.4
|
1.0
|
|
C
|
B:TYR559
|
3.3
|
15.0
|
1.0
|
|
C
|
B:LEU562
|
3.3
|
24.7
|
1.0
|
|
C
|
B:PHE556
|
3.4
|
17.6
|
1.0
|
|
C
|
B:PRO560
|
3.6
|
19.8
|
1.0
|
|
CA
|
B:PRO560
|
3.7
|
14.1
|
1.0
|
|
N
|
B:PRO560
|
3.9
|
17.9
|
1.0
|
|
N
|
B:LEU562
|
4.0
|
13.0
|
1.0
|
|
CA
|
B:PHE556
|
4.0
|
15.3
|
1.0
|
|
O
|
B:HOH8894
|
4.0
|
23.1
|
1.0
|
|
CA
|
B:LEU562
|
4.1
|
13.5
|
1.0
|
|
CB
|
B:LEU562
|
4.2
|
10.6
|
1.0
|
|
N
|
B:GLN563
|
4.3
|
16.7
|
1.0
|
|
CA
|
B:TYR559
|
4.3
|
15.2
|
1.0
|
|
N
|
B:TYR559
|
4.3
|
15.8
|
1.0
|
|
CA
|
B:GLN563
|
4.4
|
13.7
|
1.0
|
|
N
|
B:ARG557
|
4.5
|
15.6
|
1.0
|
|
N
|
B:ARG561
|
4.5
|
11.6
|
1.0
|
|
CA
|
B:ARG557
|
4.7
|
17.3
|
1.0
|
|
CB
|
B:PHE556
|
4.7
|
14.5
|
1.0
|
|
CG
|
B:GLN563
|
4.7
|
13.3
|
1.0
|
|
C
|
B:ARG557
|
4.7
|
19.4
|
1.0
|
|
O
|
B:ARG557
|
4.8
|
19.2
|
1.0
|
|
O
|
B:ALA555
|
4.8
|
16.6
|
1.0
|
|
CD1
|
B:LEU350
|
4.8
|
13.8
|
1.0
|
|
CB
|
B:TYR559
|
4.9
|
14.0
|
1.0
|
|
C
|
B:ARG561
|
4.9
|
14.1
|
1.0
|
|
Sodium binding site 7 out
of 16 in 1jz5
Go back to
Sodium Binding Sites List in 1jz5
Sodium binding site 7 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on
 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 D-Galctopyranosyl-1- on within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3103
b:29.9
occ:1.00
|
O
|
B:PRO932
|
2.4
|
28.1
|
1.0
|
|
O
|
B:HOH9283
|
2.4
|
42.6
|
1.0
|
|
O
|
B:LEU967
|
2.4
|
25.0
|
1.0
|
|
O
|
B:THR970
|
2.7
|
42.1
|
1.0
|
|
O
|
B:HOH8817
|
2.7
|
24.9
|
1.0
|
|
C
|
B:PRO932
|
3.4
|
23.9
|
1.0
|
|
CZ
|
B:PHE931
|
3.4
|
31.0
|
1.0
|
|
C
|
B:LEU967
|
3.6
|
20.6
|
1.0
|
|
O
|
B:HOH9130
|
3.7
|
32.7
|
1.0
|
|
CE2
|
B:PHE931
|
3.7
|
28.4
|
1.0
|
|
C
|
B:THR970
|
3.8
|
39.3
|
1.0
|
|
CE1
|
B:PHE931
|
3.8
|
19.6
|
1.0
|
|
CA
|
B:MET968
|
3.8
|
21.5
|
1.0
|
|
O
|
B:MET968
|
4.0
|
26.7
|
1.0
|
|
C
|
B:MET968
|
4.0
|
35.2
|
1.0
|
|
CB
|
B:PRO932
|
4.1
|
19.4
|
1.0
|
|
CA
|
B:PRO932
|
4.1
|
17.3
|
1.0
|
|
N
|
B:PRO932
|
4.2
|
25.4
|
1.0
|
|
N
|
B:MET968
|
4.2
|
17.6
|
1.0
|
|
N
|
B:THR970
|
4.3
|
21.1
|
1.0
|
|
CD
|
B:PRO932
|
4.3
|
28.9
|
1.0
|
|
CD2
|
B:PHE931
|
4.4
|
20.9
|
1.0
|
|
N
|
B:SER933
|
4.4
|
17.4
|
1.0
|
|
CD1
|
B:PHE931
|
4.4
|
20.9
|
1.0
|
|
CA
|
B:THR970
|
4.6
|
26.0
|
1.0
|
|
CG
|
B:PRO932
|
4.6
|
23.5
|
1.0
|
|
CA
|
B:SER933
|
4.7
|
16.4
|
1.0
|
|
CG
|
B:PHE931
|
4.7
|
25.3
|
1.0
|
|
N
|
B:SER971
|
4.7
|
34.2
|
1.0
|
|
CA
|
B:LEU967
|
4.7
|
21.3
|
1.0
|
|
CA
|
B:SER971
|
4.8
|
30.4
|
1.0
|
|
N
|
B:GLU969
|
4.8
|
24.2
|
1.0
|
|
C
|
B:PHE931
|
4.9
|
26.2
|
1.0
|
|
O
|
B:HOH9304
|
4.9
|
44.1
|
1.0
|
|
CB
|
B:MET968
|
4.9
|
25.8
|
1.0
|
|
Sodium binding site 8 out
of 16 in 1jz5
Go back to
Sodium Binding Sites List in 1jz5
Sodium binding site 8 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on
 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 D-Galctopyranosyl-1- on within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3104
b:33.5
occ:1.00
|
O
|
B:DMS8425
|
2.0
|
31.5
|
1.0
|
|
O
|
B:HOH9407
|
2.5
|
43.9
|
1.0
|
|
O
|
B:SER647
|
2.5
|
21.9
|
1.0
|
|
O
|
B:LEU670
|
2.5
|
26.7
|
1.0
|
|
O
|
B:GLU650
|
2.6
|
26.1
|
1.0
|
|
O
|
B:HOH9293
|
2.8
|
32.2
|
1.0
|
|
S
|
B:DMS8425
|
3.2
|
49.7
|
1.0
|
|
N
|
B:GLU650
|
3.5
|
24.0
|
1.0
|
|
C
|
B:GLU650
|
3.6
|
30.6
|
1.0
|
|
C
|
B:LEU670
|
3.6
|
28.3
|
1.0
|
|
C
|
B:SER647
|
3.7
|
22.8
|
1.0
|
|
C2
|
B:DMS8425
|
3.7
|
43.0
|
1.0
|
|
N
|
B:LEU670
|
3.8
|
28.8
|
1.0
|
|
CA
|
B:GLU650
|
4.0
|
16.9
|
1.0
|
|
CB
|
B:LEU670
|
4.0
|
27.8
|
1.0
|
|
CA
|
B:LEU670
|
4.1
|
26.9
|
1.0
|
|
CA
|
B:ASP648
|
4.2
|
28.3
|
1.0
|
|
OG
|
B:SER647
|
4.2
|
19.4
|
1.0
|
|
N
|
B:ASN649
|
4.2
|
20.9
|
1.0
|
|
C
|
B:ASP648
|
4.3
|
32.3
|
1.0
|
|
CB
|
B:GLU650
|
4.3
|
16.2
|
1.0
|
|
N
|
B:ASP648
|
4.4
|
17.1
|
1.0
|
|
C1
|
B:DMS8425
|
4.6
|
24.3
|
1.0
|
|
CB
|
B:SER647
|
4.7
|
25.9
|
1.0
|
|
C
|
B:ASN649
|
4.7
|
26.9
|
1.0
|
|
N
|
B:ASP671
|
4.7
|
20.8
|
1.0
|
|
CA
|
B:ASP671
|
4.7
|
20.0
|
1.0
|
|
C
|
B:PRO669
|
4.8
|
22.1
|
1.0
|
|
CA
|
B:SER647
|
4.8
|
21.2
|
1.0
|
|
N
|
B:LEU651
|
4.8
|
22.5
|
1.0
|
|
O
|
B:HOH9391
|
4.8
|
38.4
|
1.0
|
|
CA
|
B:ASN649
|
4.9
|
18.4
|
1.0
|
|
O
|
B:ASP648
|
4.9
|
24.1
|
1.0
|
|
OE1
|
B:GLU650
|
5.0
|
23.8
|
1.0
|
|
Sodium binding site 9 out
of 16 in 1jz5
Go back to
Sodium Binding Sites List in 1jz5
Sodium binding site 9 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on
 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 D-Galctopyranosyl-1- on within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na3101
b:19.7
occ:1.00
|
O6
|
C:1492001
|
2.3
|
17.5
|
1.0
|
|
OD2
|
C:ASP201
|
2.4
|
16.8
|
1.0
|
|
O
|
C:PHE601
|
2.5
|
18.4
|
1.0
|
|
O
|
C:HOH8897
|
2.5
|
26.3
|
1.0
|
|
OD1
|
C:ASN604
|
2.5
|
16.4
|
1.0
|
|
CD2
|
C:PHE601
|
3.1
|
33.8
|
1.0
|
|
CE2
|
C:PHE601
|
3.1
|
28.5
|
1.0
|
|
CG
|
C:ASP201
|
3.3
|
24.1
|
1.0
|
|
C6
|
C:1492001
|
3.4
|
22.2
|
1.0
|
|
CG
|
C:ASN604
|
3.5
|
22.1
|
1.0
|
|
C
|
C:PHE601
|
3.6
|
21.5
|
1.0
|
|
OD1
|
C:ASP201
|
3.7
|
18.2
|
1.0
|
|
ND2
|
C:ASN604
|
3.7
|
26.4
|
1.0
|
|
OH
|
C:TYR100
|
3.8
|
20.9
|
1.0
|
|
CG
|
C:PHE601
|
3.9
|
27.2
|
1.0
|
|
CZ
|
C:PHE601
|
4.0
|
19.6
|
1.0
|
|
C4
|
C:1492001
|
4.1
|
26.1
|
1.0
|
|
O4
|
C:1492001
|
4.1
|
21.1
|
1.0
|
|
NE1
|
C:TRP568
|
4.3
|
18.8
|
1.0
|
|
C5
|
C:1492001
|
4.3
|
26.0
|
1.0
|
|
CA
|
C:CYS602
|
4.3
|
22.4
|
1.0
|
|
N
|
C:CYS602
|
4.4
|
21.0
|
1.0
|
|
CB
|
C:ASP201
|
4.5
|
21.6
|
1.0
|
|
NE2
|
C:HIS540
|
4.5
|
17.6
|
1.0
|
|
CD1
|
C:PHE601
|
4.6
|
22.3
|
1.0
|
|
CA
|
C:PHE601
|
4.6
|
19.1
|
1.0
|
|
CB
|
C:PHE601
|
4.6
|
21.5
|
1.0
|
|
O
|
C:HOH8676
|
4.6
|
17.4
|
1.0
|
|
CE1
|
C:PHE601
|
4.6
|
23.6
|
1.0
|
|
O
|
C:ASP201
|
4.8
|
15.2
|
1.0
|
|
C
|
C:CYS602
|
4.9
|
30.1
|
1.0
|
|
CB
|
C:ASN604
|
4.9
|
12.4
|
1.0
|
|
CZ
|
C:TYR100
|
4.9
|
29.8
|
1.0
|
|
CE2
|
C:TRP568
|
5.0
|
17.9
|
1.0
|
|
CE1
|
C:HIS540
|
5.0
|
21.9
|
1.0
|
|
Sodium binding site 10 out
of 16 in 1jz5
Go back to
Sodium Binding Sites List in 1jz5
Sodium binding site 10 out
of 16 in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on
 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 D-Galctopyranosyl-1- on within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na3102
b:19.5
occ:1.00
|
O
|
C:PHE556
|
2.2
|
15.7
|
1.0
|
|
O
|
C:TYR559
|
2.3
|
17.3
|
1.0
|
|
O
|
C:LEU562
|
2.4
|
16.3
|
1.0
|
|
O
|
C:HOH9016
|
2.5
|
28.3
|
1.0
|
|
O
|
C:HOH9210
|
2.6
|
37.1
|
1.0
|
|
O
|
C:PRO560
|
3.2
|
16.6
|
1.0
|
|
C
|
C:TYR559
|
3.3
|
16.1
|
1.0
|
|
C
|
C:PHE556
|
3.4
|
17.7
|
1.0
|
|
C
|
C:LEU562
|
3.5
|
20.9
|
1.0
|
|
C
|
C:PRO560
|
3.6
|
18.7
|
1.0
|
|
CA
|
C:PRO560
|
3.7
|
18.6
|
1.0
|
|
N
|
C:PRO560
|
3.9
|
16.6
|
1.0
|
|
N
|
C:LEU562
|
4.0
|
13.4
|
1.0
|
|
O
|
C:HOH8904
|
4.0
|
22.7
|
1.0
|
|
CA
|
C:PHE556
|
4.1
|
15.5
|
1.0
|
|
CA
|
C:LEU562
|
4.2
|
12.0
|
1.0
|
|
CB
|
C:LEU562
|
4.3
|
11.1
|
1.0
|
|
N
|
C:ARG557
|
4.4
|
15.4
|
1.0
|
|
N
|
C:TYR559
|
4.4
|
17.2
|
1.0
|
|
CA
|
C:TYR559
|
4.4
|
14.2
|
1.0
|
|
N
|
C:GLN563
|
4.4
|
14.7
|
1.0
|
|
N
|
C:ARG561
|
4.5
|
13.8
|
1.0
|
|
CA
|
C:GLN563
|
4.5
|
12.8
|
1.0
|
|
CA
|
C:ARG557
|
4.6
|
15.2
|
1.0
|
|
C
|
C:ARG557
|
4.7
|
23.9
|
1.0
|
|
CB
|
C:PHE556
|
4.7
|
17.8
|
1.0
|
|
O
|
C:ARG557
|
4.7
|
19.2
|
1.0
|
|
O
|
C:ALA555
|
4.8
|
19.0
|
1.0
|
|
CG
|
C:GLN563
|
4.8
|
15.7
|
1.0
|
|
CB
|
C:TYR559
|
4.9
|
15.9
|
1.0
|
|
C
|
C:ARG561
|
4.9
|
15.1
|
1.0
|
|
CD1
|
C:LEU350
|
5.0
|
13.9
|
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 19:10:54 2024
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