Fluorine in PDB 1rbm: Human Gar Tfase Complex Structure with Polyglutamated 10- (Trifluoroacetyl)-5,10-Dideazaacyclic-5,6,7,8- Tetrahydrofolic Acid
Enzymatic activity of Human Gar Tfase Complex Structure with Polyglutamated 10- (Trifluoroacetyl)-5,10-Dideazaacyclic-5,6,7,8- Tetrahydrofolic Acid
All present enzymatic activity of Human Gar Tfase Complex Structure with Polyglutamated 10- (Trifluoroacetyl)-5,10-Dideazaacyclic-5,6,7,8- Tetrahydrofolic Acid:
2.1.2.2;
Protein crystallography data
The structure of Human Gar Tfase Complex Structure with Polyglutamated 10- (Trifluoroacetyl)-5,10-Dideazaacyclic-5,6,7,8- Tetrahydrofolic Acid, PDB code: 1rbm
was solved by
Y.Zhang,
J.Desharnais,
D.L.Boger,
I.A.Wilson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
31.47 /
2.30
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
126.099,
126.099,
94.269,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
23.6 /
26.6
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Human Gar Tfase Complex Structure with Polyglutamated 10- (Trifluoroacetyl)-5,10-Dideazaacyclic-5,6,7,8- Tetrahydrofolic Acid
(pdb code 1rbm). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Human Gar Tfase Complex Structure with Polyglutamated 10- (Trifluoroacetyl)-5,10-Dideazaacyclic-5,6,7,8- Tetrahydrofolic Acid, PDB code: 1rbm:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 1rbm
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Fluorine Binding Sites List in 1rbm
Fluorine binding site 1 out
of 6 in the Human Gar Tfase Complex Structure with Polyglutamated 10- (Trifluoroacetyl)-5,10-Dideazaacyclic-5,6,7,8- Tetrahydrofolic Acid
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Human Gar Tfase Complex Structure with Polyglutamated 10- (Trifluoroacetyl)-5,10-Dideazaacyclic-5,6,7,8- Tetrahydrofolic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F510
b:23.4
occ:1.00
|
F2
|
A:KT5510
|
0.0
|
23.4
|
1.0
|
C6
|
A:KT5510
|
1.4
|
22.4
|
1.0
|
F1
|
A:KT5510
|
2.1
|
21.8
|
1.0
|
F3
|
A:KT5510
|
2.2
|
23.3
|
1.0
|
C5
|
A:KT5510
|
2.5
|
25.5
|
1.0
|
OA1
|
A:KT5510
|
2.7
|
21.9
|
1.0
|
C10
|
A:KT5510
|
3.0
|
24.6
|
1.0
|
C11
|
A:KT5510
|
3.2
|
23.8
|
1.0
|
C16
|
A:KT5510
|
3.2
|
24.1
|
1.0
|
CE
|
A:MET89
|
3.3
|
29.3
|
1.0
|
O
|
A:HOH579
|
3.4
|
34.5
|
1.0
|
CA
|
A:SER118
|
3.5
|
21.5
|
1.0
|
CB
|
A:SER118
|
3.6
|
22.3
|
1.0
|
OA2
|
A:KT5510
|
3.6
|
24.8
|
1.0
|
SD
|
A:MET89
|
3.6
|
27.2
|
1.0
|
C12
|
A:KT5510
|
4.2
|
22.9
|
1.0
|
C15
|
A:KT5510
|
4.2
|
23.8
|
1.0
|
N
|
A:SER118
|
4.3
|
22.0
|
1.0
|
O
|
A:HOH565
|
4.3
|
34.9
|
1.0
|
C1
|
A:KT5510
|
4.5
|
26.7
|
1.0
|
O
|
A:GLY117
|
4.6
|
21.1
|
1.0
|
C
|
A:SER118
|
4.6
|
21.6
|
1.0
|
C
|
A:GLY117
|
4.7
|
22.0
|
1.0
|
O
|
A:SER118
|
4.7
|
21.8
|
1.0
|
O
|
A:PHE88
|
4.8
|
18.2
|
1.0
|
O
|
A:HOH530
|
4.9
|
21.9
|
1.0
|
ND1
|
A:HIS108
|
4.9
|
17.4
|
1.0
|
OG
|
A:SER118
|
5.0
|
21.9
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 1rbm
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Fluorine Binding Sites List in 1rbm
Fluorine binding site 2 out
of 6 in the Human Gar Tfase Complex Structure with Polyglutamated 10- (Trifluoroacetyl)-5,10-Dideazaacyclic-5,6,7,8- Tetrahydrofolic Acid
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Human Gar Tfase Complex Structure with Polyglutamated 10- (Trifluoroacetyl)-5,10-Dideazaacyclic-5,6,7,8- Tetrahydrofolic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F510
b:21.8
occ:1.00
|
F1
|
A:KT5510
|
0.0
|
21.8
|
1.0
|
C6
|
A:KT5510
|
1.3
|
22.4
|
1.0
|
F2
|
A:KT5510
|
2.1
|
23.4
|
1.0
|
C5
|
A:KT5510
|
2.2
|
25.5
|
1.0
|
F3
|
A:KT5510
|
2.2
|
23.3
|
1.0
|
C10
|
A:KT5510
|
2.8
|
24.6
|
1.0
|
OA2
|
A:KT5510
|
2.9
|
24.8
|
1.0
|
O
|
A:HOH530
|
3.1
|
21.9
|
1.0
|
O
|
A:HOH542
|
3.2
|
23.6
|
1.0
|
OA1
|
A:KT5510
|
3.4
|
21.9
|
1.0
|
CE
|
A:MET89
|
3.7
|
29.3
|
1.0
|
C11
|
A:KT5510
|
3.8
|
23.8
|
1.0
|
O
|
A:PHE88
|
3.8
|
18.2
|
1.0
|
C16
|
A:KT5510
|
3.8
|
24.1
|
1.0
|
OD1
|
A:ASN106
|
3.9
|
20.0
|
1.0
|
C1
|
A:KT5510
|
4.0
|
26.7
|
1.0
|
O
|
A:ILE107
|
4.1
|
19.5
|
1.0
|
ND2
|
A:ASN106
|
4.3
|
18.1
|
1.0
|
CG
|
A:ASN106
|
4.5
|
20.3
|
1.0
|
O
|
A:HOH579
|
4.5
|
34.5
|
1.0
|
C2
|
A:KT5510
|
4.6
|
23.9
|
1.0
|
SD
|
A:MET89
|
4.6
|
27.2
|
1.0
|
C
|
A:PHE88
|
4.9
|
19.3
|
1.0
|
ND1
|
A:HIS108
|
4.9
|
17.4
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 1rbm
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Fluorine Binding Sites List in 1rbm
Fluorine binding site 3 out
of 6 in the Human Gar Tfase Complex Structure with Polyglutamated 10- (Trifluoroacetyl)-5,10-Dideazaacyclic-5,6,7,8- Tetrahydrofolic Acid
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Human Gar Tfase Complex Structure with Polyglutamated 10- (Trifluoroacetyl)-5,10-Dideazaacyclic-5,6,7,8- Tetrahydrofolic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F510
b:23.3
occ:1.00
|
F3
|
A:KT5510
|
0.0
|
23.3
|
1.0
|
C6
|
A:KT5510
|
1.3
|
22.4
|
1.0
|
F2
|
A:KT5510
|
2.2
|
23.4
|
1.0
|
F1
|
A:KT5510
|
2.2
|
21.8
|
1.0
|
C5
|
A:KT5510
|
2.3
|
25.5
|
1.0
|
OA1
|
A:KT5510
|
2.7
|
21.9
|
1.0
|
OA2
|
A:KT5510
|
2.7
|
24.8
|
1.0
|
O
|
A:HOH579
|
3.1
|
34.5
|
1.0
|
CD
|
A:PRO109
|
3.3
|
19.5
|
1.0
|
ND1
|
A:HIS108
|
3.4
|
17.4
|
1.0
|
O
|
A:HOH565
|
3.7
|
34.9
|
1.0
|
C10
|
A:KT5510
|
3.8
|
24.6
|
1.0
|
CE1
|
A:HIS108
|
4.0
|
19.4
|
1.0
|
O
|
A:HOH530
|
4.1
|
21.9
|
1.0
|
O
|
A:ILE107
|
4.1
|
19.5
|
1.0
|
CG
|
A:PRO109
|
4.2
|
20.3
|
1.0
|
CA
|
A:HIS108
|
4.3
|
19.5
|
1.0
|
CG
|
A:HIS108
|
4.3
|
20.3
|
1.0
|
O
|
A:GLY117
|
4.4
|
21.1
|
1.0
|
CA
|
A:SER118
|
4.5
|
21.5
|
1.0
|
CE
|
A:MET89
|
4.6
|
29.3
|
1.0
|
CB
|
A:HIS108
|
4.6
|
19.4
|
1.0
|
N
|
A:PRO109
|
4.6
|
19.7
|
1.0
|
C11
|
A:KT5510
|
4.6
|
23.8
|
1.0
|
C1
|
A:KT5510
|
4.9
|
26.7
|
1.0
|
ND2
|
A:ASN106
|
5.0
|
18.1
|
1.0
|
OD1
|
A:ASP144
|
5.0
|
19.4
|
1.0
|
C
|
A:HIS108
|
5.0
|
19.4
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 1rbm
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Fluorine Binding Sites List in 1rbm
Fluorine binding site 4 out
of 6 in the Human Gar Tfase Complex Structure with Polyglutamated 10- (Trifluoroacetyl)-5,10-Dideazaacyclic-5,6,7,8- Tetrahydrofolic Acid
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Human Gar Tfase Complex Structure with Polyglutamated 10- (Trifluoroacetyl)-5,10-Dideazaacyclic-5,6,7,8- Tetrahydrofolic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F610
b:28.9
occ:1.00
|
F2
|
B:KT5610
|
0.0
|
28.9
|
1.0
|
C6
|
B:KT5610
|
1.4
|
31.6
|
1.0
|
F1
|
B:KT5610
|
2.2
|
30.2
|
1.0
|
F3
|
B:KT5610
|
2.3
|
33.1
|
1.0
|
C5
|
B:KT5610
|
2.5
|
33.4
|
1.0
|
OA1
|
B:KT5610
|
2.8
|
33.9
|
1.0
|
C10
|
B:KT5610
|
3.0
|
34.7
|
1.0
|
C11
|
B:KT5610
|
3.1
|
36.0
|
1.0
|
C16
|
B:KT5610
|
3.2
|
37.4
|
1.0
|
SD
|
B:MET89
|
3.5
|
39.7
|
1.0
|
OA2
|
B:KT5610
|
3.5
|
32.3
|
1.0
|
O
|
B:HOH686
|
3.5
|
37.4
|
1.0
|
CA
|
B:SER118
|
3.8
|
31.8
|
1.0
|
CB
|
B:SER118
|
4.0
|
32.9
|
1.0
|
C12
|
B:KT5610
|
4.0
|
36.3
|
1.0
|
CE
|
B:MET89
|
4.2
|
41.4
|
1.0
|
O
|
B:HOH635
|
4.2
|
30.4
|
1.0
|
C15
|
B:KT5610
|
4.2
|
38.8
|
1.0
|
C1
|
B:KT5610
|
4.5
|
34.8
|
1.0
|
N
|
B:SER118
|
4.5
|
31.5
|
1.0
|
O
|
B:GLY117
|
4.6
|
29.2
|
1.0
|
C
|
B:GLY117
|
4.8
|
30.3
|
1.0
|
C
|
B:SER118
|
4.8
|
31.1
|
1.0
|
O
|
B:SER118
|
4.8
|
31.4
|
1.0
|
C13
|
B:KT5610
|
4.8
|
38.5
|
1.0
|
C14
|
B:KT5610
|
4.9
|
39.8
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 1rbm
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Fluorine Binding Sites List in 1rbm
Fluorine binding site 5 out
of 6 in the Human Gar Tfase Complex Structure with Polyglutamated 10- (Trifluoroacetyl)-5,10-Dideazaacyclic-5,6,7,8- Tetrahydrofolic Acid
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Human Gar Tfase Complex Structure with Polyglutamated 10- (Trifluoroacetyl)-5,10-Dideazaacyclic-5,6,7,8- Tetrahydrofolic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F610
b:30.2
occ:1.00
|
F1
|
B:KT5610
|
0.0
|
30.2
|
1.0
|
C6
|
B:KT5610
|
1.3
|
31.6
|
1.0
|
C5
|
B:KT5610
|
2.1
|
33.4
|
1.0
|
F2
|
B:KT5610
|
2.2
|
28.9
|
1.0
|
F3
|
B:KT5610
|
2.2
|
33.1
|
1.0
|
C10
|
B:KT5610
|
2.7
|
34.7
|
1.0
|
OA2
|
B:KT5610
|
2.7
|
32.3
|
1.0
|
O
|
B:HOH667
|
3.2
|
25.3
|
1.0
|
O
|
B:HOH647
|
3.2
|
25.4
|
1.0
|
OA1
|
B:KT5610
|
3.5
|
33.9
|
1.0
|
C11
|
B:KT5610
|
3.7
|
36.0
|
1.0
|
C16
|
B:KT5610
|
3.8
|
37.4
|
1.0
|
C1
|
B:KT5610
|
3.9
|
34.8
|
1.0
|
O
|
B:PHE88
|
4.1
|
29.8
|
1.0
|
OD1
|
B:ASN106
|
4.1
|
28.7
|
1.0
|
O
|
B:ILE107
|
4.1
|
23.5
|
1.0
|
C2
|
B:KT5610
|
4.3
|
32.9
|
1.0
|
SD
|
B:MET89
|
4.3
|
39.7
|
1.0
|
ND2
|
B:ASN106
|
4.3
|
25.6
|
1.0
|
O
|
B:HOH686
|
4.6
|
37.4
|
1.0
|
CG
|
B:ASN106
|
4.7
|
27.6
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 1rbm
Go back to
Fluorine Binding Sites List in 1rbm
Fluorine binding site 6 out
of 6 in the Human Gar Tfase Complex Structure with Polyglutamated 10- (Trifluoroacetyl)-5,10-Dideazaacyclic-5,6,7,8- Tetrahydrofolic Acid
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Human Gar Tfase Complex Structure with Polyglutamated 10- (Trifluoroacetyl)-5,10-Dideazaacyclic-5,6,7,8- Tetrahydrofolic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F610
b:33.1
occ:1.00
|
F3
|
B:KT5610
|
0.0
|
33.1
|
1.0
|
C6
|
B:KT5610
|
1.3
|
31.6
|
1.0
|
F1
|
B:KT5610
|
2.2
|
30.2
|
1.0
|
F2
|
B:KT5610
|
2.3
|
28.9
|
1.0
|
C5
|
B:KT5610
|
2.4
|
33.4
|
1.0
|
OA2
|
B:KT5610
|
2.6
|
32.3
|
1.0
|
OA1
|
B:KT5610
|
2.8
|
33.9
|
1.0
|
O
|
B:HOH686
|
3.1
|
37.4
|
1.0
|
CD
|
B:PRO109
|
3.4
|
20.6
|
1.0
|
O
|
B:HOH635
|
3.5
|
30.4
|
1.0
|
ND1
|
B:HIS108
|
3.6
|
24.5
|
1.0
|
C10
|
B:KT5610
|
3.8
|
34.7
|
1.0
|
O
|
B:HOH667
|
4.1
|
25.3
|
1.0
|
O
|
B:ILE107
|
4.1
|
23.5
|
1.0
|
CG
|
B:PRO109
|
4.2
|
19.3
|
1.0
|
CA
|
B:HIS108
|
4.3
|
22.0
|
1.0
|
CE1
|
B:HIS108
|
4.3
|
24.0
|
1.0
|
CG
|
B:HIS108
|
4.5
|
24.1
|
1.0
|
O
|
B:GLY117
|
4.6
|
29.2
|
1.0
|
C11
|
B:KT5610
|
4.6
|
36.0
|
1.0
|
CB
|
B:HIS108
|
4.6
|
22.3
|
1.0
|
N
|
B:PRO109
|
4.6
|
20.4
|
1.0
|
O
|
B:HOH680
|
4.8
|
26.6
|
1.0
|
CA
|
B:SER118
|
4.9
|
31.8
|
1.0
|
C1
|
B:KT5610
|
4.9
|
34.8
|
1.0
|
|
Reference:
Y.Zhang,
J.Desharnais,
D.L.Boger,
I.A.Wilson.
Human Gar Tfase Complex Structure To Be Published.
Page generated: Wed Jul 31 12:35:52 2024
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