Sodium in PDB 1jz4: E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris)
Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris)
All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris):
3.2.1.23;
Protein crystallography data
The structure of E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris), PDB code: 1jz4
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)
|
40.00 /
2.10
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
149.500,
169.000,
200.800,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.4 /
26.7
|
Other elements in 1jz4:
The structure of E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris) 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-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris)
(pdb code 1jz4). 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-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris), PDB code: 1jz4:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 15 in 1jz4
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Sodium Binding Sites List in 1jz4
Sodium binding site 1 out
of 15 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris)
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-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3101
b:13.3
occ:1.00
|
O
|
A:HOH8875
|
2.2
|
8.8
|
1.0
|
OD1
|
A:ASN604
|
2.4
|
13.2
|
1.0
|
O
|
A:PHE601
|
2.5
|
13.1
|
1.0
|
O6
|
A:2DG2001
|
2.5
|
10.3
|
1.0
|
OD2
|
A:ASP201
|
2.5
|
11.6
|
1.0
|
O
|
A:HOH9311
|
2.8
|
33.7
|
1.0
|
CG
|
A:ASP201
|
3.2
|
11.7
|
1.0
|
CG
|
A:ASN604
|
3.5
|
16.5
|
1.0
|
OD1
|
A:ASP201
|
3.5
|
14.6
|
1.0
|
C
|
A:PHE601
|
3.6
|
13.2
|
1.0
|
C6
|
A:2DG2001
|
3.7
|
14.5
|
1.0
|
ND2
|
A:ASN604
|
3.8
|
8.9
|
1.0
|
OH
|
A:TYR100
|
3.9
|
13.6
|
1.0
|
NE1
|
A:TRP568
|
4.1
|
10.1
|
1.0
|
C4
|
A:2DG2001
|
4.1
|
10.9
|
1.0
|
O4
|
A:2DG2001
|
4.2
|
16.5
|
1.0
|
CB
|
A:PHE601
|
4.4
|
14.0
|
1.0
|
CA
|
A:CYS602
|
4.4
|
11.9
|
1.0
|
CB
|
A:ASP201
|
4.4
|
13.5
|
1.0
|
C5
|
A:2DG2001
|
4.5
|
15.9
|
1.0
|
N
|
A:CYS602
|
4.5
|
10.8
|
1.0
|
CA
|
A:PHE601
|
4.5
|
12.9
|
1.0
|
O
|
A:HOH8652
|
4.6
|
9.3
|
1.0
|
CD2
|
A:PHE601
|
4.6
|
23.3
|
1.0
|
NE2
|
A:HIS540
|
4.6
|
11.6
|
1.0
|
O
|
A:ASP201
|
4.8
|
10.1
|
1.0
|
CE2
|
A:TRP568
|
4.9
|
13.6
|
1.0
|
CB
|
A:ASN604
|
4.9
|
9.3
|
1.0
|
C
|
A:CYS602
|
4.9
|
18.4
|
1.0
|
CE1
|
A:HIS540
|
4.9
|
12.1
|
1.0
|
CZ2
|
A:TRP568
|
5.0
|
8.3
|
1.0
|
CG
|
A:PHE601
|
5.0
|
30.4
|
1.0
|
|
Sodium binding site 2 out
of 15 in 1jz4
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Sodium Binding Sites List in 1jz4
Sodium binding site 2 out
of 15 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris)
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-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3102
b:15.6
occ:1.00
|
O
|
A:TYR559
|
2.3
|
13.8
|
1.0
|
O
|
A:LEU562
|
2.3
|
18.5
|
1.0
|
O
|
A:PHE556
|
2.3
|
9.8
|
1.0
|
O
|
A:HOH9205
|
2.4
|
19.5
|
1.0
|
O
|
A:HOH8994
|
2.5
|
25.5
|
1.0
|
O
|
A:PRO560
|
3.3
|
10.2
|
1.0
|
C
|
A:TYR559
|
3.3
|
11.5
|
1.0
|
C
|
A:LEU562
|
3.4
|
8.4
|
1.0
|
C
|
A:PHE556
|
3.5
|
11.6
|
1.0
|
C
|
A:PRO560
|
3.6
|
11.6
|
1.0
|
CA
|
A:PRO560
|
3.7
|
1.0
|
1.0
|
N
|
A:PRO560
|
3.9
|
12.2
|
1.0
|
N
|
A:LEU562
|
3.9
|
6.4
|
1.0
|
O
|
A:HOH8882
|
4.1
|
12.1
|
1.0
|
CA
|
A:LEU562
|
4.1
|
11.6
|
1.0
|
CA
|
A:PHE556
|
4.2
|
6.6
|
1.0
|
N
|
A:TYR559
|
4.4
|
5.9
|
1.0
|
N
|
A:GLN563
|
4.4
|
13.9
|
1.0
|
CB
|
A:LEU562
|
4.4
|
11.4
|
1.0
|
CA
|
A:TYR559
|
4.4
|
5.4
|
1.0
|
N
|
A:ARG561
|
4.5
|
2.5
|
1.0
|
N
|
A:ARG557
|
4.5
|
4.7
|
1.0
|
CA
|
A:GLN563
|
4.6
|
17.9
|
1.0
|
CA
|
A:ARG557
|
4.6
|
1.0
|
1.0
|
O
|
A:ARG557
|
4.6
|
7.9
|
1.0
|
C
|
A:ARG557
|
4.6
|
9.0
|
1.0
|
CG
|
A:GLN563
|
4.7
|
3.8
|
1.0
|
CB
|
A:PHE556
|
4.8
|
4.1
|
1.0
|
O
|
A:ALA555
|
4.8
|
10.2
|
1.0
|
C
|
A:ARG561
|
4.9
|
13.2
|
1.0
|
O
|
A:HOH9373
|
5.0
|
43.2
|
1.0
|
CB
|
A:TYR559
|
5.0
|
5.6
|
1.0
|
|
Sodium binding site 3 out
of 15 in 1jz4
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Sodium Binding Sites List in 1jz4
Sodium binding site 3 out
of 15 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris)
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-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3103
b:25.3
occ:1.00
|
O
|
A:HOH9288
|
2.1
|
38.5
|
1.0
|
O
|
A:PRO932
|
2.5
|
12.5
|
1.0
|
O
|
A:LEU967
|
2.6
|
17.1
|
1.0
|
O
|
A:HOH8805
|
2.6
|
17.0
|
1.0
|
O
|
A:THR970
|
2.7
|
27.9
|
1.0
|
CZ
|
A:PHE931
|
3.5
|
20.6
|
1.0
|
C
|
A:PRO932
|
3.6
|
11.7
|
1.0
|
O
|
A:HOH9125
|
3.7
|
28.7
|
1.0
|
C
|
A:THR970
|
3.8
|
22.7
|
1.0
|
C
|
A:LEU967
|
3.8
|
14.8
|
1.0
|
CE1
|
A:PHE931
|
3.8
|
24.2
|
1.0
|
O
|
A:MET968
|
3.8
|
21.0
|
1.0
|
CE2
|
A:PHE931
|
3.9
|
8.6
|
1.0
|
CA
|
A:MET968
|
3.9
|
9.5
|
1.0
|
C
|
A:MET968
|
4.0
|
21.5
|
1.0
|
CB
|
A:PRO932
|
4.1
|
19.8
|
1.0
|
CD
|
A:PRO932
|
4.2
|
4.4
|
1.0
|
CG
|
A:PRO932
|
4.3
|
21.7
|
1.0
|
N
|
A:THR970
|
4.3
|
16.5
|
1.0
|
CA
|
A:PRO932
|
4.3
|
12.0
|
1.0
|
N
|
A:MET968
|
4.4
|
11.8
|
1.0
|
N
|
A:PRO932
|
4.4
|
13.2
|
1.0
|
CD1
|
A:PHE931
|
4.4
|
10.2
|
1.0
|
CD2
|
A:PHE931
|
4.5
|
9.0
|
1.0
|
N
|
A:SER971
|
4.6
|
21.1
|
1.0
|
CA
|
A:THR970
|
4.6
|
21.7
|
1.0
|
N
|
A:SER933
|
4.6
|
5.1
|
1.0
|
CA
|
A:SER971
|
4.7
|
20.2
|
1.0
|
N
|
A:GLU969
|
4.7
|
8.7
|
1.0
|
CG
|
A:PHE931
|
4.7
|
10.4
|
1.0
|
CA
|
A:SER933
|
4.9
|
9.9
|
1.0
|
CA
|
A:LEU967
|
5.0
|
20.0
|
1.0
|
|
Sodium binding site 4 out
of 15 in 1jz4
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Sodium Binding Sites List in 1jz4
Sodium binding site 4 out
of 15 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris)
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-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3104
b:21.9
occ:1.00
|
O
|
A:DMS8425
|
2.2
|
45.9
|
1.0
|
O
|
A:HOH9302
|
2.3
|
31.8
|
1.0
|
O
|
A:LEU670
|
2.3
|
8.4
|
1.0
|
O
|
A:SER647
|
2.4
|
12.7
|
1.0
|
O
|
A:GLU650
|
2.6
|
18.8
|
1.0
|
O
|
A:HOH9451
|
2.8
|
45.0
|
1.0
|
S
|
A:DMS8425
|
3.4
|
45.5
|
1.0
|
C
|
A:LEU670
|
3.5
|
16.4
|
1.0
|
N
|
A:GLU650
|
3.5
|
18.5
|
1.0
|
C
|
A:SER647
|
3.6
|
18.0
|
1.0
|
C
|
A:GLU650
|
3.6
|
15.5
|
1.0
|
C2
|
A:DMS8425
|
3.8
|
40.5
|
1.0
|
N
|
A:LEU670
|
3.9
|
24.1
|
1.0
|
CA
|
A:GLU650
|
4.1
|
13.9
|
1.0
|
N
|
A:ASN649
|
4.1
|
19.3
|
1.0
|
CA
|
A:ASP648
|
4.1
|
21.0
|
1.0
|
C
|
A:ASP648
|
4.2
|
20.0
|
1.0
|
CA
|
A:LEU670
|
4.2
|
19.4
|
1.0
|
N
|
A:ASP648
|
4.3
|
19.4
|
1.0
|
OG
|
A:SER647
|
4.3
|
9.3
|
1.0
|
CB
|
A:LEU670
|
4.3
|
16.2
|
1.0
|
CB
|
A:GLU650
|
4.4
|
10.3
|
1.0
|
CB
|
A:SER647
|
4.5
|
16.0
|
1.0
|
N
|
A:ASP671
|
4.6
|
11.0
|
1.0
|
C
|
A:ASN649
|
4.6
|
18.8
|
1.0
|
CA
|
A:SER647
|
4.7
|
12.2
|
1.0
|
CA
|
A:ASP671
|
4.7
|
15.2
|
1.0
|
CA
|
A:ASN649
|
4.8
|
15.4
|
1.0
|
O
|
A:ASP648
|
4.8
|
14.6
|
1.0
|
N
|
A:LEU651
|
4.8
|
9.6
|
1.0
|
C
|
A:PRO669
|
4.9
|
19.4
|
1.0
|
OE1
|
A:GLU650
|
4.9
|
19.6
|
1.0
|
C1
|
A:DMS8425
|
4.9
|
34.2
|
1.0
|
|
Sodium binding site 5 out
of 15 in 1jz4
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Sodium Binding Sites List in 1jz4
Sodium binding site 5 out
of 15 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris)
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-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3101
b:14.0
occ:1.00
|
O
|
B:HOH8890
|
2.3
|
10.2
|
1.0
|
OD1
|
B:ASN604
|
2.3
|
11.9
|
1.0
|
O
|
B:PHE601
|
2.4
|
14.5
|
1.0
|
OD2
|
B:ASP201
|
2.5
|
11.4
|
1.0
|
O6
|
B:2DG2001
|
2.6
|
19.5
|
1.0
|
O
|
B:HOH9551
|
3.0
|
33.1
|
1.0
|
CG
|
B:ASN604
|
3.3
|
9.1
|
1.0
|
CG
|
B:ASP201
|
3.3
|
16.4
|
1.0
|
C
|
B:PHE601
|
3.5
|
5.6
|
1.0
|
OD1
|
B:ASP201
|
3.5
|
14.0
|
1.0
|
ND2
|
B:ASN604
|
3.6
|
10.5
|
1.0
|
C6
|
B:2DG2001
|
3.8
|
13.2
|
1.0
|
OH
|
B:TYR100
|
4.0
|
10.9
|
1.0
|
C4
|
B:2DG2001
|
4.0
|
13.6
|
1.0
|
NE1
|
B:TRP568
|
4.1
|
3.6
|
1.0
|
O4
|
B:2DG2001
|
4.1
|
13.8
|
1.0
|
NE2
|
B:HIS540
|
4.3
|
1.0
|
1.0
|
N
|
B:CYS602
|
4.4
|
6.7
|
1.0
|
CB
|
B:PHE601
|
4.4
|
15.0
|
1.0
|
C5
|
B:2DG2001
|
4.4
|
15.8
|
1.0
|
CA
|
B:CYS602
|
4.4
|
7.4
|
1.0
|
CA
|
B:PHE601
|
4.4
|
13.5
|
1.0
|
O
|
B:HOH8668
|
4.5
|
12.2
|
1.0
|
CB
|
B:ASP201
|
4.6
|
16.6
|
1.0
|
CB
|
B:ASN604
|
4.7
|
5.8
|
1.0
|
O
|
B:ASP201
|
4.8
|
10.9
|
1.0
|
CE2
|
B:TRP568
|
4.9
|
11.6
|
1.0
|
CE1
|
B:HIS540
|
4.9
|
3.1
|
1.0
|
|
Sodium binding site 6 out
of 15 in 1jz4
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Sodium Binding Sites List in 1jz4
Sodium binding site 6 out
of 15 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris)
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-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3102
b:13.6
occ:1.00
|
O
|
B:PHE556
|
2.1
|
8.7
|
1.0
|
O
|
B:TYR559
|
2.2
|
14.3
|
1.0
|
O
|
B:LEU562
|
2.3
|
9.2
|
1.0
|
O
|
B:HOH9224
|
2.3
|
17.5
|
1.0
|
O
|
B:HOH9012
|
2.6
|
16.4
|
1.0
|
C
|
B:TYR559
|
3.2
|
11.9
|
1.0
|
C
|
B:PHE556
|
3.3
|
12.0
|
1.0
|
O
|
B:PRO560
|
3.3
|
14.5
|
1.0
|
C
|
B:LEU562
|
3.4
|
4.8
|
1.0
|
C
|
B:PRO560
|
3.6
|
18.5
|
1.0
|
CA
|
B:PRO560
|
3.7
|
9.4
|
1.0
|
N
|
B:PRO560
|
3.9
|
9.8
|
1.0
|
N
|
B:LEU562
|
3.9
|
7.5
|
1.0
|
O
|
B:HOH9423
|
4.0
|
37.7
|
1.0
|
O
|
B:HOH9383
|
4.0
|
33.2
|
1.0
|
CA
|
B:PHE556
|
4.0
|
6.5
|
1.0
|
O
|
B:HOH8897
|
4.1
|
12.1
|
1.0
|
CA
|
B:LEU562
|
4.1
|
10.5
|
1.0
|
CB
|
B:LEU562
|
4.2
|
12.5
|
1.0
|
N
|
B:ARG557
|
4.3
|
4.0
|
1.0
|
N
|
B:GLN563
|
4.3
|
6.9
|
1.0
|
CA
|
B:TYR559
|
4.4
|
8.8
|
1.0
|
N
|
B:TYR559
|
4.4
|
8.8
|
1.0
|
CA
|
B:ARG557
|
4.5
|
13.7
|
1.0
|
N
|
B:ARG561
|
4.5
|
7.1
|
1.0
|
CA
|
B:GLN563
|
4.5
|
4.2
|
1.0
|
C
|
B:ARG557
|
4.6
|
14.3
|
1.0
|
CB
|
B:PHE556
|
4.6
|
1.0
|
1.0
|
O
|
B:ARG557
|
4.7
|
19.1
|
1.0
|
CG
|
B:GLN563
|
4.8
|
11.7
|
1.0
|
C
|
B:ARG561
|
4.9
|
13.5
|
1.0
|
O
|
B:ALA555
|
4.9
|
11.4
|
1.0
|
CD1
|
B:LEU350
|
4.9
|
1.0
|
1.0
|
CB
|
B:TYR559
|
4.9
|
8.5
|
1.0
|
|
Sodium binding site 7 out
of 15 in 1jz4
Go back to
Sodium Binding Sites List in 1jz4
Sodium binding site 7 out
of 15 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris)
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-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3103
b:19.8
occ:1.00
|
O
|
B:PRO932
|
2.4
|
16.4
|
1.0
|
O
|
B:THR970
|
2.5
|
43.2
|
1.0
|
O
|
B:LEU967
|
2.6
|
19.0
|
1.0
|
O
|
B:HOH8820
|
2.7
|
11.6
|
1.0
|
O
|
B:HOH9311
|
2.7
|
32.1
|
1.0
|
CZ
|
B:PHE931
|
3.3
|
12.1
|
1.0
|
C
|
B:PRO932
|
3.4
|
16.1
|
1.0
|
CE1
|
B:PHE931
|
3.5
|
11.3
|
1.0
|
O
|
B:HOH9148
|
3.6
|
21.9
|
1.0
|
C
|
B:THR970
|
3.6
|
34.7
|
1.0
|
CE2
|
B:PHE931
|
3.7
|
10.8
|
1.0
|
C
|
B:LEU967
|
3.8
|
26.9
|
1.0
|
CA
|
B:MET968
|
3.9
|
8.1
|
1.0
|
O
|
B:MET968
|
4.0
|
18.9
|
1.0
|
C
|
B:MET968
|
4.1
|
24.9
|
1.0
|
CA
|
B:PRO932
|
4.1
|
8.7
|
1.0
|
CB
|
B:PRO932
|
4.1
|
15.2
|
1.0
|
N
|
B:PRO932
|
4.1
|
14.7
|
1.0
|
CD
|
B:PRO932
|
4.1
|
15.0
|
1.0
|
CD1
|
B:PHE931
|
4.2
|
14.9
|
1.0
|
N
|
B:THR970
|
4.2
|
21.1
|
1.0
|
CD2
|
B:PHE931
|
4.4
|
12.3
|
1.0
|
N
|
B:MET968
|
4.4
|
10.6
|
1.0
|
N
|
B:SER971
|
4.4
|
25.0
|
1.0
|
N
|
B:SER933
|
4.5
|
8.7
|
1.0
|
CA
|
B:THR970
|
4.5
|
24.2
|
1.0
|
CA
|
B:SER971
|
4.5
|
22.6
|
1.0
|
CG
|
B:PRO932
|
4.5
|
12.8
|
1.0
|
CG
|
B:PHE931
|
4.6
|
14.2
|
1.0
|
CA
|
B:SER933
|
4.8
|
14.2
|
1.0
|
C
|
B:PHE931
|
4.8
|
11.9
|
1.0
|
N
|
B:GLU969
|
4.9
|
18.7
|
1.0
|
O
|
B:HOH9335
|
4.9
|
28.3
|
1.0
|
CA
|
B:LEU967
|
5.0
|
19.6
|
1.0
|
|
Sodium binding site 8 out
of 15 in 1jz4
Go back to
Sodium Binding Sites List in 1jz4
Sodium binding site 8 out
of 15 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris)
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-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3104
b:38.0
occ:1.00
|
O
|
B:DMS8425
|
2.1
|
33.0
|
1.0
|
O
|
B:SER647
|
2.4
|
24.0
|
1.0
|
O
|
B:LEU670
|
2.4
|
20.9
|
1.0
|
O
|
B:GLU650
|
2.8
|
14.7
|
1.0
|
O
|
B:HOH9325
|
3.0
|
29.2
|
1.0
|
S
|
B:DMS8425
|
3.3
|
54.8
|
1.0
|
N
|
B:GLU650
|
3.5
|
15.7
|
1.0
|
C
|
B:LEU670
|
3.5
|
18.5
|
1.0
|
C
|
B:SER647
|
3.6
|
26.0
|
1.0
|
N
|
B:LEU670
|
3.7
|
24.5
|
1.0
|
C
|
B:GLU650
|
3.7
|
14.3
|
1.0
|
N
|
B:ASN649
|
3.8
|
15.2
|
1.0
|
C
|
B:ASP648
|
3.9
|
23.5
|
1.0
|
C2
|
B:DMS8425
|
3.9
|
22.9
|
1.0
|
CA
|
B:ASP648
|
4.0
|
22.4
|
1.0
|
CA
|
B:GLU650
|
4.0
|
12.4
|
1.0
|
CA
|
B:LEU670
|
4.1
|
17.6
|
1.0
|
OG
|
B:SER647
|
4.1
|
13.3
|
1.0
|
CB
|
B:GLU650
|
4.2
|
11.7
|
1.0
|
CB
|
B:LEU670
|
4.2
|
11.1
|
1.0
|
N
|
B:ASP648
|
4.2
|
17.3
|
1.0
|
O
|
B:ASP648
|
4.5
|
16.7
|
1.0
|
CA
|
B:ASN649
|
4.6
|
12.3
|
1.0
|
C
|
B:PRO669
|
4.6
|
28.0
|
1.0
|
C
|
B:ASN649
|
4.6
|
20.9
|
1.0
|
N
|
B:ASP671
|
4.6
|
15.2
|
1.0
|
CB
|
B:SER647
|
4.7
|
21.9
|
1.0
|
CA
|
B:ASP671
|
4.7
|
15.4
|
1.0
|
OE1
|
B:GLU650
|
4.7
|
12.7
|
1.0
|
CB
|
B:PRO669
|
4.7
|
48.8
|
1.0
|
CA
|
B:SER647
|
4.7
|
19.1
|
1.0
|
C1
|
B:DMS8425
|
4.8
|
30.1
|
1.0
|
CA
|
B:PRO669
|
4.8
|
43.0
|
1.0
|
N
|
B:LEU651
|
4.9
|
25.5
|
1.0
|
|
Sodium binding site 9 out
of 15 in 1jz4
Go back to
Sodium Binding Sites List in 1jz4
Sodium binding site 9 out
of 15 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris)
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-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na3101
b:11.4
occ:1.00
|
OD2
|
C:ASP201
|
2.2
|
14.4
|
1.0
|
O
|
C:HOH8894
|
2.3
|
15.3
|
1.0
|
O6
|
C:2DG2001
|
2.4
|
16.0
|
1.0
|
O
|
C:PHE601
|
2.4
|
11.7
|
1.0
|
OD1
|
C:ASN604
|
2.5
|
13.6
|
1.0
|
CG
|
C:ASP201
|
3.2
|
12.1
|
1.0
|
CG
|
C:ASN604
|
3.4
|
15.7
|
1.0
|
C
|
C:PHE601
|
3.5
|
11.7
|
1.0
|
ND2
|
C:ASN604
|
3.6
|
10.9
|
1.0
|
OD1
|
C:ASP201
|
3.7
|
11.2
|
1.0
|
C6
|
C:2DG2001
|
3.7
|
19.4
|
1.0
|
OH
|
C:TYR100
|
3.8
|
7.3
|
1.0
|
NE1
|
C:TRP568
|
4.1
|
6.9
|
1.0
|
C4
|
C:2DG2001
|
4.1
|
17.1
|
1.0
|
CB
|
C:PHE601
|
4.3
|
16.5
|
1.0
|
NE2
|
C:HIS540
|
4.3
|
10.3
|
1.0
|
O4
|
C:2DG2001
|
4.3
|
15.8
|
1.0
|
CB
|
C:ASP201
|
4.3
|
8.2
|
1.0
|
C5
|
C:2DG2001
|
4.4
|
26.5
|
1.0
|
CA
|
C:PHE601
|
4.4
|
11.3
|
1.0
|
N
|
C:CYS602
|
4.4
|
15.1
|
1.0
|
CA
|
C:CYS602
|
4.5
|
12.0
|
1.0
|
O
|
C:HOH8672
|
4.6
|
8.3
|
1.0
|
CD2
|
C:PHE601
|
4.8
|
39.2
|
1.0
|
CE1
|
C:HIS540
|
4.9
|
10.9
|
1.0
|
O
|
C:ASP201
|
4.9
|
13.6
|
1.0
|
CB
|
C:ASN604
|
4.9
|
9.3
|
1.0
|
CE2
|
C:TRP568
|
4.9
|
11.5
|
1.0
|
CD1
|
C:TRP568
|
4.9
|
11.1
|
1.0
|
CZ
|
C:TYR100
|
5.0
|
8.0
|
1.0
|
|
Sodium binding site 10 out
of 15 in 1jz4
Go back to
Sodium Binding Sites List in 1jz4
Sodium binding site 10 out
of 15 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris)
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-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na3102
b:16.6
occ:1.00
|
O
|
C:PHE556
|
2.3
|
9.0
|
1.0
|
O
|
C:LEU562
|
2.3
|
5.6
|
1.0
|
O
|
C:HOH9216
|
2.4
|
20.0
|
1.0
|
O
|
C:TYR559
|
2.4
|
17.5
|
1.0
|
O
|
C:HOH9014
|
2.6
|
16.1
|
1.0
|
C
|
C:PHE556
|
3.3
|
6.6
|
1.0
|
O
|
C:PRO560
|
3.4
|
13.8
|
1.0
|
C
|
C:TYR559
|
3.4
|
17.2
|
1.0
|
C
|
C:LEU562
|
3.5
|
8.5
|
1.0
|
C
|
C:PRO560
|
3.8
|
15.0
|
1.0
|
CA
|
C:PRO560
|
3.9
|
6.9
|
1.0
|
CA
|
C:PHE556
|
4.0
|
5.2
|
1.0
|
N
|
C:LEU562
|
4.0
|
7.1
|
1.0
|
N
|
C:PRO560
|
4.1
|
6.8
|
1.0
|
O
|
C:HOH8900
|
4.2
|
22.0
|
1.0
|
CA
|
C:LEU562
|
4.3
|
7.0
|
1.0
|
N
|
C:GLN563
|
4.4
|
8.8
|
1.0
|
CA
|
C:GLN563
|
4.4
|
9.7
|
1.0
|
CB
|
C:LEU562
|
4.4
|
2.5
|
1.0
|
N
|
C:TYR559
|
4.4
|
13.0
|
1.0
|
N
|
C:ARG557
|
4.4
|
18.5
|
1.0
|
CA
|
C:TYR559
|
4.5
|
7.3
|
1.0
|
O
|
C:HOH9391
|
4.6
|
47.4
|
1.0
|
CA
|
C:ARG557
|
4.6
|
10.2
|
1.0
|
O
|
C:ARG557
|
4.6
|
17.2
|
1.0
|
CB
|
C:PHE556
|
4.6
|
13.8
|
1.0
|
C
|
C:ARG557
|
4.7
|
19.8
|
1.0
|
N
|
C:ARG561
|
4.7
|
10.8
|
1.0
|
CG
|
C:GLN563
|
4.7
|
16.4
|
1.0
|
CD1
|
C:LEU350
|
4.7
|
1.4
|
1.0
|
O
|
C:ALA555
|
4.9
|
10.8
|
1.0
|
CB
|
C:TYR559
|
5.0
|
10.4
|
1.0
|
C
|
C:ARG561
|
5.0
|
15.5
|
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 19:10:01 2024
|