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Fluorine in PDB 5cll: Truncated Ran Wild Type in Complex with Gdp-Bef and RANBD1

Protein crystallography data

The structure of Truncated Ran Wild Type in Complex with Gdp-Bef and RANBD1, PDB code: 5cll was solved by I.R.Vetter, S.Brucker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.81 / 2.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.600, 55.780, 122.930, 90.00, 90.05, 90.00
R / Rfree (%) 23.5 / 27.2

Other elements in 5cll:

The structure of Truncated Ran Wild Type in Complex with Gdp-Bef and RANBD1 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Truncated Ran Wild Type in Complex with Gdp-Bef and RANBD1 (pdb code 5cll). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Truncated Ran Wild Type in Complex with Gdp-Bef and RANBD1, PDB code: 5cll:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5cll

Go back to Fluorine Binding Sites List in 5cll
Fluorine binding site 1 out of 6 in the Truncated Ran Wild Type in Complex with Gdp-Bef and RANBD1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Truncated Ran Wild Type in Complex with Gdp-Bef and RANBD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:24.4
occ:1.00
 F1 A:BEF201 0.0 24.4 1.0
MG A:MG202 1.6 27.4 1.0
BE A:BEF201 1.7 24.0 1.0
OG1 A:THR42 2.5 29.0 1.0
O A:HOH301 2.6 17.5 1.0
O2B A:GDP200 2.6 24.4 1.0
O3B A:GDP200 2.7 24.0 1.0
O A:HOH302 2.9 19.5 1.0
F3 A:BEF201 3.0 25.2 1.0
CB A:THR42 3.1 30.1 1.0
F2 A:BEF201 3.1 24.0 1.0
PB A:GDP200 3.1 24.6 1.0
N A:THR42 3.1 33.3 1.0
OG1 A:THR24 3.5 27.6 1.0
CA A:THR42 3.7 32.7 1.0
O2A A:GDP200 4.2 24.6 1.0
C A:ALA41 4.2 35.4 1.0
O3A A:GDP200 4.2 25.5 1.0
CA A:ALA41 4.3 35.7 1.0
O1B A:GDP200 4.3 24.7 1.0
CG2 A:THR42 4.4 29.8 1.0
NZ A:LYS23 4.4 26.9 1.0
O A:THR66 4.5 31.9 1.0
O A:VAL40 4.5 33.0 1.0
CA A:ALA67 4.6 35.1 1.0
CB A:THR24 4.6 27.3 1.0
CE1 A:TYR39 4.7 36.9 1.0
C A:THR42 4.8 34.8 1.0
CE A:LYS23 4.8 25.9 1.0
PA A:GDP200 4.8 24.2 1.0
O A:THR42 4.9 35.2 1.0
CB A:ALA67 5.0 36.2 1.0

Fluorine binding site 2 out of 6 in 5cll

Go back to Fluorine Binding Sites List in 5cll
Fluorine binding site 2 out of 6 in the Truncated Ran Wild Type in Complex with Gdp-Bef and RANBD1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Truncated Ran Wild Type in Complex with Gdp-Bef and RANBD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:24.0
occ:1.00
 F2 A:BEF201 0.0 24.0 1.0
BE A:BEF201 1.7 24.0 1.0
NZ A:LYS23 2.5 26.9 1.0
N A:GLY68 2.7 37.5 1.0
O2B A:GDP200 2.7 24.4 1.0
F3 A:BEF201 2.8 25.2 1.0
F1 A:BEF201 3.1 24.4 1.0
CA A:GLY19 3.3 31.2 1.0
CA A:GLY68 3.4 38.7 1.0
CE A:LYS23 3.5 25.9 1.0
C A:ALA67 3.6 35.6 1.0
CA A:ALA67 3.6 35.1 1.0
N A:GLY19 3.7 31.0 1.0
PB A:GDP200 3.8 24.6 1.0
O A:THR66 4.0 31.9 1.0
O A:HOH302 4.1 19.5 1.0
O A:ASP18 4.1 28.8 1.0
C A:ASP18 4.1 30.0 1.0
O A:GLY17 4.2 29.1 1.0
O1B A:GDP200 4.2 24.7 1.0
NE2 A:GLN69 4.3 49.9 1.0
O3B A:GDP200 4.4 24.0 1.0
MG A:MG202 4.4 27.4 1.0
C A:GLY19 4.4 31.8 1.0
C A:GLY68 4.5 41.5 1.0
CB A:ALA67 4.5 36.2 1.0
N A:GLY20 4.5 30.7 1.0
N A:GLN69 4.7 44.1 1.0
O A:ALA67 4.7 34.9 1.0
N A:ALA67 4.7 32.9 1.0
C A:THR66 4.8 31.8 1.0
OH A:TYR39 4.8 39.1 1.0
CD A:LYS23 4.9 24.8 1.0

Fluorine binding site 3 out of 6 in 5cll

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Fluorine binding site 3 out of 6 in the Truncated Ran Wild Type in Complex with Gdp-Bef and RANBD1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Truncated Ran Wild Type in Complex with Gdp-Bef and RANBD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:25.2
occ:1.00
 F3 A:BEF201 0.0 25.2 1.0
BE A:BEF201 1.7 24.0 1.0
OH A:TYR39 2.4 39.1 1.0
O2B A:GDP200 2.6 24.4 1.0
F2 A:BEF201 2.8 24.0 1.0
F1 A:BEF201 3.0 24.4 1.0
CE1 A:TYR39 3.2 36.9 1.0
CZ A:TYR39 3.2 38.9 1.0
NE2 A:GLN69 3.4 49.9 1.0
CA A:ALA41 3.4 35.7 1.0
CB A:ALA41 3.5 37.7 1.0
CA A:GLY19 3.6 31.2 1.0
N A:THR42 3.7 33.3 1.0
C A:ALA41 4.1 35.4 1.0
PB A:GDP200 4.1 24.6 1.0
N A:GLY20 4.1 30.7 1.0
O A:HOH301 4.3 17.5 1.0
C A:GLY19 4.4 31.8 1.0
CD A:GLN69 4.5 52.0 1.0
MG A:MG202 4.5 27.4 1.0
N A:ALA41 4.5 36.6 1.0
CE2 A:TYR39 4.6 41.2 1.0
CD1 A:TYR39 4.6 37.0 1.0
N A:GLY68 4.6 37.5 1.0
O3B A:GDP200 4.7 24.0 1.0
OE1 A:GLN69 4.7 53.3 1.0
O3A A:GDP200 4.7 25.5 1.0
N A:GLY19 4.8 31.0 1.0
CA A:THR42 4.9 32.7 1.0

Fluorine binding site 4 out of 6 in 5cll

Go back to Fluorine Binding Sites List in 5cll
Fluorine binding site 4 out of 6 in the Truncated Ran Wild Type in Complex with Gdp-Bef and RANBD1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Truncated Ran Wild Type in Complex with Gdp-Bef and RANBD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F201

b:26.1
occ:1.00
 F1 C:BEF201 0.0 26.1 1.0
BE C:BEF201 1.8 25.5 1.0
NZ C:LYS23 2.5 25.7 1.0
N C:GLY68 2.6 35.4 1.0
O3B C:GDP200 2.8 25.3 1.0
F3 C:BEF201 3.0 25.5 1.0
F2 C:BEF201 3.1 25.5 1.0
CA C:GLY68 3.3 36.9 1.0
CE C:LYS23 3.3 25.4 1.0
CA C:GLY19 3.4 31.6 1.0
C C:ALA67 3.5 34.0 1.0
CA C:ALA67 3.6 33.7 1.0
PB C:GDP200 3.8 25.4 1.0
O C:THR66 3.8 30.0 1.0
N C:GLY19 3.8 30.9 1.0
O C:GLY17 4.0 27.9 1.0
O C:HOH302 4.1 19.3 1.0
O2B C:GDP200 4.1 24.8 1.0
O C:ASP18 4.1 28.9 1.0
C C:ASP18 4.2 29.8 1.0
O1B C:GDP200 4.2 25.6 1.0
MG C:MG202 4.2 33.2 1.0
NE2 C:GLN69 4.4 47.2 1.0
C C:GLY68 4.5 39.5 1.0
CB C:ALA67 4.5 34.8 1.0
C C:GLY19 4.6 32.0 1.0
O C:ALA67 4.6 33.3 1.0
N C:ALA67 4.6 31.9 1.0
C C:THR66 4.6 30.6 1.0
N C:GLY20 4.6 31.6 1.0
N C:GLN69 4.7 41.9 1.0
CD C:LYS23 4.7 24.2 1.0
O C:HOH309 4.9 25.3 1.0

Fluorine binding site 5 out of 6 in 5cll

Go back to Fluorine Binding Sites List in 5cll
Fluorine binding site 5 out of 6 in the Truncated Ran Wild Type in Complex with Gdp-Bef and RANBD1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Truncated Ran Wild Type in Complex with Gdp-Bef and RANBD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F201

b:25.5
occ:1.00
 F2 C:BEF201 0.0 25.5 1.0
MG C:MG202 1.7 33.2 1.0
BE C:BEF201 1.7 25.5 1.0
OG1 C:THR42 2.5 31.5 1.0
O C:HOH301 2.6 17.0 1.0
O1B C:GDP200 2.7 25.6 1.0
O3B C:GDP200 2.7 25.3 1.0
F3 C:BEF201 2.8 25.5 1.0
N C:THR42 3.0 34.6 1.0
O C:HOH302 3.0 19.3 1.0
CB C:THR42 3.0 32.6 1.0
F1 C:BEF201 3.1 26.1 1.0
PB C:GDP200 3.2 25.4 1.0
OG1 C:THR24 3.5 29.4 1.0
CA C:THR42 3.6 35.0 1.0
C C:ALA41 4.0 36.6 1.0
CA C:ALA41 4.2 36.8 1.0
O1A C:GDP200 4.3 24.1 1.0
O3A C:GDP200 4.3 25.1 1.0
CG2 C:THR42 4.4 32.5 1.0
O2B C:GDP200 4.4 24.8 1.0
CA C:ALA67 4.5 33.7 1.0
O C:VAL40 4.5 34.7 1.0
NZ C:LYS23 4.5 25.7 1.0
O C:THR66 4.6 30.0 1.0
CE1 C:TYR39 4.7 35.7 1.0
C C:THR42 4.7 37.6 1.0
CB C:THR24 4.7 28.8 1.0
O C:THR42 4.7 37.7 1.0
CE C:LYS23 4.9 25.4 1.0
CB C:ALA67 4.9 34.8 1.0
PA C:GDP200 4.9 23.5 1.0

Fluorine binding site 6 out of 6 in 5cll

Go back to Fluorine Binding Sites List in 5cll
Fluorine binding site 6 out of 6 in the Truncated Ran Wild Type in Complex with Gdp-Bef and RANBD1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Truncated Ran Wild Type in Complex with Gdp-Bef and RANBD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F201

b:25.5
occ:1.00
 F3 C:BEF201 0.0 25.5 1.0
BE C:BEF201 1.7 25.5 1.0
OH C:TYR39 2.5 37.5 1.0
O3B C:GDP200 2.5 25.3 1.0
F2 C:BEF201 2.8 25.5 1.0
F1 C:BEF201 3.0 26.1 1.0
CE1 C:TYR39 3.2 35.7 1.0
CZ C:TYR39 3.2 37.6 1.0
CA C:ALA41 3.3 36.8 1.0
CB C:ALA41 3.4 38.4 1.0
NE2 C:GLN69 3.5 47.2 1.0
N C:THR42 3.6 34.6 1.0
CA C:GLY19 3.7 31.6 1.0
PB C:GDP200 4.0 25.4 1.0
C C:ALA41 4.0 36.6 1.0
N C:GLY20 4.2 31.6 1.0
O C:HOH301 4.2 17.0 1.0
MG C:MG202 4.4 33.2 1.0
N C:ALA41 4.4 37.5 1.0
O1B C:GDP200 4.4 25.6 1.0
C C:GLY19 4.5 32.0 1.0
CD1 C:TYR39 4.5 36.1 1.0
CE2 C:TYR39 4.6 39.8 1.0
CD C:GLN69 4.6 49.0 1.0
O3A C:GDP200 4.7 25.1 1.0
N C:GLY68 4.7 35.4 1.0
OE1 C:GLN69 4.8 50.1 1.0
CA C:THR42 4.8 35.0 1.0
N C:GLY19 4.9 30.9 1.0
OG1 C:THR42 5.0 31.5 1.0

Reference:

T.Rudack, S.Jenrich, S.Brucker, I.R.Vetter, K.Gerwert, C.Kotting. Catalysis of Gtp Hydrolysis By Small Gtpases at Atomic Detail By Integration of X-Ray Crystallography, Experimental, and Theoretical Ir Spectroscopy. J.Biol.Chem. V. 290 24079 2015.
ISSN: ESSN 1083-351X
PubMed: 26272610
DOI: 10.1074/JBC.M115.648071
Page generated: Thu Aug 1 08:33:40 2024

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