Sodium in PDB 1hn1: E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic)
Enzymatic activity of E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic)
All present enzymatic activity of E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic):
3.1.2.23;
Protein crystallography data
The structure of E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic), PDB code: 1hn1
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)
|
15.00 /
3.00
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
153.900,
171.400,
204.500,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
n/a /
n/a
|
Other elements in 1hn1:
The structure of E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic) also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic)
(pdb code 1hn1). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the
E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic), PDB code: 1hn1:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
Sodium binding site 1 out
of 7 in 1hn1
Go back to
Sodium Binding Sites List in 1hn1
Sodium binding site 1 out
of 7 in the E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic)
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3101
b:52.1
occ:1.00
|
OD2
|
A:ASP201
|
2.7
|
63.2
|
1.0
|
O
|
A:PHE601
|
2.7
|
37.7
|
1.0
|
OD1
|
A:ASN604
|
2.9
|
69.9
|
1.0
|
ND2
|
A:ASN604
|
2.9
|
7.9
|
1.0
|
CG
|
A:ASN604
|
3.2
|
54.3
|
1.0
|
NE1
|
A:TRP568
|
3.9
|
27.2
|
1.0
|
CG
|
A:ASP201
|
3.9
|
72.2
|
1.0
|
C
|
A:PHE601
|
3.9
|
29.9
|
1.0
|
NE2
|
A:HIS540
|
4.1
|
50.0
|
1.0
|
OD1
|
A:ASP201
|
4.4
|
89.2
|
1.0
|
OH
|
A:TYR100
|
4.4
|
34.8
|
1.0
|
CD1
|
A:TRP568
|
4.6
|
27.5
|
1.0
|
CB
|
A:ASN604
|
4.6
|
41.0
|
1.0
|
CB
|
A:PHE601
|
4.7
|
31.2
|
1.0
|
CA
|
A:CYS602
|
4.7
|
30.2
|
1.0
|
CE2
|
A:TRP568
|
4.7
|
33.5
|
1.0
|
N
|
A:CYS602
|
4.7
|
30.3
|
1.0
|
CA
|
A:PHE601
|
4.7
|
24.2
|
1.0
|
CE1
|
A:HIS540
|
4.8
|
48.6
|
1.0
|
CD2
|
A:PHE601
|
4.8
|
47.5
|
1.0
|
O
|
A:HOH4052
|
4.8
|
25.6
|
1.0
|
CZ2
|
A:TRP568
|
5.0
|
36.3
|
1.0
|
CB
|
A:ASP201
|
5.0
|
35.0
|
1.0
|
|
Sodium binding site 2 out
of 7 in 1hn1
Go back to
Sodium Binding Sites List in 1hn1
Sodium binding site 2 out
of 7 in the E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic)
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3102
b:24.3
occ:1.00
|
O
|
A:PHE556
|
2.4
|
31.6
|
1.0
|
O
|
A:LEU562
|
2.5
|
38.0
|
1.0
|
O
|
A:TYR559
|
2.7
|
25.2
|
1.0
|
O
|
A:PRO560
|
3.5
|
11.1
|
1.0
|
C
|
A:LEU562
|
3.6
|
33.7
|
1.0
|
C
|
A:PHE556
|
3.6
|
24.8
|
1.0
|
C
|
A:TYR559
|
3.7
|
21.9
|
1.0
|
C
|
A:PRO560
|
3.9
|
14.1
|
1.0
|
CA
|
A:PRO560
|
4.0
|
15.7
|
1.0
|
N
|
A:LEU562
|
4.2
|
29.0
|
1.0
|
N
|
A:PRO560
|
4.3
|
25.2
|
1.0
|
CA
|
A:LEU562
|
4.4
|
34.5
|
1.0
|
CD1
|
A:LEU350
|
4.4
|
11.5
|
1.0
|
N
|
A:GLN563
|
4.4
|
18.2
|
1.0
|
CA
|
A:PHE556
|
4.5
|
12.1
|
1.0
|
CA
|
A:GLN563
|
4.5
|
15.2
|
1.0
|
N
|
A:ARG557
|
4.5
|
15.8
|
1.0
|
CB
|
A:LEU562
|
4.5
|
35.3
|
1.0
|
CA
|
A:ARG557
|
4.6
|
22.6
|
1.0
|
CG
|
A:GLN563
|
4.8
|
14.4
|
1.0
|
C
|
A:ARG557
|
4.8
|
17.2
|
1.0
|
CA
|
A:TYR559
|
4.8
|
9.9
|
1.0
|
N
|
A:ARG561
|
4.9
|
19.1
|
1.0
|
N
|
A:TYR559
|
5.0
|
11.9
|
1.0
|
O
|
A:ARG557
|
5.0
|
17.1
|
1.0
|
CB
|
A:PHE556
|
5.0
|
16.7
|
1.0
|
|
Sodium binding site 3 out
of 7 in 1hn1
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Sodium Binding Sites List in 1hn1
Sodium binding site 3 out
of 7 in the E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic)
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3102
b:32.3
occ:1.00
|
O
|
B:TYR559
|
2.5
|
23.8
|
1.0
|
O
|
B:PHE556
|
2.6
|
26.6
|
1.0
|
O
|
B:LEU562
|
2.8
|
13.0
|
1.0
|
C
|
B:TYR559
|
3.4
|
28.9
|
1.0
|
O
|
B:PRO560
|
3.5
|
27.6
|
1.0
|
C
|
B:PHE556
|
3.7
|
26.2
|
1.0
|
CA
|
B:PRO560
|
3.7
|
24.2
|
1.0
|
C
|
B:LEU562
|
3.8
|
19.4
|
1.0
|
N
|
B:PRO560
|
3.9
|
31.0
|
1.0
|
C
|
B:PRO560
|
3.9
|
22.6
|
1.0
|
CA
|
B:PHE556
|
4.5
|
18.2
|
1.0
|
O
|
B:ARG557
|
4.5
|
31.1
|
1.0
|
N
|
B:ARG557
|
4.6
|
17.2
|
1.0
|
CA
|
B:TYR559
|
4.6
|
19.8
|
1.0
|
N
|
B:LEU562
|
4.6
|
17.6
|
1.0
|
N
|
B:GLN563
|
4.6
|
21.7
|
1.0
|
N
|
B:TYR559
|
4.7
|
24.4
|
1.0
|
C
|
B:ARG557
|
4.7
|
15.7
|
1.0
|
CA
|
B:GLN563
|
4.7
|
20.5
|
1.0
|
CA
|
B:LEU562
|
4.7
|
12.8
|
1.0
|
CD1
|
B:LEU350
|
4.7
|
25.2
|
1.0
|
CA
|
B:ARG557
|
4.7
|
14.6
|
1.0
|
CB
|
B:LEU562
|
4.8
|
10.6
|
1.0
|
CB
|
B:PHE556
|
4.9
|
20.5
|
1.0
|
|
Sodium binding site 4 out
of 7 in 1hn1
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Sodium Binding Sites List in 1hn1
Sodium binding site 4 out
of 7 in the E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic)
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3103
b:45.8
occ:1.00
|
O
|
B:PRO932
|
2.3
|
39.6
|
1.0
|
O
|
B:LEU967
|
2.6
|
29.9
|
1.0
|
O
|
B:THR970
|
2.8
|
34.1
|
1.0
|
C
|
B:PRO932
|
3.2
|
31.8
|
1.0
|
CG
|
B:PRO932
|
3.4
|
35.4
|
1.0
|
CB
|
B:PRO932
|
3.4
|
33.8
|
1.0
|
CZ
|
B:PHE931
|
3.6
|
27.6
|
1.0
|
C
|
B:LEU967
|
3.7
|
32.8
|
1.0
|
CE1
|
B:PHE931
|
3.7
|
29.8
|
1.0
|
O
|
B:MET968
|
3.8
|
58.2
|
1.0
|
CA
|
B:PRO932
|
3.8
|
29.9
|
1.0
|
C
|
B:THR970
|
4.0
|
35.8
|
1.0
|
CE2
|
B:PHE931
|
4.0
|
38.9
|
1.0
|
N
|
B:PRO932
|
4.0
|
28.5
|
1.0
|
CD
|
B:PRO932
|
4.0
|
27.2
|
1.0
|
C
|
B:MET968
|
4.1
|
42.3
|
1.0
|
CA
|
B:MET968
|
4.1
|
21.2
|
1.0
|
CD1
|
B:PHE931
|
4.2
|
33.0
|
1.0
|
N
|
B:SER933
|
4.3
|
25.9
|
1.0
|
N
|
B:MET968
|
4.3
|
15.1
|
1.0
|
CD2
|
B:PHE931
|
4.5
|
43.8
|
1.0
|
CG
|
B:PHE931
|
4.6
|
34.5
|
1.0
|
N
|
B:THR970
|
4.6
|
34.1
|
1.0
|
C
|
B:PHE931
|
4.7
|
32.4
|
1.0
|
CA
|
B:SER933
|
4.7
|
28.2
|
1.0
|
CA
|
B:LEU967
|
4.8
|
37.6
|
1.0
|
O
|
B:PRO788
|
4.9
|
45.7
|
1.0
|
CA
|
B:THR970
|
4.9
|
26.3
|
1.0
|
N
|
B:SER971
|
4.9
|
38.0
|
1.0
|
CA
|
B:SER971
|
4.9
|
33.6
|
1.0
|
N
|
B:GLU969
|
5.0
|
38.9
|
1.0
|
|
Sodium binding site 5 out
of 7 in 1hn1
Go back to
Sodium Binding Sites List in 1hn1
Sodium binding site 5 out
of 7 in the E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic)
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na3101
b:49.3
occ:1.00
|
OD2
|
C:ASP201
|
2.2
|
62.9
|
1.0
|
O
|
C:PHE601
|
2.6
|
33.6
|
1.0
|
OD1
|
C:ASN604
|
2.6
|
5.0
|
1.0
|
CG
|
C:ASP201
|
3.1
|
36.9
|
1.0
|
OD1
|
C:ASP201
|
3.5
|
31.4
|
1.0
|
C
|
C:PHE601
|
3.6
|
35.2
|
1.0
|
CG
|
C:ASN604
|
3.7
|
70.9
|
1.0
|
OH
|
C:TYR100
|
3.9
|
26.6
|
1.0
|
ND2
|
C:ASN604
|
4.1
|
43.8
|
1.0
|
NE1
|
C:TRP568
|
4.2
|
23.0
|
1.0
|
CB
|
C:PHE601
|
4.2
|
38.0
|
1.0
|
CB
|
C:ASP201
|
4.3
|
31.1
|
1.0
|
N
|
C:CYS602
|
4.4
|
40.3
|
1.0
|
CA
|
C:PHE601
|
4.5
|
34.6
|
1.0
|
CA
|
C:CYS602
|
4.5
|
43.8
|
1.0
|
CZ2
|
C:TRP568
|
4.7
|
29.1
|
1.0
|
NE2
|
C:HIS540
|
4.7
|
20.3
|
1.0
|
CE2
|
C:TRP568
|
4.8
|
27.0
|
1.0
|
ND2
|
C:ASN102
|
4.8
|
22.1
|
1.0
|
O
|
C:ASP201
|
4.8
|
23.8
|
1.0
|
CZ
|
C:TYR100
|
5.0
|
31.5
|
1.0
|
CB
|
C:ASN604
|
5.0
|
21.8
|
1.0
|
C
|
C:CYS602
|
5.0
|
38.2
|
1.0
|
|
Sodium binding site 6 out
of 7 in 1hn1
Go back to
Sodium Binding Sites List in 1hn1
Sodium binding site 6 out
of 7 in the E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic)
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na3102
b:24.6
occ:1.00
|
O
|
C:PHE556
|
2.4
|
23.5
|
1.0
|
O
|
C:LEU562
|
2.6
|
9.7
|
1.0
|
O
|
C:TYR559
|
2.7
|
22.9
|
1.0
|
O
|
C:PRO560
|
3.5
|
30.5
|
1.0
|
C
|
C:TYR559
|
3.6
|
31.5
|
1.0
|
C
|
C:PHE556
|
3.6
|
27.2
|
1.0
|
C
|
C:LEU562
|
3.7
|
18.2
|
1.0
|
CD1
|
C:LEU350
|
3.8
|
30.8
|
1.0
|
CA
|
C:PRO560
|
4.0
|
20.8
|
1.0
|
C
|
C:PRO560
|
4.0
|
17.9
|
1.0
|
N
|
C:PRO560
|
4.1
|
29.1
|
1.0
|
CA
|
C:PHE556
|
4.4
|
22.4
|
1.0
|
N
|
C:LEU562
|
4.4
|
11.6
|
1.0
|
N
|
C:GLN563
|
4.5
|
21.3
|
1.0
|
CA
|
C:LEU562
|
4.5
|
13.6
|
1.0
|
CA
|
C:GLN563
|
4.6
|
14.1
|
1.0
|
N
|
C:ARG557
|
4.7
|
19.8
|
1.0
|
CA
|
C:ARG557
|
4.7
|
17.7
|
1.0
|
CA
|
C:TYR559
|
4.7
|
25.5
|
1.0
|
O
|
C:ARG557
|
4.8
|
43.2
|
1.0
|
C
|
C:ARG557
|
4.8
|
27.6
|
1.0
|
N
|
C:TYR559
|
4.8
|
30.8
|
1.0
|
CB
|
C:PHE556
|
4.8
|
30.9
|
1.0
|
CB
|
C:LEU562
|
4.8
|
24.3
|
1.0
|
CG
|
C:GLN563
|
4.9
|
11.6
|
1.0
|
|
Sodium binding site 7 out
of 7 in 1hn1
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Sodium Binding Sites List in 1hn1
Sodium binding site 7 out
of 7 in the E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic)
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na3102
b:47.7
occ:1.00
|
O
|
D:PHE556
|
2.3
|
31.9
|
1.0
|
O
|
D:LEU562
|
2.5
|
30.8
|
1.0
|
O
|
D:TYR559
|
2.5
|
31.6
|
1.0
|
C
|
D:PHE556
|
3.4
|
23.2
|
1.0
|
C
|
D:TYR559
|
3.5
|
19.4
|
1.0
|
C
|
D:LEU562
|
3.7
|
30.5
|
1.0
|
O
|
D:PRO560
|
3.7
|
34.8
|
1.0
|
CA
|
D:PRO560
|
3.9
|
17.9
|
1.0
|
C
|
D:PRO560
|
4.0
|
37.2
|
1.0
|
N
|
D:PRO560
|
4.1
|
15.7
|
1.0
|
CA
|
D:PHE556
|
4.3
|
14.2
|
1.0
|
O
|
D:ARG557
|
4.3
|
26.1
|
1.0
|
N
|
D:ARG557
|
4.3
|
5.3
|
1.0
|
CD1
|
D:LEU350
|
4.4
|
8.9
|
1.0
|
N
|
D:TYR559
|
4.4
|
10.4
|
1.0
|
C
|
D:ARG557
|
4.5
|
20.1
|
1.0
|
CA
|
D:ARG557
|
4.5
|
9.5
|
1.0
|
CA
|
D:TYR559
|
4.5
|
8.8
|
1.0
|
CB
|
D:LEU562
|
4.5
|
19.2
|
1.0
|
N
|
D:LEU562
|
4.5
|
17.6
|
1.0
|
CA
|
D:LEU562
|
4.5
|
19.1
|
1.0
|
N
|
D:GLN563
|
4.6
|
20.6
|
1.0
|
CA
|
D:GLN563
|
4.7
|
8.8
|
1.0
|
CB
|
D:PHE556
|
4.8
|
17.7
|
1.0
|
O
|
D:ALA555
|
4.9
|
24.8
|
1.0
|
N
|
D:ARG561
|
4.9
|
33.3
|
1.0
|
|
Reference:
D.H.Juers,
B.W.Matthews.
Reversible Lattice Repacking Illustrates the Temperature Dependence of Macromolecular Interactions. J.Mol.Biol. V. 311 851 2001.
ISSN: ISSN 0022-2836
PubMed: 11518535
DOI: 10.1006/JMBI.2001.4891
Page generated: Sun Oct 6 18:46:07 2024
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