Sodium in PDB 1dp0: E. Coli Beta-Galactosidase at 1.7 Angstrom
Enzymatic activity of E. Coli Beta-Galactosidase at 1.7 Angstrom
All present enzymatic activity of E. Coli Beta-Galactosidase at 1.7 Angstrom:
3.2.1.23;
Protein crystallography data
The structure of E. Coli Beta-Galactosidase at 1.7 Angstrom, PDB code: 1dp0
was solved by
D.H.Juers,
R.H.Jacobson,
D.Wigley,
X.J.Zhang,
R.E.Huber,
D.E.Tronrud,
B.W.Matthews,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
15.00 /
1.70
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
149.600,
168.380,
200.690,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
15.7 /
21.1
|
Other elements in 1dp0:
The structure of E. Coli Beta-Galactosidase at 1.7 Angstrom also contains other interesting chemical elements:
Sodium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Binding sites:
The binding sites of Sodium atom in the E. Coli Beta-Galactosidase at 1.7 Angstrom
(pdb code 1dp0). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 20 binding sites of Sodium where determined in the
E. Coli Beta-Galactosidase at 1.7 Angstrom, PDB code: 1dp0:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 20 in 1dp0
Go back to
Sodium Binding Sites List in 1dp0
Sodium binding site 1 out
of 20 in the E. Coli Beta-Galactosidase at 1.7 Angstrom
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of E. Coli Beta-Galactosidase at 1.7 Angstrom within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3101
b:16.6
occ:1.00
|
O
|
A:HOH8875
|
2.3
|
18.0
|
1.0
|
|
O
|
A:HOH8770
|
2.3
|
18.4
|
1.0
|
|
O
|
A:PHE601
|
2.4
|
12.1
|
1.0
|
|
OD2
|
A:ASP201
|
2.4
|
11.7
|
1.0
|
|
OD1
|
A:ASN604
|
2.4
|
14.4
|
1.0
|
|
CG
|
A:ASP201
|
3.3
|
17.0
|
1.0
|
|
CG
|
A:ASN604
|
3.4
|
18.8
|
1.0
|
|
C
|
A:PHE601
|
3.5
|
17.8
|
1.0
|
|
O
|
A:HOH8882
|
3.5
|
20.8
|
1.0
|
|
OD1
|
A:ASP201
|
3.5
|
16.2
|
1.0
|
|
ND2
|
A:ASN604
|
3.6
|
13.2
|
1.0
|
|
OH
|
A:TYR100
|
3.7
|
17.1
|
1.0
|
|
O
|
A:HOH9371
|
3.9
|
31.0
|
1.0
|
|
NE1
|
A:TRP568
|
4.2
|
12.1
|
1.0
|
|
CA
|
A:CYS602
|
4.3
|
14.3
|
1.0
|
|
N
|
A:CYS602
|
4.4
|
12.4
|
1.0
|
|
O
|
A:HOH9273
|
4.4
|
29.0
|
1.0
|
|
CB
|
A:PHE601
|
4.4
|
12.4
|
1.0
|
|
CA
|
A:PHE601
|
4.5
|
16.4
|
1.0
|
|
CB
|
A:ASP201
|
4.5
|
12.1
|
1.0
|
|
O
|
A:HOH8654
|
4.5
|
17.0
|
1.0
|
|
NE2
|
A:HIS540
|
4.6
|
11.7
|
1.0
|
|
ND2
|
A:ASN102
|
4.7
|
25.4
|
1.0
|
|
O
|
A:ASP201
|
4.8
|
11.7
|
1.0
|
|
CB
|
A:ASN604
|
4.8
|
10.2
|
1.0
|
|
CZ
|
A:TYR100
|
4.8
|
19.7
|
1.0
|
|
C
|
A:CYS602
|
4.8
|
15.3
|
1.0
|
|
CD2
|
A:PHE601
|
4.9
|
13.2
|
1.0
|
|
Sodium binding site 2 out
of 20 in 1dp0
Go back to
Sodium Binding Sites List in 1dp0
Sodium binding site 2 out
of 20 in the E. Coli Beta-Galactosidase at 1.7 Angstrom
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of E. Coli Beta-Galactosidase at 1.7 Angstrom within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3102
b:12.6
occ:1.00
|
O
|
A:PHE556
|
2.3
|
12.1
|
1.0
|
|
O
|
A:TYR559
|
2.3
|
12.4
|
1.0
|
|
O
|
A:LEU562
|
2.3
|
10.0
|
1.0
|
|
O
|
A:HOH9240
|
2.5
|
21.8
|
1.0
|
|
O
|
A:HOH9004
|
2.5
|
22.5
|
1.0
|
|
O
|
A:PRO560
|
3.2
|
12.7
|
1.0
|
|
C
|
A:TYR559
|
3.4
|
12.3
|
1.0
|
|
C
|
A:LEU562
|
3.4
|
12.6
|
1.0
|
|
C
|
A:PHE556
|
3.4
|
14.0
|
1.0
|
|
C
|
A:PRO560
|
3.6
|
10.7
|
1.0
|
|
CA
|
A:PRO560
|
3.6
|
9.6
|
1.0
|
|
N
|
A:LEU562
|
3.9
|
9.0
|
1.0
|
|
N
|
A:PRO560
|
3.9
|
13.2
|
1.0
|
|
O
|
A:HOH8883
|
4.0
|
16.2
|
1.0
|
|
CA
|
A:LEU562
|
4.1
|
10.4
|
1.0
|
|
CA
|
A:PHE556
|
4.1
|
10.8
|
1.0
|
|
O
|
A:HOH9436
|
4.2
|
39.0
|
1.0
|
|
CB
|
A:LEU562
|
4.3
|
9.0
|
1.0
|
|
N
|
A:GLN563
|
4.3
|
8.6
|
1.0
|
|
CA
|
A:GLN563
|
4.4
|
8.8
|
1.0
|
|
N
|
A:TYR559
|
4.5
|
9.9
|
1.0
|
|
CA
|
A:TYR559
|
4.5
|
8.6
|
1.0
|
|
N
|
A:ARG557
|
4.5
|
9.0
|
1.0
|
|
N
|
A:ARG561
|
4.5
|
9.7
|
1.0
|
|
CA
|
A:ARG557
|
4.6
|
4.7
|
1.0
|
|
O
|
A:ARG557
|
4.7
|
12.1
|
1.0
|
|
C
|
A:ARG557
|
4.7
|
11.7
|
1.0
|
|
CG
|
A:GLN563
|
4.7
|
10.0
|
1.0
|
|
CB
|
A:PHE556
|
4.8
|
8.4
|
1.0
|
|
O
|
A:ALA555
|
4.8
|
11.6
|
1.0
|
|
C
|
A:ARG561
|
4.8
|
9.7
|
1.0
|
|
CD1
|
A:LEU350
|
4.9
|
9.8
|
1.0
|
|
O
|
A:HOH9451
|
4.9
|
45.4
|
1.0
|
|
Sodium binding site 3 out
of 20 in 1dp0
Go back to
Sodium Binding Sites List in 1dp0
Sodium binding site 3 out
of 20 in the E. Coli Beta-Galactosidase at 1.7 Angstrom
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of E. Coli Beta-Galactosidase at 1.7 Angstrom within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3103
b:26.9
occ:1.00
|
O
|
A:HOH9348
|
2.3
|
39.5
|
1.0
|
|
O
|
A:LEU967
|
2.5
|
18.4
|
1.0
|
|
O
|
A:PRO932
|
2.6
|
17.2
|
1.0
|
|
O
|
A:THR970
|
2.7
|
22.4
|
1.0
|
|
O
|
A:HOH8806
|
2.8
|
16.1
|
1.0
|
|
O
|
A:HOH9150
|
3.3
|
27.2
|
1.0
|
|
CZ
|
A:PHE931
|
3.4
|
23.6
|
1.0
|
|
C
|
A:PRO932
|
3.6
|
14.2
|
1.0
|
|
C
|
A:LEU967
|
3.7
|
18.0
|
1.0
|
|
CE1
|
A:PHE931
|
3.7
|
19.1
|
1.0
|
|
C
|
A:THR970
|
3.8
|
25.7
|
1.0
|
|
O
|
A:MET968
|
3.8
|
22.5
|
1.0
|
|
CE2
|
A:PHE931
|
3.9
|
16.1
|
1.0
|
|
CB
|
A:PRO932
|
3.9
|
12.1
|
1.0
|
|
C
|
A:MET968
|
3.9
|
23.0
|
1.0
|
|
CA
|
A:MET968
|
4.0
|
15.5
|
1.0
|
|
CA
|
A:PRO932
|
4.1
|
13.7
|
1.0
|
|
CD
|
A:PRO932
|
4.2
|
12.4
|
1.0
|
|
N
|
A:PRO932
|
4.2
|
14.5
|
1.0
|
|
N
|
A:THR970
|
4.3
|
15.5
|
1.0
|
|
N
|
A:MET968
|
4.3
|
13.4
|
1.0
|
|
CD1
|
A:PHE931
|
4.4
|
12.3
|
1.0
|
|
CG
|
A:PRO932
|
4.5
|
21.2
|
1.0
|
|
CD2
|
A:PHE931
|
4.5
|
14.7
|
1.0
|
|
N
|
A:SER933
|
4.7
|
10.2
|
1.0
|
|
CA
|
A:THR970
|
4.7
|
16.8
|
1.0
|
|
N
|
A:SER971
|
4.7
|
19.5
|
1.0
|
|
CA
|
A:SER971
|
4.7
|
23.4
|
1.0
|
|
CG
|
A:PHE931
|
4.8
|
12.5
|
1.0
|
|
N
|
A:GLU969
|
4.8
|
12.0
|
1.0
|
|
CA
|
A:LEU967
|
4.9
|
17.0
|
1.0
|
|
CA
|
A:SER933
|
4.9
|
12.0
|
1.0
|
|
C
|
A:PHE931
|
4.9
|
19.0
|
1.0
|
|
C
|
A:GLU969
|
5.0
|
32.2
|
1.0
|
|
Sodium binding site 4 out
of 20 in 1dp0
Go back to
Sodium Binding Sites List in 1dp0
Sodium binding site 4 out
of 20 in the E. Coli Beta-Galactosidase at 1.7 Angstrom
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of E. Coli Beta-Galactosidase at 1.7 Angstrom within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3104
b:25.3
occ:1.00
|
O
|
A:DMS8425
|
2.0
|
32.8
|
1.0
|
|
O
|
A:LEU670
|
2.3
|
15.3
|
1.0
|
|
O
|
A:SER647
|
2.4
|
14.1
|
1.0
|
|
O
|
A:HOH9361
|
2.6
|
40.8
|
1.0
|
|
O
|
A:GLU650
|
2.6
|
18.9
|
1.0
|
|
O
|
A:HOH9556
|
2.8
|
52.9
|
1.0
|
|
S
|
A:DMS8425
|
3.3
|
39.5
|
1.0
|
|
C
|
A:LEU670
|
3.4
|
21.7
|
1.0
|
|
N
|
A:GLU650
|
3.6
|
13.6
|
1.0
|
|
C
|
A:SER647
|
3.6
|
18.6
|
1.0
|
|
C
|
A:GLU650
|
3.7
|
16.9
|
1.0
|
|
C1
|
A:DMS8425
|
3.8
|
36.2
|
1.0
|
|
N
|
A:LEU670
|
3.9
|
21.4
|
1.0
|
|
CA
|
A:GLU650
|
4.1
|
13.9
|
1.0
|
|
N
|
A:ASN649
|
4.1
|
15.8
|
1.0
|
|
CA
|
A:LEU670
|
4.1
|
17.9
|
1.0
|
|
CA
|
A:ASP648
|
4.1
|
14.3
|
1.0
|
|
C
|
A:ASP648
|
4.1
|
22.4
|
1.0
|
|
CB
|
A:GLU650
|
4.2
|
11.1
|
1.0
|
|
OG
|
A:SER647
|
4.2
|
16.4
|
1.0
|
|
CB
|
A:LEU670
|
4.2
|
20.9
|
1.0
|
|
N
|
A:ASP648
|
4.3
|
15.4
|
1.0
|
|
CB
|
A:SER647
|
4.5
|
17.5
|
1.0
|
|
N
|
A:ASP671
|
4.5
|
20.6
|
1.0
|
|
C
|
A:ASN649
|
4.6
|
16.7
|
1.0
|
|
CA
|
A:SER647
|
4.7
|
11.2
|
1.0
|
|
CA
|
A:ASP671
|
4.7
|
19.1
|
1.0
|
|
OD1
|
A:ASP671
|
4.7
|
0.0
|
1.0
|
|
O
|
A:ASP648
|
4.8
|
16.7
|
1.0
|
|
C2
|
A:DMS8425
|
4.8
|
39.9
|
1.0
|
|
CA
|
A:ASN649
|
4.8
|
14.5
|
1.0
|
|
OE1
|
A:GLU650
|
4.8
|
16.9
|
1.0
|
|
N
|
A:LEU651
|
4.9
|
15.0
|
1.0
|
|
C
|
A:PRO669
|
4.9
|
19.1
|
1.0
|
|
Sodium binding site 5 out
of 20 in 1dp0
Go back to
Sodium Binding Sites List in 1dp0
Sodium binding site 5 out
of 20 in the E. Coli Beta-Galactosidase at 1.7 Angstrom
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of E. Coli Beta-Galactosidase at 1.7 Angstrom within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3105
b:35.9
occ:0.50
|
O
|
A:HOH9216
|
1.7
|
20.7
|
0.5
|
|
O
|
A:HOH9093
|
2.2
|
37.0
|
1.0
|
|
O
|
A:HOH9704
|
2.3
|
48.5
|
1.0
|
|
O
|
A:ASN597
|
2.3
|
16.5
|
1.0
|
|
O
|
A:HOH9048
|
2.6
|
25.0
|
1.0
|
|
O
|
A:HOH8822
|
3.0
|
27.6
|
1.0
|
|
C
|
A:ASN597
|
3.5
|
23.5
|
1.0
|
|
N
|
A:ASN597
|
3.9
|
16.7
|
1.0
|
|
OE2
|
A:GLU797
|
4.0
|
0.0
|
1.0
|
|
O
|
A:HOH9358
|
4.0
|
29.8
|
1.0
|
|
OD1
|
A:ASP598
|
4.2
|
20.0
|
1.0
|
|
OE1
|
A:GLU797
|
4.3
|
53.8
|
1.0
|
|
CA
|
A:ASN597
|
4.4
|
14.3
|
1.0
|
|
CD
|
A:GLU797
|
4.4
|
44.3
|
1.0
|
|
N
|
A:ASP598
|
4.5
|
14.7
|
1.0
|
|
CA
|
A:ASP598
|
4.5
|
11.4
|
1.0
|
|
OD1
|
A:ASN597
|
4.6
|
16.7
|
1.0
|
|
O
|
A:HOH9435
|
4.7
|
36.9
|
1.0
|
|
O
|
A:HOH9051
|
4.8
|
27.8
|
1.0
|
|
CG
|
A:ASN597
|
4.8
|
40.5
|
1.0
|
|
NH1
|
A:ARG800
|
4.8
|
56.0
|
1.0
|
|
CG
|
A:ASP598
|
4.9
|
27.3
|
1.0
|
|
Sodium binding site 6 out
of 20 in 1dp0
Go back to
Sodium Binding Sites List in 1dp0
Sodium binding site 6 out
of 20 in the E. Coli Beta-Galactosidase at 1.7 Angstrom
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of E. Coli Beta-Galactosidase at 1.7 Angstrom within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3101
b:14.7
occ:1.00
|
O
|
B:HOH8788
|
2.2
|
19.9
|
1.0
|
|
O
|
B:HOH8894
|
2.3
|
17.3
|
1.0
|
|
OD2
|
B:ASP201
|
2.3
|
13.7
|
1.0
|
|
O
|
B:PHE601
|
2.4
|
12.5
|
1.0
|
|
OD1
|
B:ASN604
|
2.4
|
12.1
|
1.0
|
|
CG
|
B:ASP201
|
3.3
|
19.6
|
1.0
|
|
CG
|
B:ASN604
|
3.4
|
17.3
|
1.0
|
|
O
|
B:HOH8901
|
3.5
|
21.7
|
1.0
|
|
C
|
B:PHE601
|
3.5
|
13.2
|
1.0
|
|
OD1
|
B:ASP201
|
3.5
|
13.1
|
1.0
|
|
OH
|
B:TYR100
|
3.6
|
14.1
|
1.0
|
|
ND2
|
B:ASN604
|
3.6
|
13.6
|
1.0
|
|
O
|
B:HOH9384
|
4.1
|
41.5
|
1.0
|
|
NE1
|
B:TRP568
|
4.2
|
9.7
|
1.0
|
|
CA
|
B:CYS602
|
4.2
|
14.2
|
1.0
|
|
N
|
B:CYS602
|
4.3
|
13.1
|
1.0
|
|
O
|
B:HOH8672
|
4.4
|
14.9
|
1.0
|
|
CA
|
B:PHE601
|
4.5
|
10.6
|
1.0
|
|
CB
|
B:PHE601
|
4.5
|
11.9
|
1.0
|
|
CB
|
B:ASP201
|
4.5
|
11.4
|
1.0
|
|
NE2
|
B:HIS540
|
4.5
|
11.3
|
1.0
|
|
ND2
|
B:ASN102
|
4.6
|
25.1
|
1.0
|
|
O
|
B:ASP201
|
4.8
|
12.0
|
1.0
|
|
CZ
|
B:TYR100
|
4.8
|
15.8
|
1.0
|
|
C
|
B:CYS602
|
4.8
|
12.3
|
1.0
|
|
CB
|
B:ASN604
|
4.8
|
10.1
|
1.0
|
|
O
|
B:HOH9286
|
4.9
|
35.6
|
1.0
|
|
CE2
|
B:TRP568
|
5.0
|
12.4
|
1.0
|
|
Sodium binding site 7 out
of 20 in 1dp0
Go back to
Sodium Binding Sites List in 1dp0
Sodium binding site 7 out
of 20 in the E. Coli Beta-Galactosidase at 1.7 Angstrom
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of E. Coli Beta-Galactosidase at 1.7 Angstrom within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3102
b:13.3
occ:1.00
|
O
|
B:TYR559
|
2.3
|
12.4
|
1.0
|
|
O
|
B:PHE556
|
2.3
|
9.9
|
1.0
|
|
O
|
B:LEU562
|
2.3
|
10.9
|
1.0
|
|
O
|
B:HOH9254
|
2.3
|
27.5
|
1.0
|
|
O
|
B:HOH9022
|
2.5
|
20.3
|
1.0
|
|
O
|
B:PRO560
|
3.2
|
11.9
|
1.0
|
|
C
|
B:TYR559
|
3.3
|
12.4
|
1.0
|
|
C
|
B:LEU562
|
3.4
|
14.5
|
1.0
|
|
C
|
B:PHE556
|
3.4
|
11.5
|
1.0
|
|
C
|
B:PRO560
|
3.6
|
12.1
|
1.0
|
|
CA
|
B:PRO560
|
3.7
|
9.8
|
1.0
|
|
N
|
B:PRO560
|
3.9
|
11.2
|
1.0
|
|
N
|
B:LEU562
|
4.0
|
8.4
|
1.0
|
|
CA
|
B:PHE556
|
4.1
|
9.3
|
1.0
|
|
O
|
B:HOH8902
|
4.1
|
13.6
|
1.0
|
|
CA
|
B:LEU562
|
4.2
|
10.3
|
1.0
|
|
O
|
B:HOH9501
|
4.3
|
34.0
|
1.0
|
|
CB
|
B:LEU562
|
4.3
|
9.0
|
1.0
|
|
N
|
B:GLN563
|
4.3
|
8.6
|
1.0
|
|
O
|
B:HOH9449
|
4.3
|
39.1
|
1.0
|
|
CA
|
B:TYR559
|
4.4
|
9.9
|
1.0
|
|
N
|
B:TYR559
|
4.4
|
10.4
|
1.0
|
|
CA
|
B:GLN563
|
4.4
|
8.7
|
1.0
|
|
N
|
B:ARG557
|
4.5
|
8.0
|
1.0
|
|
N
|
B:ARG561
|
4.5
|
9.9
|
1.0
|
|
CA
|
B:ARG557
|
4.6
|
8.4
|
1.0
|
|
CB
|
B:PHE556
|
4.7
|
8.4
|
1.0
|
|
C
|
B:ARG557
|
4.7
|
16.3
|
1.0
|
|
O
|
B:ARG557
|
4.7
|
14.8
|
1.0
|
|
CG
|
B:GLN563
|
4.8
|
9.8
|
1.0
|
|
CD1
|
B:LEU350
|
4.8
|
10.8
|
1.0
|
|
O
|
B:ALA555
|
4.9
|
10.7
|
1.0
|
|
C
|
B:ARG561
|
4.9
|
8.9
|
1.0
|
|
CB
|
B:TYR559
|
4.9
|
8.3
|
1.0
|
|
Sodium binding site 8 out
of 20 in 1dp0
Go back to
Sodium Binding Sites List in 1dp0
Sodium binding site 8 out
of 20 in the E. Coli Beta-Galactosidase at 1.7 Angstrom
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of E. Coli Beta-Galactosidase at 1.7 Angstrom within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3103
b:23.2
occ:1.00
|
O
|
B:PRO932
|
2.4
|
14.3
|
1.0
|
|
O
|
B:LEU967
|
2.5
|
16.0
|
1.0
|
|
O
|
B:HOH8824
|
2.7
|
18.0
|
1.0
|
|
O
|
B:THR970
|
2.9
|
26.1
|
1.0
|
|
CZ
|
B:PHE931
|
3.3
|
15.3
|
1.0
|
|
C
|
B:PRO932
|
3.5
|
14.2
|
1.0
|
|
CE1
|
B:PHE931
|
3.6
|
15.9
|
1.0
|
|
O
|
B:HOH9166
|
3.7
|
25.9
|
1.0
|
|
C
|
B:LEU967
|
3.7
|
18.4
|
1.0
|
|
CE2
|
B:PHE931
|
3.8
|
15.6
|
1.0
|
|
O
|
B:HOH9360
|
3.9
|
51.7
|
1.0
|
|
O
|
B:MET968
|
3.9
|
20.9
|
1.0
|
|
CA
|
B:MET968
|
3.9
|
12.9
|
1.0
|
|
C
|
B:THR970
|
4.0
|
24.3
|
1.0
|
|
C
|
B:MET968
|
4.1
|
23.9
|
1.0
|
|
CB
|
B:PRO932
|
4.1
|
16.4
|
1.0
|
|
CA
|
B:PRO932
|
4.1
|
14.5
|
1.0
|
|
CD
|
B:PRO932
|
4.2
|
16.3
|
1.0
|
|
N
|
B:PRO932
|
4.2
|
14.4
|
1.0
|
|
CD1
|
B:PHE931
|
4.3
|
14.4
|
1.0
|
|
N
|
B:THR970
|
4.3
|
15.2
|
1.0
|
|
CD2
|
B:PHE931
|
4.4
|
12.3
|
1.0
|
|
N
|
B:MET968
|
4.4
|
12.5
|
1.0
|
|
N
|
B:SER933
|
4.4
|
12.5
|
1.0
|
|
CG
|
B:PRO932
|
4.6
|
11.7
|
1.0
|
|
CG
|
B:PHE931
|
4.6
|
13.8
|
1.0
|
|
CA
|
B:SER933
|
4.7
|
11.0
|
1.0
|
|
CA
|
B:SER971
|
4.8
|
18.4
|
1.0
|
|
CA
|
B:THR970
|
4.8
|
12.8
|
1.0
|
|
N
|
B:SER971
|
4.8
|
18.8
|
1.0
|
|
CA
|
B:LEU967
|
4.8
|
15.7
|
1.0
|
|
C
|
B:PHE931
|
4.8
|
19.9
|
1.0
|
|
N
|
B:GLU969
|
4.9
|
14.9
|
1.0
|
|
O
|
B:HOH9390
|
5.0
|
34.6
|
1.0
|
|
Sodium binding site 9 out
of 20 in 1dp0
Go back to
Sodium Binding Sites List in 1dp0
Sodium binding site 9 out
of 20 in the E. Coli Beta-Galactosidase at 1.7 Angstrom
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 9 of E. Coli Beta-Galactosidase at 1.7 Angstrom within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3104
b:29.8
occ:1.00
|
O
|
B:DMS8425
|
2.0
|
31.9
|
1.0
|
|
O
|
B:LEU670
|
2.4
|
21.8
|
1.0
|
|
O
|
B:SER647
|
2.5
|
16.7
|
1.0
|
|
O
|
B:HOH9545
|
2.5
|
33.6
|
1.0
|
|
O
|
B:GLU650
|
2.6
|
18.5
|
1.0
|
|
O
|
B:HOH9375
|
2.8
|
28.5
|
1.0
|
|
S
|
B:DMS8425
|
3.2
|
43.0
|
1.0
|
|
N
|
B:GLU650
|
3.4
|
15.6
|
1.0
|
|
C
|
B:LEU670
|
3.5
|
18.1
|
1.0
|
|
C
|
B:GLU650
|
3.6
|
19.4
|
1.0
|
|
C
|
B:SER647
|
3.6
|
20.1
|
1.0
|
|
N
|
B:LEU670
|
3.8
|
22.7
|
1.0
|
|
C1
|
B:DMS8425
|
3.8
|
35.9
|
1.0
|
|
CA
|
B:GLU650
|
4.0
|
12.5
|
1.0
|
|
CA
|
B:ASP648
|
4.0
|
16.6
|
1.0
|
|
N
|
B:ASN649
|
4.0
|
19.3
|
1.0
|
|
C
|
B:ASP648
|
4.1
|
17.3
|
1.0
|
|
CA
|
B:LEU670
|
4.1
|
16.4
|
1.0
|
|
CB
|
B:LEU670
|
4.1
|
21.2
|
1.0
|
|
CB
|
B:GLU650
|
4.1
|
13.6
|
1.0
|
|
OG
|
B:SER647
|
4.3
|
16.1
|
1.0
|
|
N
|
B:ASP648
|
4.3
|
15.5
|
1.0
|
|
C
|
B:ASN649
|
4.5
|
24.3
|
1.0
|
|
N
|
B:ASP671
|
4.6
|
17.3
|
1.0
|
|
CB
|
B:SER647
|
4.7
|
18.6
|
1.0
|
|
O
|
B:ASP648
|
4.7
|
17.8
|
1.0
|
|
CA
|
B:ASN649
|
4.7
|
13.6
|
1.0
|
|
C2
|
B:DMS8425
|
4.7
|
24.8
|
1.0
|
|
C
|
B:PRO669
|
4.8
|
22.8
|
1.0
|
|
N
|
B:LEU651
|
4.8
|
15.5
|
1.0
|
|
CA
|
B:SER647
|
4.8
|
12.9
|
1.0
|
|
O
|
B:HOH9518
|
4.8
|
34.7
|
1.0
|
|
CA
|
B:ASP671
|
4.8
|
19.5
|
1.0
|
|
OE1
|
B:GLU650
|
4.8
|
15.5
|
1.0
|
|
Sodium binding site 10 out
of 20 in 1dp0
Go back to
Sodium Binding Sites List in 1dp0
Sodium binding site 10 out
of 20 in the E. Coli Beta-Galactosidase at 1.7 Angstrom
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 10 of E. Coli Beta-Galactosidase at 1.7 Angstrom within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3105
b:31.6
occ:0.50
|
O
|
B:HOH9230
|
1.7
|
24.9
|
0.5
|
|
O
|
B:HOH9109
|
2.1
|
38.2
|
1.0
|
|
O
|
B:ASN597
|
2.2
|
14.6
|
1.0
|
|
O
|
B:HOH9064
|
2.3
|
24.6
|
1.0
|
|
O
|
B:HOH8841
|
2.7
|
24.0
|
1.0
|
|
C
|
B:ASN597
|
3.4
|
19.1
|
1.0
|
|
N
|
B:ASN597
|
3.9
|
15.6
|
1.0
|
|
OE1
|
B:GLU797
|
4.1
|
51.5
|
1.0
|
|
O
|
B:HOH9446
|
4.2
|
32.9
|
1.0
|
|
OD1
|
B:ASN597
|
4.3
|
15.4
|
1.0
|
|
O
|
B:HOH9372
|
4.3
|
46.9
|
1.0
|
|
CA
|
B:ASN597
|
4.3
|
10.4
|
1.0
|
|
OD1
|
B:ASP598
|
4.4
|
20.1
|
1.0
|
|
N
|
B:ASP598
|
4.4
|
13.8
|
1.0
|
|
CA
|
B:ASP598
|
4.4
|
12.0
|
1.0
|
|
CG
|
B:ASN597
|
4.5
|
15.9
|
1.0
|
|
O
|
B:HOH9523
|
4.5
|
27.0
|
1.0
|
|
OE2
|
B:GLU797
|
4.6
|
37.4
|
1.0
|
|
CD
|
B:GLU797
|
4.6
|
35.9
|
1.0
|
|
ND2
|
B:ASN597
|
4.8
|
15.3
|
1.0
|
|
O
|
B:HOH9067
|
4.9
|
25.1
|
1.0
|
|
C
|
B:PRO596
|
4.9
|
23.6
|
1.0
|
|
CB
|
B:PRO596
|
4.9
|
21.9
|
1.0
|
|
CG
|
B:ASP598
|
5.0
|
25.9
|
1.0
|
|
Reference:
D.H.Juers,
R.H.Jacobson,
D.Wigley,
X.J.Zhang,
R.E.Huber,
D.E.Tronrud,
B.W.Matthews.
High Resolution Refinement of Beta-Galactosidase in A New Crystal Form Reveals Multiple Metal-Binding Sites and Provides A Structural Basis For Alpha-Complementation. Protein Sci. V. 9 1685 2000.
ISSN: ISSN 0961-8368
PubMed: 11045615
Page generated: Sun Oct 6 18:18:44 2024
|
