Sodium in PDB 3i3b: E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on
Enzymatic activity of E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on
All present enzymatic activity of E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on:
3.2.1.23;
Protein crystallography data
The structure of E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on, PDB code: 3i3b
was solved by
M.L.Dugdale,
D.Dymianiw,
B.Minhas,
R.E.Huber,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
14.18 /
2.20
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
149.600,
168.420,
201.310,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.3 /
24.4
|
Other elements in 3i3b:
The structure of E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-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 (M542A) in Complex with D- Galactopyranosyl-1-on
(pdb code 3i3b). 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 (M542A) in Complex with D- Galactopyranosyl-1-on, PDB code: 3i3b:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 16 in 3i3b
Go back to
Sodium Binding Sites List in 3i3b
Sodium binding site 1 out
of 16 in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-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 (M542A) in Complex with D- Galactopyranosyl-1-on within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3101
b:13.8
occ:1.00
|
O6
|
A:1492001
|
2.3
|
14.0
|
1.0
|
OD1
|
A:ASN604
|
2.3
|
12.1
|
1.0
|
OD2
|
A:ASP201
|
2.4
|
18.2
|
1.0
|
O
|
A:HOH4270
|
2.4
|
13.5
|
1.0
|
O
|
A:PHE601
|
2.4
|
19.5
|
1.0
|
CG
|
A:ASP201
|
3.4
|
17.5
|
1.0
|
CG
|
A:ASN604
|
3.4
|
14.9
|
1.0
|
C6
|
A:1492001
|
3.4
|
13.3
|
1.0
|
CD1
|
A:PHE601
|
3.6
|
17.7
|
1.0
|
C
|
A:PHE601
|
3.6
|
19.2
|
1.0
|
CE1
|
A:PHE601
|
3.7
|
17.2
|
1.0
|
OD1
|
A:ASP201
|
3.8
|
18.4
|
1.0
|
ND2
|
A:ASN604
|
3.8
|
15.3
|
1.0
|
CG
|
A:PHE601
|
3.9
|
19.6
|
1.0
|
OH
|
A:TYR100
|
3.9
|
18.2
|
1.0
|
O4
|
A:1492001
|
4.0
|
18.0
|
1.0
|
CZ
|
A:PHE601
|
4.1
|
17.5
|
1.0
|
C4
|
A:1492001
|
4.1
|
15.2
|
1.0
|
NE1
|
A:TRP568
|
4.2
|
10.9
|
1.0
|
CD2
|
A:PHE601
|
4.3
|
17.5
|
1.0
|
C5
|
A:1492001
|
4.3
|
12.9
|
1.0
|
CA
|
A:CYS602
|
4.4
|
17.2
|
1.0
|
CE2
|
A:PHE601
|
4.4
|
17.8
|
1.0
|
NE2
|
A:HIS540
|
4.4
|
11.5
|
1.0
|
N
|
A:CYS602
|
4.5
|
18.1
|
1.0
|
O
|
A:HOH4050
|
4.5
|
18.3
|
1.0
|
CB
|
A:PHE601
|
4.6
|
19.2
|
1.0
|
CB
|
A:ASP201
|
4.6
|
15.8
|
1.0
|
CA
|
A:PHE601
|
4.6
|
20.8
|
1.0
|
CB
|
A:ASN604
|
4.7
|
11.0
|
1.0
|
O
|
A:ASP201
|
4.7
|
12.2
|
1.0
|
C
|
A:CYS602
|
4.9
|
16.9
|
1.0
|
CE2
|
A:TRP568
|
4.9
|
13.1
|
1.0
|
CE1
|
A:HIS540
|
5.0
|
12.9
|
1.0
|
|
Sodium binding site 2 out
of 16 in 3i3b
Go back to
Sodium Binding Sites List in 3i3b
Sodium binding site 2 out
of 16 in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-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 (M542A) in Complex with D- Galactopyranosyl-1-on within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3102
b:21.8
occ:1.00
|
O
|
A:PHE556
|
2.3
|
15.3
|
1.0
|
O
|
A:LEU562
|
2.3
|
8.7
|
1.0
|
O
|
A:TYR559
|
2.4
|
13.2
|
1.0
|
O
|
A:HOH4387
|
2.7
|
22.9
|
1.0
|
O
|
A:HOH4557
|
2.8
|
32.4
|
1.0
|
O
|
A:PRO560
|
3.2
|
10.7
|
1.0
|
C
|
A:TYR559
|
3.3
|
11.8
|
1.0
|
C
|
A:LEU562
|
3.4
|
7.8
|
1.0
|
C
|
A:PHE556
|
3.4
|
14.5
|
1.0
|
C
|
A:PRO560
|
3.6
|
10.6
|
1.0
|
CA
|
A:PRO560
|
3.7
|
9.6
|
1.0
|
O
|
A:HOH4277
|
3.9
|
14.1
|
1.0
|
O
|
A:HOH4672
|
3.9
|
46.6
|
1.0
|
N
|
A:PRO560
|
3.9
|
10.2
|
1.0
|
N
|
A:LEU562
|
3.9
|
7.3
|
1.0
|
CA
|
A:PHE556
|
4.1
|
12.9
|
1.0
|
CA
|
A:LEU562
|
4.2
|
8.4
|
1.0
|
CB
|
A:LEU562
|
4.3
|
6.9
|
1.0
|
N
|
A:GLN563
|
4.3
|
9.9
|
1.0
|
CA
|
A:GLN563
|
4.4
|
10.8
|
1.0
|
CA
|
A:TYR559
|
4.5
|
11.8
|
1.0
|
N
|
A:ARG557
|
4.5
|
12.9
|
1.0
|
N
|
A:ARG561
|
4.5
|
9.4
|
1.0
|
N
|
A:TYR559
|
4.5
|
12.6
|
1.0
|
CG
|
A:GLN563
|
4.6
|
10.5
|
1.0
|
CA
|
A:ARG557
|
4.7
|
12.3
|
1.0
|
CB
|
A:PHE556
|
4.7
|
13.4
|
1.0
|
C
|
A:ARG561
|
4.8
|
9.0
|
1.0
|
C
|
A:ARG557
|
4.8
|
12.3
|
1.0
|
O
|
A:ALA555
|
4.9
|
13.0
|
1.0
|
|
Sodium binding site 3 out
of 16 in 3i3b
Go back to
Sodium Binding Sites List in 3i3b
Sodium binding site 3 out
of 16 in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-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 (M542A) in Complex with D- Galactopyranosyl-1-on within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3103
b:39.5
occ:1.00
|
O
|
A:THR970
|
2.5
|
26.4
|
1.0
|
O
|
A:LEU967
|
2.9
|
21.6
|
1.0
|
O
|
A:PRO932
|
3.0
|
17.5
|
1.0
|
O
|
A:HOH4807
|
3.1
|
39.4
|
1.0
|
CZ
|
A:PHE931
|
3.2
|
28.1
|
1.0
|
O
|
A:HOH4624
|
3.3
|
37.7
|
1.0
|
CE1
|
A:PHE931
|
3.4
|
28.8
|
1.0
|
O
|
A:HOH4202
|
3.4
|
17.2
|
1.0
|
C
|
A:THR970
|
3.6
|
27.0
|
1.0
|
O
|
A:MET968
|
3.7
|
24.8
|
1.0
|
CE2
|
A:PHE931
|
3.8
|
27.5
|
1.0
|
C
|
A:PRO932
|
3.9
|
17.7
|
1.0
|
CD1
|
A:PHE931
|
4.1
|
27.2
|
1.0
|
CD
|
A:PRO932
|
4.1
|
18.5
|
1.0
|
C
|
A:MET968
|
4.1
|
26.4
|
1.0
|
C
|
A:LEU967
|
4.1
|
22.2
|
1.0
|
CB
|
A:PRO932
|
4.1
|
19.2
|
1.0
|
N
|
A:THR970
|
4.3
|
26.8
|
1.0
|
N
|
A:PRO932
|
4.3
|
20.3
|
1.0
|
CA
|
A:PRO932
|
4.3
|
19.0
|
1.0
|
CD2
|
A:PHE931
|
4.4
|
27.0
|
1.0
|
CA
|
A:MET968
|
4.4
|
25.8
|
1.0
|
N
|
A:SER971
|
4.4
|
25.4
|
1.0
|
CA
|
A:SER971
|
4.4
|
24.7
|
1.0
|
CA
|
A:THR970
|
4.5
|
27.7
|
1.0
|
CG
|
A:PHE931
|
4.6
|
25.8
|
1.0
|
CG
|
A:PRO932
|
4.7
|
18.5
|
1.0
|
N
|
A:MET968
|
4.7
|
23.1
|
1.0
|
N
|
A:GLU969
|
4.8
|
26.0
|
1.0
|
C
|
A:GLU969
|
4.9
|
27.8
|
1.0
|
|
Sodium binding site 4 out
of 16 in 3i3b
Go back to
Sodium Binding Sites List in 3i3b
Sodium binding site 4 out
of 16 in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-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 (M542A) in Complex with D- Galactopyranosyl-1-on within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na3104
b:28.4
occ:1.00
|
O
|
A:DMS5018
|
2.4
|
55.2
|
1.0
|
O
|
A:LEU670
|
2.6
|
27.9
|
1.0
|
O
|
A:SER647
|
2.6
|
24.8
|
1.0
|
O
|
A:GLU650
|
2.7
|
20.4
|
1.0
|
S
|
A:DMS5018
|
3.5
|
56.3
|
1.0
|
N
|
A:GLU650
|
3.6
|
21.7
|
1.0
|
C
|
A:LEU670
|
3.6
|
28.2
|
1.0
|
C
|
A:GLU650
|
3.7
|
22.6
|
1.0
|
C1
|
A:DMS5018
|
3.8
|
55.2
|
1.0
|
C
|
A:SER647
|
3.8
|
23.9
|
1.0
|
N
|
A:LEU670
|
3.9
|
29.5
|
1.0
|
C
|
A:ASP648
|
4.1
|
24.2
|
1.0
|
N
|
A:ASN649
|
4.1
|
23.4
|
1.0
|
CA
|
A:LEU670
|
4.1
|
29.3
|
1.0
|
CA
|
A:GLU650
|
4.2
|
21.7
|
1.0
|
CA
|
A:ASP648
|
4.2
|
24.6
|
1.0
|
CB
|
A:LEU670
|
4.2
|
29.6
|
1.0
|
OG
|
A:SER647
|
4.4
|
20.4
|
1.0
|
N
|
A:ASP648
|
4.5
|
23.2
|
1.0
|
O
|
A:ASP648
|
4.6
|
23.4
|
1.0
|
CB
|
A:GLU650
|
4.6
|
20.3
|
1.0
|
C
|
A:ASN649
|
4.6
|
21.6
|
1.0
|
CA
|
A:ASN649
|
4.7
|
21.6
|
1.0
|
N
|
A:ASP671
|
4.7
|
27.5
|
1.0
|
CB
|
A:SER647
|
4.8
|
21.7
|
1.0
|
O
|
A:HOH4674
|
4.9
|
34.8
|
1.0
|
OE1
|
A:GLU650
|
4.9
|
15.3
|
1.0
|
N
|
A:LEU651
|
4.9
|
23.6
|
1.0
|
C
|
A:PRO669
|
4.9
|
29.6
|
1.0
|
CA
|
A:SER647
|
5.0
|
23.1
|
1.0
|
C2
|
A:DMS5018
|
5.0
|
55.5
|
1.0
|
|
Sodium binding site 5 out
of 16 in 3i3b
Go back to
Sodium Binding Sites List in 3i3b
Sodium binding site 5 out
of 16 in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-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 (M542A) in Complex with D- Galactopyranosyl-1-on within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3101
b:15.9
occ:1.00
|
O6
|
B:1492001
|
2.3
|
12.3
|
1.0
|
OD2
|
B:ASP201
|
2.5
|
17.8
|
1.0
|
O
|
B:PHE601
|
2.5
|
14.7
|
1.0
|
OD1
|
B:ASN604
|
2.5
|
12.6
|
1.0
|
O
|
B:HOH4270
|
2.6
|
12.0
|
1.0
|
CD1
|
B:PHE601
|
3.3
|
14.4
|
1.0
|
CE1
|
B:PHE601
|
3.3
|
14.3
|
1.0
|
C6
|
B:1492001
|
3.3
|
11.1
|
1.0
|
CG
|
B:ASP201
|
3.4
|
14.2
|
1.0
|
CG
|
B:ASN604
|
3.5
|
12.8
|
1.0
|
C
|
B:PHE601
|
3.7
|
15.0
|
1.0
|
ND2
|
B:ASN604
|
3.8
|
10.9
|
1.0
|
OD1
|
B:ASP201
|
3.8
|
16.3
|
1.0
|
OH
|
B:TYR100
|
3.9
|
12.5
|
1.0
|
CG
|
B:PHE601
|
3.9
|
16.1
|
1.0
|
O4
|
B:1492001
|
4.0
|
16.4
|
1.0
|
CZ
|
B:PHE601
|
4.0
|
13.2
|
1.0
|
C4
|
B:1492001
|
4.1
|
13.6
|
1.0
|
NE1
|
B:TRP568
|
4.2
|
4.9
|
1.0
|
C5
|
B:1492001
|
4.2
|
12.6
|
1.0
|
NE2
|
B:HIS540
|
4.4
|
12.3
|
1.0
|
CA
|
B:CYS602
|
4.4
|
16.2
|
1.0
|
CD2
|
B:PHE601
|
4.5
|
16.0
|
1.0
|
N
|
B:CYS602
|
4.5
|
14.0
|
1.0
|
CE2
|
B:PHE601
|
4.5
|
16.1
|
1.0
|
O
|
B:HOH4052
|
4.6
|
12.7
|
1.0
|
CB
|
B:PHE601
|
4.6
|
15.1
|
1.0
|
CB
|
B:ASP201
|
4.7
|
14.5
|
1.0
|
CA
|
B:PHE601
|
4.7
|
15.9
|
1.0
|
O
|
B:ASP201
|
4.7
|
12.8
|
1.0
|
CB
|
B:ASN604
|
4.8
|
12.6
|
1.0
|
C
|
B:CYS602
|
4.9
|
16.1
|
1.0
|
CE1
|
B:HIS540
|
4.9
|
12.0
|
1.0
|
CE2
|
B:TRP568
|
5.0
|
6.2
|
1.0
|
|
Sodium binding site 6 out
of 16 in 3i3b
Go back to
Sodium Binding Sites List in 3i3b
Sodium binding site 6 out
of 16 in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-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 (M542A) in Complex with D- Galactopyranosyl-1-on within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3102
b:16.4
occ:1.00
|
O
|
B:TYR559
|
2.2
|
13.8
|
1.0
|
O
|
B:PHE556
|
2.3
|
7.4
|
1.0
|
O
|
B:LEU562
|
2.4
|
10.8
|
1.0
|
O
|
B:HOH4387
|
2.6
|
32.7
|
1.0
|
O
|
B:HOH4575
|
2.8
|
21.7
|
1.0
|
C
|
B:TYR559
|
3.2
|
14.1
|
1.0
|
O
|
B:PRO560
|
3.4
|
14.0
|
1.0
|
C
|
B:LEU562
|
3.4
|
9.6
|
1.0
|
C
|
B:PHE556
|
3.5
|
9.7
|
1.0
|
C
|
B:PRO560
|
3.6
|
11.9
|
1.0
|
CA
|
B:PRO560
|
3.6
|
11.9
|
1.0
|
N
|
B:PRO560
|
3.8
|
12.4
|
1.0
|
N
|
B:LEU562
|
3.9
|
8.9
|
1.0
|
O
|
B:HOH4277
|
4.1
|
17.6
|
1.0
|
CA
|
B:LEU562
|
4.1
|
10.5
|
1.0
|
CA
|
B:PHE556
|
4.2
|
8.5
|
1.0
|
CB
|
B:LEU562
|
4.3
|
5.7
|
1.0
|
N
|
B:GLN563
|
4.3
|
9.8
|
1.0
|
CA
|
B:TYR559
|
4.3
|
13.5
|
1.0
|
CA
|
B:GLN563
|
4.4
|
9.4
|
1.0
|
N
|
B:TYR559
|
4.4
|
13.2
|
1.0
|
N
|
B:ARG561
|
4.5
|
10.9
|
1.0
|
N
|
B:ARG557
|
4.5
|
9.9
|
1.0
|
CG
|
B:GLN563
|
4.7
|
10.4
|
1.0
|
CA
|
B:ARG557
|
4.7
|
10.1
|
1.0
|
CB
|
B:PHE556
|
4.8
|
8.7
|
1.0
|
C
|
B:ARG561
|
4.8
|
10.6
|
1.0
|
C
|
B:ARG557
|
4.8
|
10.6
|
1.0
|
CB
|
B:TYR559
|
4.9
|
12.4
|
1.0
|
CD1
|
B:LEU350
|
4.9
|
8.3
|
1.0
|
O
|
B:ARG557
|
4.9
|
9.0
|
1.0
|
O
|
B:ALA555
|
5.0
|
8.9
|
1.0
|
|
Sodium binding site 7 out
of 16 in 3i3b
Go back to
Sodium Binding Sites List in 3i3b
Sodium binding site 7 out
of 16 in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-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 (M542A) in Complex with D- Galactopyranosyl-1-on within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3103
b:23.9
occ:1.00
|
O
|
B:LEU967
|
2.5
|
16.3
|
1.0
|
O
|
B:PRO932
|
2.6
|
21.7
|
1.0
|
O
|
B:THR970
|
2.8
|
24.6
|
1.0
|
O
|
B:HOH4204
|
3.0
|
22.5
|
1.0
|
C
|
B:PRO932
|
3.5
|
20.3
|
1.0
|
CZ
|
B:PHE931
|
3.5
|
18.7
|
1.0
|
O
|
B:HOH4651
|
3.6
|
35.1
|
1.0
|
C
|
B:LEU967
|
3.7
|
17.2
|
1.0
|
CE2
|
B:PHE931
|
3.7
|
20.6
|
1.0
|
C
|
B:THR970
|
3.8
|
24.2
|
1.0
|
CB
|
B:PRO932
|
3.8
|
21.3
|
1.0
|
O
|
B:HOH4510
|
3.9
|
23.9
|
1.0
|
O
|
B:MET968
|
4.0
|
22.3
|
1.0
|
CA
|
B:PRO932
|
4.0
|
20.8
|
1.0
|
CE1
|
B:PHE931
|
4.0
|
20.2
|
1.0
|
C
|
B:MET968
|
4.1
|
23.3
|
1.0
|
N
|
B:PRO932
|
4.1
|
21.6
|
1.0
|
CA
|
B:MET968
|
4.1
|
22.4
|
1.0
|
CD
|
B:PRO932
|
4.3
|
20.6
|
1.0
|
N
|
B:THR970
|
4.3
|
23.8
|
1.0
|
CD2
|
B:PHE931
|
4.3
|
19.9
|
1.0
|
N
|
B:MET968
|
4.3
|
18.7
|
1.0
|
N
|
B:SER933
|
4.5
|
17.4
|
1.0
|
N
|
B:SER971
|
4.5
|
23.7
|
1.0
|
CD1
|
B:PHE931
|
4.6
|
19.8
|
1.0
|
CA
|
B:SER971
|
4.6
|
22.6
|
1.0
|
CG
|
B:PRO932
|
4.6
|
20.2
|
1.0
|
CA
|
B:THR970
|
4.7
|
23.3
|
1.0
|
CG
|
B:PHE931
|
4.7
|
20.7
|
1.0
|
N
|
B:GLU969
|
4.7
|
24.3
|
1.0
|
C
|
B:PHE931
|
4.8
|
20.5
|
1.0
|
CA
|
B:LEU967
|
4.8
|
17.1
|
1.0
|
CA
|
B:SER933
|
4.9
|
16.1
|
1.0
|
|
Sodium binding site 8 out
of 16 in 3i3b
Go back to
Sodium Binding Sites List in 3i3b
Sodium binding site 8 out
of 16 in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-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 (M542A) in Complex with D- Galactopyranosyl-1-on within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na3104
b:31.1
occ:1.00
|
O
|
B:DMS5021
|
2.4
|
66.5
|
1.0
|
O
|
B:GLU650
|
2.5
|
23.4
|
1.0
|
O
|
B:SER647
|
2.6
|
14.9
|
1.0
|
O
|
B:LEU670
|
2.8
|
22.4
|
1.0
|
O
|
B:HOH4662
|
3.0
|
43.7
|
1.0
|
C1
|
B:DMS5021
|
3.1
|
66.6
|
1.0
|
N
|
B:GLU650
|
3.1
|
20.0
|
1.0
|
S
|
B:DMS5021
|
3.3
|
66.7
|
1.0
|
C
|
B:GLU650
|
3.4
|
22.5
|
1.0
|
N
|
B:ASN649
|
3.6
|
20.2
|
1.0
|
C
|
B:SER647
|
3.7
|
16.1
|
1.0
|
CA
|
B:GLU650
|
3.7
|
21.6
|
1.0
|
C
|
B:ASP648
|
3.8
|
20.5
|
1.0
|
CA
|
B:ASP648
|
3.9
|
20.1
|
1.0
|
C
|
B:LEU670
|
3.9
|
23.8
|
1.0
|
N
|
B:LEU670
|
4.1
|
25.2
|
1.0
|
C
|
B:ASN649
|
4.1
|
19.4
|
1.0
|
CA
|
B:ASN649
|
4.2
|
18.3
|
1.0
|
N
|
B:ASP648
|
4.2
|
18.3
|
1.0
|
CB
|
B:GLU650
|
4.2
|
21.4
|
1.0
|
C2
|
B:DMS5021
|
4.2
|
67.1
|
1.0
|
O
|
B:ASP648
|
4.4
|
19.9
|
1.0
|
CA
|
B:LEU670
|
4.4
|
24.2
|
1.0
|
CB
|
B:LEU670
|
4.5
|
24.2
|
1.0
|
OE1
|
B:GLU650
|
4.6
|
18.4
|
1.0
|
N
|
B:LEU651
|
4.7
|
22.5
|
1.0
|
OG
|
B:SER647
|
4.7
|
14.2
|
1.0
|
CB
|
B:SER647
|
4.8
|
16.6
|
1.0
|
O
|
B:HOH4704
|
4.8
|
40.0
|
1.0
|
CA
|
B:SER647
|
4.9
|
15.6
|
1.0
|
C
|
B:PRO669
|
5.0
|
25.9
|
1.0
|
|
Sodium binding site 9 out
of 16 in 3i3b
Go back to
Sodium Binding Sites List in 3i3b
Sodium binding site 9 out
of 16 in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-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 (M542A) in Complex with D- Galactopyranosyl-1-on within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na3101
b:13.8
occ:1.00
|
O6
|
C:1492001
|
2.3
|
9.3
|
1.0
|
OD2
|
C:ASP201
|
2.4
|
10.9
|
1.0
|
OD1
|
C:ASN604
|
2.4
|
12.8
|
1.0
|
O
|
C:PHE601
|
2.5
|
14.7
|
1.0
|
O
|
C:HOH4276
|
2.6
|
15.4
|
1.0
|
CD2
|
C:PHE601
|
3.2
|
12.7
|
1.0
|
CE2
|
C:PHE601
|
3.3
|
12.5
|
1.0
|
C6
|
C:1492001
|
3.3
|
9.9
|
1.0
|
CG
|
C:ASN604
|
3.4
|
13.6
|
1.0
|
CG
|
C:ASP201
|
3.5
|
11.3
|
1.0
|
C
|
C:PHE601
|
3.6
|
16.3
|
1.0
|
ND2
|
C:ASN604
|
3.7
|
11.8
|
1.0
|
CG
|
C:PHE601
|
3.8
|
12.6
|
1.0
|
OD1
|
C:ASP201
|
3.9
|
11.7
|
1.0
|
CZ
|
C:PHE601
|
3.9
|
10.0
|
1.0
|
OH
|
C:TYR100
|
3.9
|
15.9
|
1.0
|
O4
|
C:1492001
|
4.0
|
13.8
|
1.0
|
C4
|
C:1492001
|
4.1
|
13.0
|
1.0
|
C5
|
C:1492001
|
4.2
|
11.5
|
1.0
|
NE1
|
C:TRP568
|
4.3
|
7.9
|
1.0
|
CD1
|
C:PHE601
|
4.4
|
10.9
|
1.0
|
NE2
|
C:HIS540
|
4.4
|
9.9
|
1.0
|
CA
|
C:CYS602
|
4.4
|
17.2
|
1.0
|
CE1
|
C:PHE601
|
4.4
|
11.8
|
1.0
|
N
|
C:CYS602
|
4.5
|
16.0
|
1.0
|
CB
|
C:PHE601
|
4.5
|
14.5
|
1.0
|
CA
|
C:PHE601
|
4.6
|
16.5
|
1.0
|
O
|
C:HOH4054
|
4.6
|
13.6
|
1.0
|
CB
|
C:ASP201
|
4.7
|
9.9
|
1.0
|
CB
|
C:ASN604
|
4.8
|
13.9
|
1.0
|
O
|
C:ASP201
|
4.9
|
11.1
|
1.0
|
CE1
|
C:HIS540
|
4.9
|
10.5
|
1.0
|
C
|
C:CYS602
|
4.9
|
16.5
|
1.0
|
CE2
|
C:TRP568
|
5.0
|
7.1
|
1.0
|
|
Sodium binding site 10 out
of 16 in 3i3b
Go back to
Sodium Binding Sites List in 3i3b
Sodium binding site 10 out
of 16 in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-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 (M542A) in Complex with D- Galactopyranosyl-1-on within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na3102
b:14.7
occ:1.00
|
O
|
C:PHE556
|
2.2
|
6.4
|
1.0
|
O
|
C:TYR559
|
2.2
|
10.3
|
1.0
|
O
|
C:LEU562
|
2.4
|
14.1
|
1.0
|
O
|
C:HOH4392
|
2.5
|
20.9
|
1.0
|
O
|
C:HOH4565
|
2.8
|
27.2
|
1.0
|
C
|
C:TYR559
|
3.2
|
10.9
|
1.0
|
O
|
C:PRO560
|
3.3
|
10.7
|
1.0
|
C
|
C:PHE556
|
3.4
|
9.3
|
1.0
|
C
|
C:LEU562
|
3.4
|
11.5
|
1.0
|
C
|
C:PRO560
|
3.6
|
10.8
|
1.0
|
CA
|
C:PRO560
|
3.6
|
9.9
|
1.0
|
N
|
C:PRO560
|
3.8
|
9.3
|
1.0
|
N
|
C:LEU562
|
3.9
|
11.0
|
1.0
|
CA
|
C:PHE556
|
4.1
|
8.9
|
1.0
|
O
|
C:HOH4283
|
4.1
|
14.2
|
1.0
|
CA
|
C:LEU562
|
4.1
|
12.0
|
1.0
|
CB
|
C:LEU562
|
4.3
|
8.2
|
1.0
|
N
|
C:GLN563
|
4.4
|
11.5
|
1.0
|
CA
|
C:TYR559
|
4.4
|
12.1
|
1.0
|
N
|
C:ARG557
|
4.4
|
11.1
|
1.0
|
N
|
C:TYR559
|
4.4
|
12.1
|
1.0
|
CA
|
C:GLN563
|
4.5
|
12.0
|
1.0
|
N
|
C:ARG561
|
4.5
|
10.3
|
1.0
|
CA
|
C:ARG557
|
4.6
|
10.1
|
1.0
|
CG
|
C:GLN563
|
4.7
|
13.8
|
1.0
|
C
|
C:ARG557
|
4.7
|
11.9
|
1.0
|
CB
|
C:PHE556
|
4.7
|
8.6
|
1.0
|
C
|
C:ARG561
|
4.8
|
11.7
|
1.0
|
O
|
C:ALA555
|
4.8
|
9.4
|
1.0
|
O
|
C:ARG557
|
4.9
|
12.8
|
1.0
|
CB
|
C:TYR559
|
5.0
|
12.1
|
1.0
|
|
Reference:
M.L.Dugdale,
D.L.Dymianiw,
B.K.Minhas,
I.D'angelo,
R.E.Huber.
Role of Met-542 As A Guide For the Conformational Changes of Phe-601 That Occur During the Reaction of β-Galactosidase (Escherichia Coli). Biochem.Cell Biol. V. 88 861 2010.
ISSN: ISSN 0829-8211
PubMed: 20921997
DOI: 10.1139/O10-009
Page generated: Mon Oct 7 10:34:02 2024
|