Fluorine in PDB 6gze: Tubulin-Gdp.Bef Complex
Protein crystallography data
The structure of Tubulin-Gdp.Bef Complex, PDB code: 6gze
was solved by
M.A.Oliva,
J.F.Diaz,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.46 /
2.49
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
104.176,
156.744,
180.587,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.2 /
25.7
|
Other elements in 6gze:
The structure of Tubulin-Gdp.Bef Complex also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Tubulin-Gdp.Bef Complex
(pdb code 6gze). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the
Tubulin-Gdp.Bef Complex, PDB code: 6gze:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 6gze
Go back to
Fluorine Binding Sites List in 6gze
Fluorine binding site 1 out
of 3 in the Tubulin-Gdp.Bef Complex
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Tubulin-Gdp.Bef Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F503
b:82.4
occ:1.00
|
F1
|
D:BEF503
|
0.0
|
82.4
|
1.0
|
BE
|
D:BEF503
|
1.5
|
84.7
|
1.0
|
O3B
|
D:GDP501
|
2.3
|
91.9
|
1.0
|
MG
|
D:MG502
|
2.4
|
0.1
|
1.0
|
F3
|
D:BEF503
|
2.5
|
81.1
|
1.0
|
F2
|
D:BEF503
|
2.6
|
80.2
|
1.0
|
O
|
D:HOH602
|
2.8
|
1.0
|
1.0
|
O
|
D:HOH601
|
3.4
|
0.2
|
1.0
|
PB
|
D:GDP501
|
3.5
|
89.0
|
1.0
|
O1A
|
D:GDP501
|
3.6
|
98.7
|
1.0
|
O1B
|
D:GDP501
|
3.6
|
93.6
|
1.0
|
OD1
|
D:ASN101
|
3.7
|
95.6
|
1.0
|
H
|
D:ASN101
|
3.8
|
99.6
|
1.0
|
HG3
|
D:GLU71
|
3.9
|
0.1
|
1.0
|
H
|
D:GLY144
|
4.1
|
88.7
|
1.0
|
H
|
D:GLY100
|
4.2
|
0.7
|
1.0
|
O3A
|
D:GDP501
|
4.2
|
83.1
|
1.0
|
O
|
D:HOH603
|
4.3
|
0.8
|
1.0
|
HA2
|
D:GLY100
|
4.4
|
0.2
|
1.0
|
N
|
D:ASN101
|
4.5
|
96.7
|
1.0
|
PA
|
D:GDP501
|
4.5
|
79.3
|
1.0
|
H
|
D:THR145
|
4.5
|
91.8
|
1.0
|
O2B
|
D:GDP501
|
4.6
|
0.4
|
1.0
|
HG1
|
D:THR145
|
4.7
|
92.0
|
1.0
|
CG
|
D:ASN101
|
4.7
|
98.7
|
1.0
|
OE2
|
D:GLU71
|
4.7
|
0.8
|
1.0
|
CG
|
D:GLU71
|
4.7
|
0.2
|
1.0
|
N
|
D:GLY100
|
4.8
|
98.0
|
1.0
|
HB2
|
D:GLN11
|
4.8
|
0.1
|
1.0
|
HG2
|
D:GLU71
|
4.8
|
0.1
|
1.0
|
N
|
D:GLY144
|
4.9
|
84.6
|
1.0
|
HA3
|
D:GLY144
|
4.9
|
87.3
|
1.0
|
CA
|
D:GLY100
|
4.9
|
0.2
|
1.0
|
HA
|
D:ASN101
|
4.9
|
98.2
|
1.0
|
|
Fluorine binding site 2 out
of 3 in 6gze
Go back to
Fluorine Binding Sites List in 6gze
Fluorine binding site 2 out
of 3 in the Tubulin-Gdp.Bef Complex
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Tubulin-Gdp.Bef Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F503
b:80.2
occ:1.00
|
F2
|
D:BEF503
|
0.0
|
80.2
|
1.0
|
BE
|
D:BEF503
|
1.6
|
84.7
|
1.0
|
HG1
|
D:THR145
|
2.3
|
92.0
|
1.0
|
O3B
|
D:GDP501
|
2.5
|
91.9
|
1.0
|
O
|
D:HOH601
|
2.5
|
0.2
|
1.0
|
F3
|
D:BEF503
|
2.5
|
81.1
|
1.0
|
F1
|
D:BEF503
|
2.6
|
82.4
|
1.0
|
OG1
|
D:THR145
|
3.0
|
89.2
|
1.0
|
H
|
D:ALA99
|
3.1
|
0.4
|
1.0
|
H
|
D:THR145
|
3.1
|
91.8
|
1.0
|
MG
|
D:MG502
|
3.3
|
0.1
|
1.0
|
HA3
|
D:GLY98
|
3.3
|
0.7
|
1.0
|
HG3
|
D:GLU71
|
3.4
|
0.1
|
1.0
|
HG2
|
D:GLU71
|
3.4
|
0.1
|
1.0
|
H
|
D:GLY100
|
3.6
|
0.7
|
1.0
|
PB
|
D:GDP501
|
3.7
|
89.0
|
1.0
|
N
|
D:ALA99
|
3.7
|
0.1
|
1.0
|
HB
|
D:THR145
|
3.8
|
91.0
|
1.0
|
N
|
D:THR145
|
3.8
|
88.2
|
1.0
|
CG
|
D:GLU71
|
3.8
|
0.2
|
1.0
|
HB3
|
D:ALA99
|
3.9
|
0.8
|
1.0
|
CB
|
D:THR145
|
3.9
|
87.3
|
1.0
|
HB2
|
D:LEU70
|
4.0
|
99.6
|
1.0
|
O2B
|
D:GDP501
|
4.0
|
0.4
|
1.0
|
HA3
|
D:GLY144
|
4.0
|
87.3
|
1.0
|
O1B
|
D:GDP501
|
4.1
|
93.6
|
1.0
|
H
|
D:ASN101
|
4.1
|
99.6
|
1.0
|
CA
|
D:GLY98
|
4.1
|
0.9
|
1.0
|
H
|
D:GLY144
|
4.1
|
88.7
|
1.0
|
OE2
|
D:GLU71
|
4.1
|
0.8
|
1.0
|
HA2
|
D:GLY98
|
4.2
|
0.7
|
1.0
|
N
|
D:GLY100
|
4.3
|
98.0
|
1.0
|
OD1
|
D:ASP69
|
4.3
|
0.3
|
1.0
|
C
|
D:GLY98
|
4.3
|
0.6
|
1.0
|
CA
|
D:THR145
|
4.5
|
87.1
|
1.0
|
CD
|
D:GLU71
|
4.5
|
0.2
|
1.0
|
CB
|
D:ALA99
|
4.6
|
0.4
|
1.0
|
CA
|
D:ALA99
|
4.6
|
0.4
|
1.0
|
CA
|
D:GLY144
|
4.6
|
84.5
|
1.0
|
HD12
|
D:LEU70
|
4.7
|
98.3
|
1.0
|
C
|
D:GLY144
|
4.7
|
82.5
|
1.0
|
H
|
D:GLU71
|
4.7
|
0.7
|
1.0
|
N
|
D:GLY144
|
4.8
|
84.6
|
1.0
|
H
|
D:LEU70
|
4.8
|
97.5
|
1.0
|
HB2
|
D:ALA99
|
4.8
|
0.8
|
1.0
|
O
|
D:HOH602
|
4.8
|
1.0
|
1.0
|
CB
|
D:LEU70
|
4.9
|
0.6
|
1.0
|
HA
|
D:THR145
|
4.9
|
91.2
|
1.0
|
C
|
D:ALA99
|
4.9
|
0.9
|
1.0
|
HA2
|
D:GLY100
|
4.9
|
0.2
|
1.0
|
N
|
D:ASN101
|
4.9
|
96.7
|
1.0
|
O3A
|
D:GDP501
|
5.0
|
83.1
|
1.0
|
|
Fluorine binding site 3 out
of 3 in 6gze
Go back to
Fluorine Binding Sites List in 6gze
Fluorine binding site 3 out
of 3 in the Tubulin-Gdp.Bef Complex
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Tubulin-Gdp.Bef Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F503
b:81.1
occ:1.00
|
F3
|
D:BEF503
|
0.0
|
81.1
|
1.0
|
BE
|
D:BEF503
|
1.5
|
84.7
|
1.0
|
H
|
D:ASN101
|
1.8
|
99.6
|
1.0
|
O3B
|
D:GDP501
|
2.4
|
91.9
|
1.0
|
F2
|
D:BEF503
|
2.5
|
80.2
|
1.0
|
HA3
|
D:GLY144
|
2.5
|
87.3
|
1.0
|
F1
|
D:BEF503
|
2.5
|
82.4
|
1.0
|
N
|
D:ASN101
|
2.6
|
96.7
|
1.0
|
H
|
D:GLY144
|
2.6
|
88.7
|
1.0
|
HA
|
D:ASN101
|
3.0
|
98.2
|
1.0
|
H
|
D:GLY100
|
3.0
|
0.7
|
1.0
|
HB3
|
D:ALA99
|
3.1
|
0.8
|
1.0
|
N
|
D:GLY144
|
3.1
|
84.6
|
1.0
|
CA
|
D:GLY144
|
3.2
|
84.5
|
1.0
|
H
|
D:THR145
|
3.3
|
91.8
|
1.0
|
N
|
D:GLY100
|
3.3
|
98.0
|
1.0
|
CA
|
D:ASN101
|
3.4
|
96.0
|
1.0
|
OD1
|
D:ASN101
|
3.4
|
95.6
|
1.0
|
C
|
D:GLY100
|
3.6
|
0.4
|
1.0
|
HA2
|
D:GLY100
|
3.7
|
0.2
|
1.0
|
CA
|
D:GLY100
|
3.7
|
0.2
|
1.0
|
H
|
D:ALA99
|
3.8
|
0.4
|
1.0
|
N
|
D:THR145
|
3.9
|
88.2
|
1.0
|
PB
|
D:GDP501
|
3.9
|
89.0
|
1.0
|
H
|
D:ASN102
|
3.9
|
0.5
|
1.0
|
HG1
|
D:THR145
|
3.9
|
92.0
|
1.0
|
HA2
|
D:GLY144
|
3.9
|
87.3
|
1.0
|
C
|
D:ALA99
|
3.9
|
0.9
|
1.0
|
CB
|
D:ALA99
|
4.0
|
0.4
|
1.0
|
C
|
D:GLY144
|
4.1
|
82.5
|
1.0
|
CG
|
D:ASN101
|
4.1
|
98.7
|
1.0
|
N
|
D:ALA99
|
4.1
|
0.1
|
1.0
|
CA
|
D:ALA99
|
4.2
|
0.4
|
1.0
|
C
|
D:GLY143
|
4.2
|
0.4
|
1.0
|
CB
|
D:ASN101
|
4.4
|
98.8
|
1.0
|
HB1
|
D:ALA99
|
4.4
|
0.8
|
1.0
|
N
|
D:ASN102
|
4.5
|
0.3
|
1.0
|
C
|
D:ASN101
|
4.5
|
96.6
|
1.0
|
O3A
|
D:GDP501
|
4.5
|
83.1
|
1.0
|
O2B
|
D:GDP501
|
4.5
|
0.4
|
1.0
|
HA2
|
D:GLY143
|
4.6
|
0.2
|
1.0
|
MG
|
D:MG502
|
4.6
|
0.1
|
1.0
|
HA3
|
D:GLY143
|
4.6
|
0.2
|
1.0
|
HB2
|
D:ALA99
|
4.6
|
0.8
|
1.0
|
HA3
|
D:GLY100
|
4.7
|
0.2
|
1.0
|
O
|
D:HOH601
|
4.7
|
0.2
|
1.0
|
OG1
|
D:THR145
|
4.8
|
89.2
|
1.0
|
CA
|
D:GLY143
|
4.8
|
0.4
|
1.0
|
O
|
D:GLY100
|
4.8
|
0.4
|
1.0
|
O
|
D:ALA99
|
4.8
|
0.3
|
1.0
|
O1B
|
D:GDP501
|
4.9
|
93.6
|
1.0
|
HA3
|
D:GLY98
|
4.9
|
0.7
|
1.0
|
HB2
|
D:ASN101
|
4.9
|
0.3
|
1.0
|
O1A
|
D:GDP501
|
5.0
|
98.7
|
1.0
|
HB3
|
D:ASN101
|
5.0
|
0.3
|
1.0
|
|
Reference:
F.Josa-Prado,
J.Estevez-Gallego,
R.M.Buey,
F.A.Balaguer,
A.E.Prota,
M.O.Steinmetz,
I.Barasoain,
S.Kamimura,
J.F.Diaz,
M.A.Oliva.
Structural Basis For Tubulin Activation Revealed By A Gtp Mimicking State To Be Published.
Page generated: Thu Aug 1 20:50:53 2024
|