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:

Magnesium (Mg) 5 atoms
Calcium (Ca) 3 atoms

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: Sun Dec 13 12:51:53 2020

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