Sodium in PDB 4cnp: Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative
Enzymatic activity of Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative
All present enzymatic activity of Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative:
4.2.1.10;
Protein crystallography data
The structure of Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative, PDB code: 4cnp
was solved by
J.M.Otero,
A.L.Llamas-Saiz,
M.Maneiro,
A.Peon,
E.Lence,
H.Lamb,
A.R.Hawkins,
C.Gonzalez-Bello,
M.J.Van Raaij,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
51.17 /
1.15
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.216,
44.473,
84.702,
90.00,
95.20,
90.00
|
R / Rfree (%)
|
13.344 /
16.031
|
Other elements in 4cnp:
The structure of Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative
(pdb code 4cnp). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the
Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative, PDB code: 4cnp:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
Sodium binding site 1 out
of 7 in 4cnp
Go back to
Sodium Binding Sites List in 4cnp
Sodium binding site 1 out
of 7 in the Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative
![](/pictures/NA/pdb/cn/4cnp-NA-sphere_01.jpg) Mono view
![](/pictures/NA/pdb/cn/4cnp-NA-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1253
b:27.6
occ:1.00
|
O
|
A:HOH2111
|
2.4
|
31.7
|
1.0
|
O
|
A:MET23
|
2.4
|
7.8
|
0.5
|
O
|
A:HOH2077
|
2.5
|
28.8
|
1.0
|
O
|
A:HOH2393
|
2.6
|
17.5
|
1.0
|
OE2
|
A:GLU33
|
3.0
|
10.5
|
0.5
|
C
|
A:MET23
|
3.5
|
7.9
|
0.5
|
CD
|
A:GLU33
|
3.6
|
10.6
|
0.5
|
O
|
A:HOH2073
|
3.7
|
9.7
|
0.5
|
CD
|
A:GLU33
|
3.8
|
10.7
|
0.5
|
OE2
|
A:GLU33
|
3.9
|
14.0
|
0.5
|
O
|
A:MET23
|
3.9
|
8.5
|
0.5
|
OE1
|
A:GLU33
|
3.9
|
12.4
|
0.5
|
C
|
A:MET23
|
4.0
|
7.8
|
0.5
|
CG
|
A:GLU33
|
4.1
|
9.5
|
0.5
|
CG
|
A:GLU33
|
4.1
|
9.5
|
0.5
|
CB
|
A:MET23
|
4.1
|
8.9
|
1.0
|
N
|
A:GLY24
|
4.2
|
7.7
|
0.5
|
CA
|
A:MET23
|
4.3
|
8.1
|
0.5
|
N
|
A:GLY24
|
4.4
|
7.0
|
0.5
|
CA
|
A:GLY24
|
4.4
|
7.3
|
0.5
|
CA
|
A:GLY24
|
4.4
|
7.0
|
0.5
|
OE1
|
A:GLU33
|
4.4
|
10.5
|
0.5
|
O
|
A:HOH2081
|
4.5
|
8.6
|
1.0
|
CA
|
A:MET23
|
4.5
|
8.0
|
0.5
|
O
|
A:HOH2097
|
4.6
|
11.8
|
1.0
|
N
|
A:MET23
|
4.8
|
7.2
|
0.5
|
N
|
A:MET23
|
4.8
|
7.7
|
0.5
|
O
|
A:HOH2076
|
4.9
|
27.2
|
1.0
|
|
Sodium binding site 2 out
of 7 in 4cnp
Go back to
Sodium Binding Sites List in 4cnp
Sodium binding site 2 out
of 7 in the Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative
![](/pictures/NA/pdb/cn/4cnp-NA-sphere_02.jpg) Mono view
![](/pictures/NA/pdb/cn/4cnp-NA-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1254
b:34.4
occ:1.00
|
O
|
A:HOH2243
|
2.2
|
24.5
|
1.0
|
O
|
A:HOH2241
|
2.3
|
28.1
|
1.0
|
O
|
A:HOH2271
|
2.6
|
27.8
|
1.0
|
O
|
A:HOH2273
|
2.8
|
26.9
|
1.0
|
O
|
A:ASN135
|
2.8
|
8.6
|
1.0
|
O
|
A:HOH2242
|
3.5
|
14.5
|
1.0
|
C
|
A:ASN135
|
3.8
|
7.0
|
1.0
|
ND2
|
A:ASN135
|
3.8
|
15.0
|
1.0
|
O
|
A:HIS134
|
4.0
|
8.6
|
1.0
|
CB
|
A:ASN135
|
4.1
|
9.7
|
1.0
|
CG
|
A:ASN135
|
4.2
|
12.5
|
1.0
|
O
|
A:HOH2239
|
4.2
|
23.4
|
1.0
|
O
|
A:HOH2244
|
4.3
|
21.1
|
1.0
|
CG2
|
A:VAL136
|
4.3
|
6.5
|
1.0
|
O
|
A:VAL110
|
4.3
|
7.8
|
1.0
|
CA
|
A:ASN135
|
4.5
|
7.9
|
1.0
|
N
|
A:VAL136
|
4.6
|
5.9
|
1.0
|
CA
|
A:VAL136
|
4.8
|
5.5
|
1.0
|
OD1
|
A:ASP111
|
4.8
|
14.2
|
1.0
|
OD1
|
A:ASN135
|
5.0
|
14.3
|
1.0
|
CA
|
A:ASP111
|
5.0
|
6.1
|
1.0
|
|
Sodium binding site 3 out
of 7 in 4cnp
Go back to
Sodium Binding Sites List in 4cnp
Sodium binding site 3 out
of 7 in the Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative
![](/pictures/NA/pdb/cn/4cnp-NA-sphere_03.jpg) Mono view
![](/pictures/NA/pdb/cn/4cnp-NA-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1255
b:18.8
occ:1.00
|
O
|
A:HOH2264
|
2.4
|
25.9
|
1.0
|
O
|
A:HOH2394
|
2.7
|
16.9
|
1.0
|
NE2
|
A:HIS134
|
2.7
|
8.5
|
1.0
|
CE1
|
A:HIS134
|
3.6
|
8.3
|
1.0
|
OH
|
A:TYR130
|
3.6
|
8.8
|
1.0
|
CD2
|
A:HIS134
|
3.8
|
8.2
|
1.0
|
CB
|
A:ASP106
|
3.9
|
6.6
|
1.0
|
CZ
|
A:TYR130
|
4.3
|
7.2
|
1.0
|
O
|
A:HOH2235
|
4.3
|
21.7
|
1.0
|
OD2
|
A:ASP106
|
4.3
|
9.0
|
1.0
|
CG
|
A:ASP106
|
4.5
|
6.9
|
1.0
|
O
|
A:HOH2237
|
4.6
|
17.6
|
1.0
|
CE1
|
A:TYR130
|
4.7
|
7.6
|
1.0
|
ND1
|
A:HIS134
|
4.7
|
8.4
|
1.0
|
CG
|
A:HIS134
|
4.9
|
7.6
|
1.0
|
|
Sodium binding site 4 out
of 7 in 4cnp
Go back to
Sodium Binding Sites List in 4cnp
Sodium binding site 4 out
of 7 in the Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative
![](/pictures/NA/pdb/cn/4cnp-NA-sphere_04.jpg) Mono view
![](/pictures/NA/pdb/cn/4cnp-NA-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1256
b:11.0
occ:1.00
|
OD1
|
A:ASN101
|
2.7
|
6.4
|
0.5
|
O
|
A:ASP114
|
2.8
|
8.8
|
1.0
|
N
|
A:PHE81
|
2.9
|
5.2
|
1.0
|
OD1
|
A:ASN101
|
2.9
|
7.0
|
0.5
|
ND2
|
A:ASN101
|
3.1
|
7.9
|
0.5
|
O
|
A:HOH2201
|
3.3
|
8.8
|
1.0
|
CG
|
A:ASN101
|
3.3
|
6.5
|
0.5
|
O
|
A:PHE79
|
3.7
|
5.1
|
1.0
|
CB
|
A:PHE81
|
3.7
|
6.2
|
1.0
|
CA
|
A:PHE81
|
3.8
|
5.7
|
1.0
|
CA
|
A:THR80
|
3.8
|
5.1
|
1.0
|
C
|
A:THR80
|
3.8
|
5.1
|
1.0
|
CG
|
A:ASN101
|
3.8
|
7.6
|
0.5
|
CE1
|
A:TYR97
|
3.9
|
6.3
|
1.0
|
O
|
A:PHE81
|
3.9
|
6.3
|
1.0
|
C
|
A:ASP114
|
3.9
|
5.9
|
1.0
|
CD1
|
A:PHE79
|
4.0
|
5.7
|
1.0
|
ND2
|
A:ASN101
|
4.1
|
8.7
|
0.5
|
CG1
|
A:ILE113
|
4.1
|
7.7
|
0.5
|
OH
|
A:TYR97
|
4.2
|
6.9
|
1.0
|
CE1
|
A:PHE79
|
4.2
|
6.2
|
1.0
|
C
|
A:PHE81
|
4.2
|
5.8
|
1.0
|
CZ
|
A:TYR97
|
4.3
|
5.9
|
1.0
|
C
|
A:PHE79
|
4.3
|
4.4
|
1.0
|
N
|
A:THR80
|
4.4
|
5.0
|
1.0
|
N
|
A:ASP114
|
4.4
|
5.5
|
1.0
|
CB
|
A:ASP114
|
4.4
|
7.5
|
1.0
|
CA
|
A:ASP114
|
4.5
|
5.8
|
1.0
|
CD1
|
A:ILE113
|
4.6
|
8.3
|
0.5
|
CD1
|
A:TYR97
|
4.7
|
6.8
|
1.0
|
CB
|
A:ASN101
|
4.8
|
6.6
|
0.5
|
O
|
A:THR80
|
5.0
|
5.6
|
1.0
|
N
|
A:LEU115
|
5.0
|
5.0
|
1.0
|
OD1
|
A:ASP114
|
5.0
|
9.7
|
1.0
|
CB
|
A:THR80
|
5.0
|
5.7
|
1.0
|
|
Sodium binding site 5 out
of 7 in 4cnp
Go back to
Sodium Binding Sites List in 4cnp
Sodium binding site 5 out
of 7 in the Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative
![](/pictures/NA/pdb/cn/4cnp-NA-sphere_05.jpg) Mono view
![](/pictures/NA/pdb/cn/4cnp-NA-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na1253
b:16.4
occ:1.00
|
O
|
B:HOH2274
|
2.6
|
14.6
|
1.0
|
OH
|
B:TYR130
|
2.7
|
9.6
|
1.0
|
CE1
|
B:HIS134
|
3.3
|
13.0
|
1.0
|
NE2
|
B:HIS134
|
3.4
|
12.6
|
1.0
|
CZ
|
B:TYR130
|
3.7
|
8.2
|
1.0
|
CB
|
B:ASP106
|
3.7
|
8.1
|
1.0
|
OD2
|
B:ASP106
|
3.9
|
10.4
|
1.0
|
CE1
|
B:TYR130
|
4.0
|
9.6
|
1.0
|
CG
|
B:ASP106
|
4.1
|
8.6
|
1.0
|
O
|
B:HOH2179
|
4.1
|
24.3
|
1.0
|
ND1
|
B:HIS134
|
4.4
|
12.2
|
1.0
|
CD2
|
B:HIS134
|
4.6
|
10.7
|
1.0
|
O
|
B:HOH2158
|
4.7
|
17.7
|
1.0
|
CE2
|
B:TYR130
|
4.8
|
8.4
|
1.0
|
|
Sodium binding site 6 out
of 7 in 4cnp
Go back to
Sodium Binding Sites List in 4cnp
Sodium binding site 6 out
of 7 in the Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative
![](/pictures/NA/pdb/cn/4cnp-NA-sphere_06.jpg) Mono view
![](/pictures/NA/pdb/cn/4cnp-NA-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na1254
b:17.0
occ:1.00
|
O
|
B:HOH2149
|
2.7
|
23.1
|
1.0
|
O
|
B:HOH2135
|
2.7
|
22.4
|
1.0
|
N
|
B:ILE92
|
3.1
|
9.5
|
1.0
|
N
|
B:ALA84
|
3.3
|
13.1
|
1.0
|
O
|
B:ILE92
|
3.4
|
10.0
|
1.0
|
O
|
B:GLN90
|
3.6
|
17.4
|
1.0
|
CA
|
B:THR91
|
3.6
|
10.7
|
1.0
|
CB
|
B:SER83
|
3.7
|
12.3
|
1.0
|
CA
|
B:SER83
|
3.7
|
11.1
|
1.0
|
C
|
B:THR91
|
3.8
|
9.7
|
1.0
|
CG1
|
B:ILE92
|
4.0
|
10.1
|
1.0
|
C
|
B:SER83
|
4.0
|
11.5
|
1.0
|
CB
|
B:ALA84
|
4.1
|
15.1
|
1.0
|
CE1
|
B:PHE81
|
4.1
|
10.0
|
1.0
|
CA
|
B:ILE92
|
4.1
|
9.4
|
1.0
|
C
|
B:ILE92
|
4.2
|
8.7
|
1.0
|
CA
|
B:ALA84
|
4.3
|
13.7
|
1.0
|
CG2
|
B:THR91
|
4.3
|
12.5
|
1.0
|
O
|
B:HOH2069
|
4.4
|
26.4
|
1.0
|
C
|
B:GLN90
|
4.4
|
11.6
|
1.0
|
N
|
B:THR91
|
4.4
|
10.2
|
1.0
|
CB
|
B:THR91
|
4.5
|
11.8
|
1.0
|
O
|
B:HOH2148
|
4.5
|
23.5
|
1.0
|
O
|
B:HOH2132
|
4.6
|
16.5
|
1.0
|
CB
|
B:ILE92
|
4.7
|
9.8
|
1.0
|
O
|
B:HOH2147
|
4.7
|
30.4
|
1.0
|
OG
|
B:SER83
|
4.8
|
13.6
|
1.0
|
CZ
|
B:PHE81
|
4.8
|
10.4
|
1.0
|
N
|
B:LYS85
|
4.8
|
13.0
|
1.0
|
OG1
|
B:THR91
|
4.8
|
14.0
|
1.0
|
|
Sodium binding site 7 out
of 7 in 4cnp
Go back to
Sodium Binding Sites List in 4cnp
Sodium binding site 7 out
of 7 in the Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative
![](/pictures/NA/pdb/cn/4cnp-NA-sphere_07.jpg) Mono view
![](/pictures/NA/pdb/cn/4cnp-NA-sphere_07_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na1255
b:12.9
occ:1.00
|
O
|
B:ASP114
|
2.7
|
10.3
|
1.0
|
OD1
|
B:ASN101
|
2.8
|
9.9
|
1.0
|
N
|
B:PHE81
|
2.9
|
6.9
|
1.0
|
ND2
|
B:ASN101
|
3.2
|
10.3
|
1.0
|
O
|
B:HOH2131
|
3.3
|
10.8
|
1.0
|
CG
|
B:ASN101
|
3.3
|
9.0
|
1.0
|
O
|
B:PHE81
|
3.7
|
8.1
|
1.0
|
CA
|
B:PHE81
|
3.7
|
7.0
|
1.0
|
CB
|
B:PHE81
|
3.7
|
7.5
|
1.0
|
O
|
B:PHE79
|
3.7
|
6.8
|
1.0
|
CA
|
B:THR80
|
3.8
|
6.4
|
1.0
|
C
|
B:THR80
|
3.8
|
6.6
|
1.0
|
C
|
B:ASP114
|
3.8
|
7.6
|
1.0
|
CE1
|
B:TYR97
|
3.9
|
8.2
|
1.0
|
C
|
B:PHE81
|
4.1
|
7.1
|
1.0
|
CD1
|
B:PHE79
|
4.2
|
6.7
|
1.0
|
CB
|
B:ASP114
|
4.2
|
8.7
|
1.0
|
OH
|
B:TYR97
|
4.2
|
8.8
|
1.0
|
N
|
B:ASP114
|
4.3
|
7.0
|
1.0
|
CA
|
B:ASP114
|
4.3
|
7.4
|
1.0
|
CZ
|
B:TYR97
|
4.4
|
7.9
|
1.0
|
C
|
B:PHE79
|
4.4
|
6.0
|
1.0
|
CE1
|
B:PHE79
|
4.4
|
7.5
|
1.0
|
N
|
B:THR80
|
4.4
|
6.0
|
1.0
|
CD1
|
B:TYR97
|
4.8
|
8.1
|
1.0
|
CB
|
B:ASN101
|
4.9
|
7.7
|
1.0
|
OD1
|
B:ASP114
|
4.9
|
10.1
|
1.0
|
N
|
B:LEU115
|
4.9
|
7.3
|
1.0
|
O
|
B:THR80
|
5.0
|
7.2
|
1.0
|
CB
|
B:THR80
|
5.0
|
6.6
|
1.0
|
|
Reference:
M.Maneiro,
A.Peon,
E.Lence,
J.M.Otero,
A.L.Llamas-Saiz,
M.J.Van Raaij,
H.Lamb,
A.R.Hawkins,
C.Gonzalez-Bello.
Mechanistic Insight Into the Reaction Catalyzed By Type I Dehydroquinase To Be Published.
Page generated: Tue Dec 15 06:35:54 2020
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