Fluorine in PDB 5eyn: Crystal Structure of Fructokinase From Vibrio Cholerae O395 in Fructose, Adp, Beryllium Trifluoride and Calcium Ion Bound Form
Enzymatic activity of Crystal Structure of Fructokinase From Vibrio Cholerae O395 in Fructose, Adp, Beryllium Trifluoride and Calcium Ion Bound Form
All present enzymatic activity of Crystal Structure of Fructokinase From Vibrio Cholerae O395 in Fructose, Adp, Beryllium Trifluoride and Calcium Ion Bound Form:
2.7.1.4;
Protein crystallography data
The structure of Crystal Structure of Fructokinase From Vibrio Cholerae O395 in Fructose, Adp, Beryllium Trifluoride and Calcium Ion Bound Form, PDB code: 5eyn
was solved by
R.Paul,
S.Nath,
U.Sen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
32.15 /
1.29
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
64.300,
107.218,
41.618,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
14.1 /
16.9
|
Other elements in 5eyn:
The structure of Crystal Structure of Fructokinase From Vibrio Cholerae O395 in Fructose, Adp, Beryllium Trifluoride and Calcium Ion Bound Form also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Fructokinase From Vibrio Cholerae O395 in Fructose, Adp, Beryllium Trifluoride and Calcium Ion Bound Form
(pdb code 5eyn). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the
Crystal Structure of Fructokinase From Vibrio Cholerae O395 in Fructose, Adp, Beryllium Trifluoride and Calcium Ion Bound Form, PDB code: 5eyn:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 5eyn
Go back to
Fluorine Binding Sites List in 5eyn
Fluorine binding site 1 out
of 3 in the Crystal Structure of Fructokinase From Vibrio Cholerae O395 in Fructose, Adp, Beryllium Trifluoride and Calcium Ion Bound Form
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Crystal Structure of Fructokinase From Vibrio Cholerae O395 in Fructose, Adp, Beryllium Trifluoride and Calcium Ion Bound Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F403
b:62.8
occ:1.00
|
F1
|
A:BEF403
|
0.0
|
62.8
|
1.0
|
BE
|
A:BEF403
|
1.5
|
14.6
|
1.0
|
O1B
|
A:ADP404
|
2.0
|
77.3
|
1.0
|
H
|
A:GLY263
|
2.0
|
12.9
|
1.0
|
PB
|
A:ADP404
|
2.5
|
25.3
|
1.0
|
F3
|
A:BEF403
|
2.5
|
17.9
|
1.0
|
F2
|
A:BEF403
|
2.6
|
38.5
|
1.0
|
O2B
|
A:ADP404
|
2.6
|
79.2
|
1.0
|
O3B
|
A:ADP404
|
2.7
|
66.6
|
1.0
|
N
|
A:GLY263
|
2.7
|
10.7
|
1.0
|
HA2
|
A:GLY263
|
3.2
|
14.3
|
1.0
|
HO6
|
A:FRU401
|
3.2
|
10.5
|
1.0
|
HA
|
A:THR262
|
3.4
|
11.0
|
1.0
|
CA
|
A:GLY263
|
3.4
|
11.9
|
1.0
|
H
|
A:ALA264
|
3.4
|
13.5
|
1.0
|
H
|
A:GLY265
|
3.4
|
9.9
|
1.0
|
O
|
A:THR261
|
3.5
|
10.8
|
1.0
|
H62
|
A:FRU401
|
3.6
|
9.2
|
1.0
|
C
|
A:THR262
|
3.7
|
10.4
|
1.0
|
N
|
A:ALA264
|
3.8
|
11.3
|
1.0
|
O6
|
A:FRU401
|
3.9
|
8.7
|
1.0
|
HA2
|
A:GLY109
|
3.9
|
20.0
|
1.0
|
C
|
A:GLY263
|
3.9
|
10.6
|
1.0
|
O
|
A:HOH583
|
4.0
|
15.2
|
1.0
|
H61
|
A:FRU401
|
4.0
|
9.2
|
1.0
|
CA
|
A:THR262
|
4.0
|
9.2
|
1.0
|
C6
|
A:FRU401
|
4.0
|
7.6
|
1.0
|
HZ
|
A:PHE113
|
4.0
|
11.9
|
1.0
|
O3A
|
A:ADP404
|
4.0
|
82.3
|
1.0
|
O
|
A:HOH501
|
4.1
|
15.7
|
1.0
|
HH22
|
A:ARG176
|
4.2
|
10.0
|
1.0
|
HA3
|
A:GLY263
|
4.3
|
14.3
|
1.0
|
N
|
A:GLY265
|
4.3
|
8.3
|
1.0
|
CA
|
A:CA402
|
4.4
|
18.3
|
1.0
|
C
|
A:THR261
|
4.4
|
9.8
|
1.0
|
HE1
|
A:PHE113
|
4.5
|
12.7
|
1.0
|
HB3
|
A:ALA264
|
4.6
|
14.1
|
1.0
|
HH21
|
A:ARG176
|
4.6
|
10.0
|
1.0
|
NH2
|
A:ARG176
|
4.7
|
8.3
|
1.0
|
HA3
|
A:GLY265
|
4.7
|
10.1
|
1.0
|
N
|
A:THR262
|
4.7
|
9.3
|
1.0
|
H
|
A:ASP266
|
4.8
|
9.9
|
1.0
|
CA
|
A:GLY109
|
4.8
|
16.7
|
1.0
|
H
|
A:GLY109
|
4.8
|
21.4
|
1.0
|
CZ
|
A:PHE113
|
4.8
|
9.9
|
1.0
|
O
|
A:THR262
|
4.8
|
12.3
|
1.0
|
HG23
|
A:THR262
|
4.8
|
13.3
|
1.0
|
CA
|
A:ALA264
|
4.9
|
10.8
|
1.0
|
O
|
A:GLY263
|
4.9
|
12.5
|
1.0
|
|
Fluorine binding site 2 out
of 3 in 5eyn
Go back to
Fluorine Binding Sites List in 5eyn
Fluorine binding site 2 out
of 3 in the Crystal Structure of Fructokinase From Vibrio Cholerae O395 in Fructose, Adp, Beryllium Trifluoride and Calcium Ion Bound Form
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Crystal Structure of Fructokinase From Vibrio Cholerae O395 in Fructose, Adp, Beryllium Trifluoride and Calcium Ion Bound Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F403
b:38.5
occ:1.00
|
F2
|
A:BEF403
|
0.0
|
38.5
|
1.0
|
BE
|
A:BEF403
|
1.6
|
14.6
|
1.0
|
HA2
|
A:GLY263
|
2.1
|
14.3
|
1.0
|
O1B
|
A:ADP404
|
2.3
|
77.3
|
1.0
|
F3
|
A:BEF403
|
2.4
|
17.9
|
1.0
|
HO6
|
A:FRU401
|
2.4
|
10.5
|
1.0
|
H
|
A:ASP266
|
2.5
|
9.9
|
1.0
|
H
|
A:GLY265
|
2.6
|
9.9
|
1.0
|
F1
|
A:BEF403
|
2.6
|
62.8
|
1.0
|
O6
|
A:FRU401
|
2.8
|
8.7
|
1.0
|
CA
|
A:GLY263
|
2.8
|
11.9
|
1.0
|
C
|
A:GLY263
|
3.1
|
10.6
|
1.0
|
H
|
A:GLY263
|
3.1
|
12.9
|
1.0
|
N
|
A:ASP266
|
3.1
|
8.3
|
1.0
|
N
|
A:GLY265
|
3.2
|
8.3
|
1.0
|
OD2
|
A:ASP266
|
3.2
|
9.3
|
1.0
|
CG
|
A:ASP266
|
3.2
|
8.5
|
1.0
|
HA3
|
A:GLY265
|
3.3
|
10.1
|
1.0
|
O
|
A:HOH607
|
3.3
|
11.8
|
1.0
|
N
|
A:GLY263
|
3.4
|
10.7
|
1.0
|
OD1
|
A:ASP266
|
3.4
|
9.1
|
1.0
|
PB
|
A:ADP404
|
3.5
|
25.3
|
1.0
|
O
|
A:GLY263
|
3.5
|
12.5
|
1.0
|
H61
|
A:FRU401
|
3.5
|
9.2
|
1.0
|
CA
|
A:GLY265
|
3.5
|
8.4
|
1.0
|
O2B
|
A:ADP404
|
3.6
|
79.2
|
1.0
|
N
|
A:ALA264
|
3.6
|
11.3
|
1.0
|
C6
|
A:FRU401
|
3.6
|
7.6
|
1.0
|
HA3
|
A:GLY263
|
3.6
|
14.3
|
1.0
|
CA
|
A:CA402
|
3.7
|
18.3
|
1.0
|
C
|
A:GLY265
|
3.8
|
8.1
|
1.0
|
H62
|
A:FRU401
|
3.8
|
9.2
|
1.0
|
H
|
A:ALA264
|
3.8
|
13.5
|
1.0
|
HB2
|
A:ASP266
|
3.9
|
9.6
|
1.0
|
CB
|
A:ASP266
|
4.0
|
8.0
|
1.0
|
HD22
|
A:ASN174
|
4.0
|
15.6
|
1.0
|
O
|
A:HOH501
|
4.1
|
15.7
|
1.0
|
CA
|
A:ASP266
|
4.1
|
8.4
|
1.0
|
C
|
A:ALA264
|
4.1
|
8.7
|
1.0
|
HH22
|
A:ARG176
|
4.2
|
10.0
|
1.0
|
O3A
|
A:ADP404
|
4.4
|
82.3
|
1.0
|
HA2
|
A:GLY265
|
4.5
|
10.1
|
1.0
|
CA
|
A:ALA264
|
4.5
|
10.8
|
1.0
|
O3B
|
A:ADP404
|
4.5
|
66.6
|
1.0
|
OD1
|
A:ASN174
|
4.5
|
11.5
|
1.0
|
HA
|
A:ASP266
|
4.6
|
10.1
|
1.0
|
C
|
A:THR262
|
4.7
|
10.4
|
1.0
|
HH21
|
A:ARG176
|
4.8
|
10.0
|
1.0
|
HD21
|
A:ASN49
|
4.8
|
9.1
|
1.0
|
ND2
|
A:ASN174
|
4.8
|
13.0
|
1.0
|
NH2
|
A:ARG176
|
4.8
|
8.3
|
1.0
|
H
|
A:ALA267
|
4.8
|
10.6
|
1.0
|
O
|
A:GLY265
|
4.9
|
9.7
|
1.0
|
HB3
|
A:ASP266
|
4.9
|
9.6
|
1.0
|
|
Fluorine binding site 3 out
of 3 in 5eyn
Go back to
Fluorine Binding Sites List in 5eyn
Fluorine binding site 3 out
of 3 in the Crystal Structure of Fructokinase From Vibrio Cholerae O395 in Fructose, Adp, Beryllium Trifluoride and Calcium Ion Bound Form
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Crystal Structure of Fructokinase From Vibrio Cholerae O395 in Fructose, Adp, Beryllium Trifluoride and Calcium Ion Bound Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F403
b:17.9
occ:1.00
|
F3
|
A:BEF403
|
0.0
|
17.9
|
1.0
|
BE
|
A:BEF403
|
1.5
|
14.6
|
1.0
|
HO6
|
A:FRU401
|
2.1
|
10.5
|
1.0
|
CA
|
A:CA402
|
2.2
|
18.3
|
1.0
|
HH22
|
A:ARG176
|
2.3
|
10.0
|
1.0
|
F2
|
A:BEF403
|
2.4
|
38.5
|
1.0
|
F1
|
A:BEF403
|
2.5
|
62.8
|
1.0
|
O2B
|
A:ADP404
|
2.8
|
79.2
|
1.0
|
O6
|
A:FRU401
|
3.0
|
8.7
|
1.0
|
OD1
|
A:ASN174
|
3.0
|
11.5
|
1.0
|
NH2
|
A:ARG176
|
3.1
|
8.3
|
1.0
|
O
|
A:HOH501
|
3.3
|
15.7
|
1.0
|
O1B
|
A:ADP404
|
3.3
|
77.3
|
1.0
|
HH21
|
A:ARG176
|
3.4
|
10.0
|
1.0
|
O
|
A:HOH619
|
3.4
|
14.9
|
1.0
|
O
|
A:HOH607
|
3.4
|
11.8
|
1.0
|
H62
|
A:FRU401
|
3.6
|
9.2
|
1.0
|
PB
|
A:ADP404
|
3.7
|
25.3
|
1.0
|
HH12
|
A:ARG176
|
3.7
|
10.1
|
1.0
|
HD22
|
A:ASN174
|
3.8
|
15.6
|
1.0
|
C6
|
A:FRU401
|
3.8
|
7.6
|
1.0
|
CG
|
A:ASN174
|
4.0
|
10.6
|
1.0
|
H
|
A:GLY263
|
4.0
|
12.9
|
1.0
|
HA2
|
A:GLY263
|
4.0
|
14.3
|
1.0
|
H
|
A:GLY265
|
4.1
|
9.9
|
1.0
|
CZ
|
A:ARG176
|
4.1
|
8.2
|
1.0
|
HA3
|
A:GLY265
|
4.1
|
10.1
|
1.0
|
NH1
|
A:ARG176
|
4.3
|
8.4
|
1.0
|
H61
|
A:FRU401
|
4.3
|
9.2
|
1.0
|
ND2
|
A:ASN174
|
4.3
|
13.0
|
1.0
|
HA2
|
A:GLY109
|
4.5
|
20.0
|
1.0
|
HE1
|
A:PHE113
|
4.5
|
12.7
|
1.0
|
OD1
|
A:ASP266
|
4.5
|
9.1
|
1.0
|
O3B
|
A:ADP404
|
4.6
|
66.6
|
1.0
|
H
|
A:ASP266
|
4.6
|
9.9
|
1.0
|
OD2
|
A:ASP266
|
4.7
|
9.3
|
1.0
|
N
|
A:GLY263
|
4.7
|
10.7
|
1.0
|
O
|
A:HOH566
|
4.7
|
11.9
|
1.0
|
CA
|
A:GLY263
|
4.7
|
11.9
|
1.0
|
N
|
A:GLY265
|
4.8
|
8.3
|
1.0
|
CG
|
A:ASP266
|
4.8
|
8.5
|
1.0
|
O3A
|
A:ADP404
|
4.8
|
82.3
|
1.0
|
CA
|
A:GLY265
|
4.9
|
8.4
|
1.0
|
HA
|
A:ASN174
|
4.9
|
10.6
|
1.0
|
|
Reference:
R.Paul,
S.Nath,
U.Sen.
Crystal Structure of Fructokinase From Vibrio Cholerae O395 in Apo Form To Be Published.
Page generated: Thu Aug 1 09:16:14 2024
|