Sodium in PDB 1jz2: E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic)
Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic)
All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic):
3.2.1.23;
Protein crystallography data
The structure of E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic), PDB code: 1jz2
was solved by
D.H.Juers,
J.D.Mccarter,
L.Mackenzie,
S.G.Withers,
B.W.Matthews,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
27.60 /
2.10
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
151.500,
167.700,
201.600,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.7 /
27
|
Other elements in 1jz2:
The structure of E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic) also contains other interesting chemical elements:
Sodium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Sodium atom in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic)
(pdb code 1jz2). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the
E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic), PDB code: 1jz2:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 12 in 1jz2
Go back to
Sodium Binding Sites List in 1jz2
Sodium binding site 1 out
of 12 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (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 (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3101
b:22.0
occ:1.00
|
OD2
|
A:ASP201
|
2.3
|
19.7
|
1.0
|
O
|
A:HOH8764
|
2.3
|
19.4
|
1.0
|
O
|
A:PHE601
|
2.4
|
25.8
|
1.0
|
OD1
|
A:ASN604
|
2.5
|
25.1
|
1.0
|
O6
|
A:2FG2001
|
2.5
|
22.0
|
1.0
|
CE2
|
A:PHE601
|
3.0
|
35.4
|
1.0
|
CD2
|
A:PHE601
|
3.0
|
43.4
|
1.0
|
CG
|
A:ASP201
|
3.3
|
36.9
|
1.0
|
CG
|
A:ASN604
|
3.4
|
22.2
|
1.0
|
C
|
A:PHE601
|
3.6
|
29.5
|
1.0
|
ND2
|
A:ASN604
|
3.6
|
19.0
|
1.0
|
OD1
|
A:ASP201
|
3.7
|
19.0
|
1.0
|
C6
|
A:2FG2001
|
3.8
|
21.8
|
1.0
|
OH
|
A:TYR100
|
3.8
|
20.9
|
1.0
|
CZ
|
A:PHE601
|
3.9
|
27.6
|
1.0
|
CG
|
A:PHE601
|
3.9
|
36.3
|
1.0
|
NE1
|
A:TRP568
|
4.1
|
20.5
|
1.0
|
C4
|
A:2FG2001
|
4.1
|
19.1
|
1.0
|
O4
|
A:2FG2001
|
4.1
|
14.7
|
1.0
|
NE2
|
A:HIS540
|
4.4
|
20.9
|
1.0
|
O
|
A:HOH8555
|
4.4
|
17.7
|
1.0
|
CB
|
A:ASP201
|
4.4
|
18.4
|
1.0
|
CA
|
A:CYS602
|
4.4
|
22.0
|
1.0
|
N
|
A:CYS602
|
4.4
|
22.8
|
1.0
|
C5
|
A:2FG2001
|
4.5
|
22.1
|
1.0
|
CE1
|
A:PHE601
|
4.5
|
36.6
|
1.0
|
CD1
|
A:PHE601
|
4.6
|
30.8
|
1.0
|
CA
|
A:PHE601
|
4.6
|
29.7
|
1.0
|
CB
|
A:PHE601
|
4.6
|
29.9
|
1.0
|
O
|
A:ASP201
|
4.8
|
23.6
|
1.0
|
CB
|
A:ASN604
|
4.8
|
17.4
|
1.0
|
CE2
|
A:TRP568
|
4.9
|
22.6
|
1.0
|
CE1
|
A:HIS540
|
5.0
|
26.5
|
1.0
|
CZ2
|
A:TRP568
|
5.0
|
26.1
|
1.0
|
|
Sodium binding site 2 out
of 12 in 1jz2
Go back to
Sodium Binding Sites List in 1jz2
Sodium binding site 2 out
of 12 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (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 (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3102
b:31.1
occ:1.00
|
O
|
A:TYR559
|
2.2
|
23.5
|
1.0
|
O
|
A:LEU562
|
2.3
|
17.0
|
1.0
|
O
|
A:PHE556
|
2.4
|
25.7
|
1.0
|
O
|
A:HOH8872
|
2.6
|
38.5
|
1.0
|
O
|
A:HOH9020
|
2.7
|
33.7
|
1.0
|
C
|
A:TYR559
|
3.1
|
16.9
|
1.0
|
O
|
A:PRO560
|
3.3
|
20.5
|
1.0
|
C
|
A:LEU562
|
3.4
|
18.3
|
1.0
|
C
|
A:PHE556
|
3.5
|
25.1
|
1.0
|
C
|
A:PRO560
|
3.6
|
20.9
|
1.0
|
CA
|
A:PRO560
|
3.6
|
17.4
|
1.0
|
N
|
A:PRO560
|
3.7
|
12.0
|
1.0
|
N
|
A:LEU562
|
3.8
|
15.6
|
1.0
|
CA
|
A:LEU562
|
4.0
|
13.5
|
1.0
|
O
|
A:HOH8771
|
4.1
|
27.6
|
1.0
|
CA
|
A:PHE556
|
4.1
|
15.9
|
1.0
|
CB
|
A:LEU562
|
4.2
|
11.3
|
1.0
|
N
|
A:TYR559
|
4.3
|
17.4
|
1.0
|
CA
|
A:TYR559
|
4.3
|
11.0
|
1.0
|
N
|
A:GLN563
|
4.3
|
14.1
|
1.0
|
CA
|
A:GLN563
|
4.4
|
12.9
|
1.0
|
N
|
A:ARG561
|
4.5
|
13.2
|
1.0
|
O
|
A:HOH9111
|
4.5
|
50.7
|
1.0
|
N
|
A:ARG557
|
4.6
|
17.9
|
1.0
|
CG
|
A:GLN563
|
4.7
|
19.4
|
1.0
|
CD1
|
A:LEU350
|
4.7
|
17.0
|
1.0
|
CA
|
A:ARG557
|
4.8
|
20.2
|
1.0
|
C
|
A:ARG561
|
4.8
|
16.1
|
1.0
|
CB
|
A:TYR559
|
4.8
|
15.2
|
1.0
|
C
|
A:ARG557
|
4.8
|
27.3
|
1.0
|
O
|
A:ALA555
|
4.8
|
18.3
|
1.0
|
CB
|
A:PHE556
|
4.8
|
14.2
|
1.0
|
O
|
A:ARG557
|
4.9
|
23.8
|
1.0
|
|
Sodium binding site 3 out
of 12 in 1jz2
Go back to
Sodium Binding Sites List in 1jz2
Sodium binding site 3 out
of 12 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (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 (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3103
b:43.0
occ:1.00
|
O
|
A:THR970
|
2.6
|
39.9
|
1.0
|
O
|
A:PRO932
|
2.8
|
32.3
|
1.0
|
O
|
A:LEU967
|
2.9
|
25.1
|
1.0
|
O
|
A:HOH9075
|
3.0
|
46.5
|
1.0
|
O
|
A:HOH8702
|
3.2
|
22.3
|
1.0
|
O
|
A:HOH8967
|
3.3
|
47.7
|
1.0
|
CZ
|
A:PHE931
|
3.3
|
15.2
|
1.0
|
CE1
|
A:PHE931
|
3.6
|
24.9
|
1.0
|
C
|
A:THR970
|
3.7
|
37.5
|
1.0
|
C
|
A:PRO932
|
3.7
|
26.1
|
1.0
|
CE2
|
A:PHE931
|
3.7
|
22.2
|
1.0
|
O
|
A:MET968
|
3.8
|
25.1
|
1.0
|
C
|
A:MET968
|
4.0
|
38.6
|
1.0
|
C
|
A:LEU967
|
4.0
|
30.3
|
1.0
|
CA
|
A:MET968
|
4.1
|
30.9
|
1.0
|
CD
|
A:PRO932
|
4.2
|
19.2
|
1.0
|
CA
|
A:PRO932
|
4.2
|
33.5
|
1.0
|
CA
|
A:SER971
|
4.2
|
37.2
|
1.0
|
N
|
A:PRO932
|
4.2
|
30.2
|
1.0
|
CD1
|
A:PHE931
|
4.2
|
30.3
|
1.0
|
CB
|
A:PRO932
|
4.3
|
31.2
|
1.0
|
CD2
|
A:PHE931
|
4.3
|
22.8
|
1.0
|
N
|
A:SER971
|
4.4
|
31.2
|
1.0
|
N
|
A:THR970
|
4.4
|
28.2
|
1.0
|
N
|
A:MET968
|
4.6
|
27.5
|
1.0
|
CG
|
A:PHE931
|
4.6
|
25.5
|
1.0
|
CG
|
A:PRO932
|
4.6
|
24.5
|
1.0
|
CA
|
A:THR970
|
4.7
|
31.4
|
1.0
|
N
|
A:GLU969
|
4.7
|
33.5
|
1.0
|
N
|
A:SER933
|
4.8
|
19.9
|
1.0
|
C
|
A:GLU969
|
4.9
|
33.6
|
1.0
|
|
Sodium binding site 4 out
of 12 in 1jz2
Go back to
Sodium Binding Sites List in 1jz2
Sodium binding site 4 out
of 12 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (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 (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3101
b:19.6
occ:1.00
|
O
|
B:HOH8781
|
2.2
|
19.9
|
1.0
|
OD1
|
B:ASN604
|
2.3
|
26.8
|
1.0
|
OD2
|
B:ASP201
|
2.3
|
19.8
|
1.0
|
O
|
B:PHE601
|
2.4
|
24.0
|
1.0
|
O6
|
B:2FG2001
|
2.5
|
19.6
|
1.0
|
CE2
|
B:PHE601
|
3.1
|
37.5
|
1.0
|
CD2
|
B:PHE601
|
3.2
|
32.4
|
1.0
|
CG
|
B:ASP201
|
3.4
|
17.8
|
1.0
|
CG
|
B:ASN604
|
3.4
|
28.5
|
1.0
|
C
|
B:PHE601
|
3.6
|
25.4
|
1.0
|
C6
|
B:2FG2001
|
3.7
|
25.1
|
1.0
|
OD1
|
B:ASP201
|
3.7
|
28.1
|
1.0
|
CZ
|
B:PHE601
|
3.8
|
35.3
|
1.0
|
OH
|
B:TYR100
|
3.8
|
22.5
|
1.0
|
ND2
|
B:ASN604
|
3.9
|
24.3
|
1.0
|
CG
|
B:PHE601
|
3.9
|
22.9
|
1.0
|
C4
|
B:2FG2001
|
4.1
|
29.1
|
1.0
|
NE1
|
B:TRP568
|
4.2
|
16.0
|
1.0
|
O4
|
B:2FG2001
|
4.2
|
28.0
|
1.0
|
O
|
B:HOH8573
|
4.4
|
26.1
|
1.0
|
CE1
|
B:PHE601
|
4.4
|
36.0
|
1.0
|
N
|
B:CYS602
|
4.4
|
19.1
|
1.0
|
CA
|
B:CYS602
|
4.4
|
18.4
|
1.0
|
NE2
|
B:HIS540
|
4.4
|
18.8
|
1.0
|
C5
|
B:2FG2001
|
4.4
|
27.7
|
1.0
|
CD1
|
B:PHE601
|
4.5
|
23.8
|
1.0
|
CA
|
B:PHE601
|
4.6
|
21.2
|
1.0
|
CB
|
B:ASP201
|
4.6
|
13.9
|
1.0
|
CB
|
B:PHE601
|
4.6
|
23.3
|
1.0
|
CB
|
B:ASN604
|
4.7
|
14.2
|
1.0
|
O
|
B:ASP201
|
4.9
|
24.3
|
1.0
|
CE2
|
B:TRP568
|
4.9
|
22.7
|
1.0
|
CZ
|
B:TYR100
|
5.0
|
21.8
|
1.0
|
|
Sodium binding site 5 out
of 12 in 1jz2
Go back to
Sodium Binding Sites List in 1jz2
Sodium binding site 5 out
of 12 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (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 (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3102
b:20.8
occ:1.00
|
O
|
B:LEU562
|
2.1
|
16.3
|
1.0
|
O
|
B:HOH9039
|
2.2
|
35.0
|
1.0
|
O
|
B:TYR559
|
2.2
|
14.6
|
1.0
|
O
|
B:PHE556
|
2.3
|
18.1
|
1.0
|
O
|
B:HOH8887
|
2.7
|
33.3
|
1.0
|
O
|
B:PRO560
|
3.1
|
28.0
|
1.0
|
C
|
B:TYR559
|
3.2
|
14.2
|
1.0
|
C
|
B:LEU562
|
3.2
|
25.6
|
1.0
|
C
|
B:PHE556
|
3.4
|
19.9
|
1.0
|
C
|
B:PRO560
|
3.5
|
24.4
|
1.0
|
CA
|
B:PRO560
|
3.6
|
16.9
|
1.0
|
N
|
B:LEU562
|
3.7
|
13.8
|
1.0
|
N
|
B:PRO560
|
3.8
|
15.8
|
1.0
|
CA
|
B:LEU562
|
3.9
|
16.6
|
1.0
|
O
|
B:HOH9155
|
4.1
|
40.4
|
1.0
|
CA
|
B:PHE556
|
4.1
|
12.2
|
1.0
|
CB
|
B:LEU562
|
4.1
|
16.1
|
1.0
|
O
|
B:HOH8788
|
4.1
|
24.8
|
1.0
|
N
|
B:GLN563
|
4.2
|
25.7
|
1.0
|
CA
|
B:TYR559
|
4.3
|
15.6
|
1.0
|
N
|
B:TYR559
|
4.3
|
24.9
|
1.0
|
CA
|
B:GLN563
|
4.4
|
21.7
|
1.0
|
N
|
B:ARG561
|
4.4
|
17.6
|
1.0
|
N
|
B:ARG557
|
4.5
|
17.9
|
1.0
|
CB
|
B:PHE556
|
4.6
|
16.3
|
1.0
|
O
|
B:ARG557
|
4.6
|
22.8
|
1.0
|
C
|
B:ARG561
|
4.7
|
20.4
|
1.0
|
C
|
B:ARG557
|
4.7
|
20.5
|
1.0
|
CG
|
B:GLN563
|
4.8
|
18.7
|
1.0
|
O
|
B:HOH9138
|
4.8
|
42.8
|
1.0
|
CA
|
B:ARG557
|
4.8
|
15.2
|
1.0
|
CB
|
B:TYR559
|
4.8
|
13.9
|
1.0
|
O
|
B:ALA555
|
4.8
|
17.6
|
1.0
|
CD1
|
B:LEU350
|
4.9
|
14.9
|
1.0
|
|
Sodium binding site 6 out
of 12 in 1jz2
Go back to
Sodium Binding Sites List in 1jz2
Sodium binding site 6 out
of 12 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (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 (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3103
b:40.9
occ:1.00
|
O
|
B:LEU967
|
2.5
|
25.2
|
1.0
|
O
|
B:THR970
|
2.6
|
40.1
|
1.0
|
O
|
B:PRO932
|
2.6
|
20.4
|
1.0
|
O
|
B:HOH9103
|
2.7
|
31.3
|
1.0
|
O
|
B:HOH8985
|
3.0
|
38.5
|
1.0
|
O
|
B:HOH8718
|
3.1
|
32.8
|
1.0
|
CZ
|
B:PHE931
|
3.4
|
31.8
|
1.0
|
O
|
B:MET968
|
3.6
|
35.9
|
1.0
|
C
|
B:PRO932
|
3.6
|
29.2
|
1.0
|
C
|
B:LEU967
|
3.6
|
23.2
|
1.0
|
C
|
B:THR970
|
3.7
|
29.8
|
1.0
|
C
|
B:MET968
|
3.7
|
42.2
|
1.0
|
CE1
|
B:PHE931
|
3.7
|
28.0
|
1.0
|
CA
|
B:MET968
|
3.7
|
29.9
|
1.0
|
CE2
|
B:PHE931
|
3.8
|
29.0
|
1.0
|
CB
|
B:PRO932
|
4.0
|
24.6
|
1.0
|
CA
|
B:PRO932
|
4.1
|
22.6
|
1.0
|
N
|
B:THR970
|
4.2
|
33.3
|
1.0
|
N
|
B:MET968
|
4.2
|
21.6
|
1.0
|
N
|
B:PRO932
|
4.2
|
26.2
|
1.0
|
CD1
|
B:PHE931
|
4.3
|
26.5
|
1.0
|
CD2
|
B:PHE931
|
4.4
|
22.4
|
1.0
|
N
|
B:GLU969
|
4.4
|
35.5
|
1.0
|
N
|
B:SER971
|
4.5
|
26.1
|
1.0
|
CA
|
B:THR970
|
4.6
|
25.8
|
1.0
|
CD
|
B:PRO932
|
4.6
|
28.0
|
1.0
|
CG
|
B:PRO932
|
4.6
|
24.7
|
1.0
|
N
|
B:SER933
|
4.6
|
22.8
|
1.0
|
CG
|
B:PHE931
|
4.7
|
28.2
|
1.0
|
CA
|
B:SER971
|
4.7
|
26.6
|
1.0
|
CA
|
B:LEU967
|
4.9
|
26.0
|
1.0
|
C
|
B:GLU969
|
4.9
|
37.1
|
1.0
|
CA
|
B:SER933
|
5.0
|
18.9
|
1.0
|
CB
|
B:MET968
|
5.0
|
33.7
|
1.0
|
|
Sodium binding site 7 out
of 12 in 1jz2
Go back to
Sodium Binding Sites List in 1jz2
Sodium binding site 7 out
of 12 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (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 (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na3101
b:19.9
occ:1.00
|
O6
|
C:2FG2001
|
2.3
|
23.8
|
1.0
|
OD2
|
C:ASP201
|
2.4
|
28.3
|
1.0
|
O
|
C:HOH8780
|
2.5
|
23.4
|
1.0
|
OD1
|
C:ASN604
|
2.5
|
22.9
|
1.0
|
O
|
C:PHE601
|
2.6
|
18.0
|
1.0
|
CE2
|
C:PHE601
|
3.0
|
39.6
|
1.0
|
CD2
|
C:PHE601
|
3.1
|
42.6
|
1.0
|
CG
|
C:ASP201
|
3.3
|
38.7
|
1.0
|
CG
|
C:ASN604
|
3.5
|
35.9
|
1.0
|
C6
|
C:2FG2001
|
3.5
|
26.5
|
1.0
|
OD1
|
C:ASP201
|
3.6
|
36.5
|
1.0
|
C
|
C:PHE601
|
3.7
|
26.5
|
1.0
|
ND2
|
C:ASN604
|
3.7
|
21.2
|
1.0
|
CZ
|
C:PHE601
|
3.8
|
42.8
|
1.0
|
CG
|
C:PHE601
|
4.0
|
31.1
|
1.0
|
OH
|
C:TYR100
|
4.0
|
30.0
|
1.0
|
C4
|
C:2FG2001
|
4.0
|
23.1
|
1.0
|
O4
|
C:2FG2001
|
4.0
|
19.7
|
1.0
|
NE1
|
C:TRP568
|
4.2
|
26.1
|
1.0
|
NE2
|
C:HIS540
|
4.3
|
18.8
|
1.0
|
C5
|
C:2FG2001
|
4.3
|
25.7
|
1.0
|
O
|
C:HOH8566
|
4.4
|
18.3
|
1.0
|
CA
|
C:CYS602
|
4.4
|
16.0
|
1.0
|
N
|
C:CYS602
|
4.5
|
20.7
|
1.0
|
CE1
|
C:PHE601
|
4.5
|
39.2
|
1.0
|
CD1
|
C:PHE601
|
4.5
|
33.5
|
1.0
|
CB
|
C:ASP201
|
4.5
|
32.3
|
1.0
|
CA
|
C:PHE601
|
4.7
|
28.9
|
1.0
|
CB
|
C:PHE601
|
4.7
|
28.7
|
1.0
|
CE1
|
C:HIS540
|
4.8
|
23.4
|
1.0
|
CB
|
C:ASN604
|
4.9
|
17.8
|
1.0
|
C
|
C:CYS602
|
4.9
|
23.7
|
1.0
|
CE2
|
C:TRP568
|
4.9
|
30.6
|
1.0
|
O
|
C:ASP201
|
4.9
|
18.2
|
1.0
|
|
Sodium binding site 8 out
of 12 in 1jz2
Go back to
Sodium Binding Sites List in 1jz2
Sodium binding site 8 out
of 12 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic)
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-F-Galactosyl- Enzyme Intermediate (Orthorhombic) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na3102
b:23.7
occ:1.00
|
O
|
C:LEU562
|
2.2
|
18.2
|
1.0
|
O
|
C:PHE556
|
2.2
|
16.1
|
1.0
|
O
|
C:TYR559
|
2.3
|
18.4
|
1.0
|
O
|
C:HOH9031
|
2.5
|
38.6
|
1.0
|
O
|
C:HOH8883
|
2.7
|
26.9
|
1.0
|
O
|
C:PRO560
|
3.2
|
20.1
|
1.0
|
C
|
C:LEU562
|
3.3
|
24.4
|
1.0
|
C
|
C:TYR559
|
3.4
|
18.5
|
1.0
|
C
|
C:PHE556
|
3.4
|
23.7
|
1.0
|
C
|
C:PRO560
|
3.6
|
24.8
|
1.0
|
CA
|
C:PRO560
|
3.6
|
13.5
|
1.0
|
N
|
C:LEU562
|
3.9
|
21.0
|
1.0
|
N
|
C:PRO560
|
4.0
|
18.2
|
1.0
|
CA
|
C:LEU562
|
4.0
|
15.5
|
1.0
|
CA
|
C:PHE556
|
4.1
|
13.7
|
1.0
|
O
|
C:HOH8787
|
4.1
|
26.8
|
1.0
|
N
|
C:GLN563
|
4.3
|
18.2
|
1.0
|
CB
|
C:LEU562
|
4.3
|
16.6
|
1.0
|
N
|
C:TYR559
|
4.4
|
23.2
|
1.0
|
N
|
C:ARG557
|
4.4
|
21.1
|
1.0
|
CA
|
C:TYR559
|
4.4
|
15.5
|
1.0
|
CA
|
C:GLN563
|
4.5
|
19.3
|
1.0
|
O
|
C:HOH9187
|
4.5
|
49.2
|
1.0
|
O
|
C:ARG557
|
4.6
|
24.1
|
1.0
|
N
|
C:ARG561
|
4.6
|
11.7
|
1.0
|
CA
|
C:ARG557
|
4.6
|
18.5
|
1.0
|
C
|
C:ARG557
|
4.6
|
29.6
|
1.0
|
CB
|
C:PHE556
|
4.7
|
16.5
|
1.0
|
CG
|
C:GLN563
|
4.8
|
11.7
|
1.0
|
O
|
C:ALA555
|
4.8
|
18.2
|
1.0
|
C
|
C:ARG561
|
4.9
|
23.6
|
1.0
|
CD1
|
C:LEU350
|
4.9
|
16.2
|
1.0
|
CB
|
C:TYR559
|
5.0
|
15.3
|
1.0
|
|
Sodium binding site 9 out
of 12 in 1jz2
Go back to
Sodium Binding Sites List in 1jz2
Sodium binding site 9 out
of 12 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic)
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-F-Galactosyl- Enzyme Intermediate (Orthorhombic) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na3103
b:48.0
occ:1.00
|
O
|
C:THR970
|
2.6
|
36.0
|
1.0
|
O
|
C:HOH8717
|
2.8
|
35.6
|
1.0
|
O
|
C:LEU967
|
2.9
|
30.4
|
1.0
|
O
|
C:PRO932
|
2.9
|
25.6
|
1.0
|
O
|
C:HOH9085
|
3.0
|
59.5
|
1.0
|
O
|
C:HOH8976
|
3.2
|
37.9
|
1.0
|
CZ
|
C:PHE931
|
3.4
|
27.8
|
1.0
|
O
|
C:MET968
|
3.4
|
35.0
|
1.0
|
C
|
C:MET968
|
3.6
|
38.0
|
1.0
|
CE1
|
C:PHE931
|
3.6
|
31.9
|
1.0
|
C
|
C:THR970
|
3.7
|
41.8
|
1.0
|
CA
|
C:MET968
|
3.8
|
29.5
|
1.0
|
CE2
|
C:PHE931
|
3.9
|
24.1
|
1.0
|
C
|
C:PRO932
|
3.9
|
21.1
|
1.0
|
C
|
C:LEU967
|
4.0
|
29.4
|
1.0
|
N
|
C:THR970
|
4.1
|
37.5
|
1.0
|
CD1
|
C:PHE931
|
4.4
|
26.2
|
1.0
|
N
|
C:GLU969
|
4.4
|
39.2
|
1.0
|
CB
|
C:PRO932
|
4.4
|
24.7
|
1.0
|
N
|
C:MET968
|
4.5
|
29.2
|
1.0
|
N
|
C:SER971
|
4.5
|
31.2
|
1.0
|
CA
|
C:THR970
|
4.5
|
40.8
|
1.0
|
CA
|
C:PRO932
|
4.6
|
26.4
|
1.0
|
CD2
|
C:PHE931
|
4.6
|
23.5
|
1.0
|
CG
|
C:PRO932
|
4.7
|
23.2
|
1.0
|
N
|
C:PRO932
|
4.7
|
26.8
|
1.0
|
CA
|
C:SER971
|
4.7
|
40.4
|
1.0
|
C
|
C:GLU969
|
4.8
|
42.1
|
1.0
|
CD
|
C:PRO932
|
4.8
|
22.1
|
1.0
|
CG
|
C:PHE931
|
4.8
|
29.3
|
1.0
|
CB
|
C:MET968
|
4.9
|
32.3
|
1.0
|
N
|
C:SER933
|
4.9
|
18.2
|
1.0
|
CA
|
C:GLU969
|
5.0
|
37.2
|
1.0
|
|
Sodium binding site 10 out
of 12 in 1jz2
Go back to
Sodium Binding Sites List in 1jz2
Sodium binding site 10 out
of 12 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic)
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-F-Galactosyl- Enzyme Intermediate (Orthorhombic) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na3101
b:21.6
occ:1.00
|
OD2
|
D:ASP201
|
2.3
|
21.6
|
1.0
|
O
|
D:HOH8796
|
2.4
|
22.3
|
1.0
|
OD1
|
D:ASN604
|
2.4
|
21.2
|
1.0
|
O
|
D:PHE601
|
2.5
|
31.5
|
1.0
|
O6
|
D:2FG2001
|
2.7
|
20.1
|
1.0
|
CE2
|
D:PHE601
|
3.0
|
42.1
|
1.0
|
CG
|
D:ASP201
|
3.2
|
33.0
|
1.0
|
CD2
|
D:PHE601
|
3.2
|
36.5
|
1.0
|
OD1
|
D:ASP201
|
3.5
|
22.9
|
1.0
|
CG
|
D:ASN604
|
3.5
|
11.5
|
1.0
|
C
|
D:PHE601
|
3.6
|
27.4
|
1.0
|
CZ
|
D:PHE601
|
3.7
|
50.0
|
1.0
|
OH
|
D:TYR100
|
3.8
|
20.1
|
1.0
|
ND2
|
D:ASN604
|
3.9
|
17.1
|
1.0
|
C6
|
D:2FG2001
|
3.9
|
23.9
|
1.0
|
O4
|
D:2FG2001
|
4.0
|
18.5
|
1.0
|
CG
|
D:PHE601
|
4.0
|
35.6
|
1.0
|
NE1
|
D:TRP568
|
4.0
|
24.9
|
1.0
|
C4
|
D:2FG2001
|
4.1
|
23.2
|
1.0
|
CA
|
D:CYS602
|
4.3
|
17.8
|
1.0
|
O
|
D:HOH8584
|
4.3
|
23.4
|
1.0
|
CB
|
D:ASP201
|
4.4
|
22.9
|
1.0
|
N
|
D:CYS602
|
4.4
|
21.2
|
1.0
|
CE1
|
D:PHE601
|
4.4
|
46.1
|
1.0
|
NE2
|
D:HIS540
|
4.5
|
24.1
|
1.0
|
CD1
|
D:PHE601
|
4.5
|
36.6
|
1.0
|
C5
|
D:2FG2001
|
4.6
|
24.2
|
1.0
|
O
|
D:ASP201
|
4.6
|
15.3
|
1.0
|
CA
|
D:PHE601
|
4.7
|
21.5
|
1.0
|
CB
|
D:PHE601
|
4.8
|
27.2
|
1.0
|
CB
|
D:ASN604
|
4.8
|
12.3
|
1.0
|
CE2
|
D:TRP568
|
4.8
|
27.3
|
1.0
|
C
|
D:CYS602
|
4.9
|
22.0
|
1.0
|
CZ2
|
D:TRP568
|
4.9
|
20.7
|
1.0
|
CZ
|
D:TYR100
|
5.0
|
26.3
|
1.0
|
CD1
|
D:TRP568
|
5.0
|
27.7
|
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 19:02:59 2024
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