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Fluorine in PDB 1k5g: Crystal Structure of Ran-Gdp-Alfx-RANBP1-Rangap Complex

Protein crystallography data

The structure of Crystal Structure of Ran-Gdp-Alfx-RANBP1-Rangap Complex, PDB code: 1k5g was solved by M.J.Seewald, C.Koerner, A.Wittinghofer, I.R.Vetter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.00 / 3.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 99.930, 102.568, 118.850, 71.67, 79.09, 67.81
R / Rfree (%) 25 / 26.9

Other elements in 1k5g:

The structure of Crystal Structure of Ran-Gdp-Alfx-RANBP1-Rangap Complex also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Aluminium (Al) 4 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Ran-Gdp-Alfx-RANBP1-Rangap Complex (pdb code 1k5g). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of Ran-Gdp-Alfx-RANBP1-Rangap Complex, PDB code: 1k5g:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 1k5g

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Fluorine binding site 1 out of 12 in the Crystal Structure of Ran-Gdp-Alfx-RANBP1-Rangap Complex


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 Ran-Gdp-Alfx-RANBP1-Rangap Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1252

b:57.3
occ:1.00
F1 A:AF31252 0.0 57.3 1.0
AL A:AF31252 1.7 57.4 1.0
N A:THR42 2.4 34.6 1.0
MG A:MG1251 2.6 31.7 1.0
F3 A:AF31252 2.7 57.5 1.0
F2 A:AF31252 3.0 57.7 1.0
CB A:THR42 3.2 33.6 1.0
CA A:THR42 3.2 34.6 1.0
C A:ALA41 3.3 24.4 1.0
CA A:ALA41 3.3 24.4 1.0
OG1 A:THR42 3.4 33.6 1.0
O2B A:GDP1250 3.5 43.3 1.0
O A:THR42 3.8 34.6 1.0
C A:THR42 3.8 34.6 1.0
CB A:ALA41 4.0 10.4 1.0
O3B A:GDP1250 4.3 43.3 1.0
O A:ALA41 4.4 24.4 1.0
PB A:GDP1250 4.5 43.3 1.0
OE1 A:GLN69 4.5 42.7 1.0
CA A:ALA67 4.5 25.9 1.0
N A:ALA41 4.6 24.4 1.0
N A:GLY68 4.6 39.6 1.0
CG2 A:THR42 4.6 33.6 1.0
O A:VAL40 4.7 26.0 1.0
O A:THR66 4.8 38.6 1.0
CB A:ALA67 4.9 1.0 1.0
OH A:TYR39 4.9 40.6 1.0
CE1 A:TYR39 4.9 40.6 1.0
N A:LEU43 5.0 22.1 1.0

Fluorine binding site 2 out of 12 in 1k5g

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Fluorine binding site 2 out of 12 in the Crystal Structure of Ran-Gdp-Alfx-RANBP1-Rangap Complex


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 Ran-Gdp-Alfx-RANBP1-Rangap Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1252

b:57.7
occ:1.00
F2 A:AF31252 0.0 57.7 1.0
AL A:AF31252 1.7 57.4 1.0
OH A:TYR39 2.8 40.6 1.0
F3 A:AF31252 2.9 57.5 1.0
NE2 A:GLN69 3.0 42.5 1.0
F1 A:AF31252 3.0 57.3 1.0
CA A:GLY19 3.1 42.9 1.0
OE1 A:GLN69 3.2 42.7 1.0
CD A:GLN69 3.5 42.5 1.0
N A:GLY20 3.6 63.3 1.0
C A:GLY19 3.7 42.9 1.0
O3B A:GDP1250 3.8 43.3 1.0
CZ A:TYR39 3.9 40.6 1.0
CE1 A:TYR39 4.1 40.6 1.0
N A:GLY19 4.3 42.9 1.0
N A:GLY68 4.3 39.6 1.0
CB A:ALA41 4.5 10.4 1.0
CA C:GLY133 4.5 27.6 1.0
CA A:ALA41 4.6 24.4 1.0
CA A:GLY68 4.6 39.6 1.0
CA A:GLY20 4.7 63.3 1.0
O A:GLY19 4.8 42.9 1.0
O2B A:GDP1250 4.8 43.3 1.0
MG A:MG1251 4.8 31.7 1.0
PB A:GDP1250 4.9 43.3 1.0
C A:GLY68 4.9 39.6 1.0
CG A:GLN69 5.0 42.1 1.0

Fluorine binding site 3 out of 12 in 1k5g

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Fluorine binding site 3 out of 12 in the Crystal Structure of Ran-Gdp-Alfx-RANBP1-Rangap Complex


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 Ran-Gdp-Alfx-RANBP1-Rangap Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1252

b:57.5
occ:1.00
F3 A:AF31252 0.0 57.5 1.0
AL A:AF31252 1.6 57.4 1.0
F1 A:AF31252 2.7 57.3 1.0
O3B A:GDP1250 2.9 43.3 1.0
MG A:MG1251 2.9 31.7 1.0
F2 A:AF31252 2.9 57.7 1.0
NZ A:LYS23 3.1 30.1 1.0
O2B A:GDP1250 3.2 43.3 1.0
CE A:LYS23 3.3 30.1 1.0
PB A:GDP1250 3.3 43.3 1.0
N A:GLY68 3.3 39.6 1.0
O1B A:GDP1250 3.4 43.3 1.0
CA A:GLY19 3.6 42.9 1.0
O A:THR66 4.0 38.6 1.0
CA A:GLY68 4.0 39.6 1.0
N A:GLY20 4.1 63.3 1.0
C A:ALA67 4.3 25.9 1.0
CA A:ALA67 4.3 25.9 1.0
C A:GLY19 4.4 42.9 1.0
N A:GLY19 4.4 42.9 1.0
O A:ASP18 4.6 41.2 1.0
CD A:LYS23 4.8 30.1 1.0
O3A A:GDP1250 4.8 43.3 1.0
C A:ASP18 4.8 41.2 1.0
O A:GLY17 4.8 40.1 1.0
OG1 A:THR42 4.8 33.6 1.0
OE1 A:GLN69 4.9 42.7 1.0
CB A:THR42 4.9 33.6 1.0
C A:THR66 5.0 38.6 1.0

Fluorine binding site 4 out of 12 in 1k5g

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Fluorine binding site 4 out of 12 in the Crystal Structure of Ran-Gdp-Alfx-RANBP1-Rangap Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Ran-Gdp-Alfx-RANBP1-Rangap Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F2252

b:57.3
occ:1.00
F1 D:AF32252 0.0 57.3 1.0
AL D:AF32252 1.7 57.4 1.0
MG D:MG2251 2.0 45.2 1.0
N D:THR42 2.5 25.1 1.0
F3 D:AF32252 2.7 57.5 1.0
OG1 D:THR42 2.9 2.1 1.0
O2B D:GDP2250 2.9 32.0 1.0
CB D:THR42 3.0 2.1 1.0
F2 D:AF32252 3.0 57.7 1.0
CA D:THR42 3.2 25.1 1.0
C D:ALA41 3.5 27.9 1.0
CA D:ALA41 3.6 27.9 1.0
O3B D:GDP2250 3.9 32.0 1.0
PB D:GDP2250 3.9 32.0 1.0
O D:THR42 4.0 25.1 1.0
C D:THR42 4.1 25.1 1.0
CB D:ALA41 4.4 52.1 1.0
CG2 D:THR42 4.4 2.1 1.0
OG1 D:THR24 4.5 24.1 1.0
O D:VAL40 4.6 19.9 1.0
O D:ALA41 4.6 27.9 1.0
O1B D:GDP2250 4.6 32.0 1.0
O D:THR66 4.7 23.3 1.0
N D:ALA41 4.7 27.9 1.0
CA D:ALA67 4.7 36.2 1.0
CE1 D:TYR39 4.9 60.1 1.0
N D:GLY68 4.9 44.9 1.0
O2A D:GDP2250 4.9 32.0 1.0

Fluorine binding site 5 out of 12 in 1k5g

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Fluorine binding site 5 out of 12 in the Crystal Structure of Ran-Gdp-Alfx-RANBP1-Rangap Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Ran-Gdp-Alfx-RANBP1-Rangap Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F2252

b:57.7
occ:1.00
F2 D:AF32252 0.0 57.7 1.0
AL D:AF32252 1.7 57.4 1.0
F3 D:AF32252 2.9 57.5 1.0
OH D:TYR39 2.9 60.1 1.0
F1 D:AF32252 3.0 57.3 1.0
OE1 D:GLN69 3.1 42.4 1.0
NE2 D:GLN69 3.1 42.2 1.0
CD D:GLN69 3.5 42.2 1.0
CA D:GLY19 3.8 32.7 1.0
CB D:ALA41 3.8 52.1 1.0
CZ D:TYR39 4.0 60.1 1.0
CA D:ALA41 4.0 27.9 1.0
O3B D:GDP2250 4.0 32.0 1.0
CE1 D:TYR39 4.1 60.1 1.0
N D:GLY20 4.1 43.9 1.0
N D:THR42 4.4 25.1 1.0
C D:GLY19 4.4 32.7 1.0
N D:GLY68 4.5 44.9 1.0
CA F:GLY133 4.5 37.7 1.0
MG D:MG2251 4.7 45.2 1.0
C D:ALA41 4.7 27.9 1.0
O2B D:GDP2250 4.8 32.0 1.0
CA D:GLY68 5.0 44.9 1.0
N D:GLY19 5.0 32.7 1.0

Fluorine binding site 6 out of 12 in 1k5g

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Fluorine binding site 6 out of 12 in the Crystal Structure of Ran-Gdp-Alfx-RANBP1-Rangap Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Ran-Gdp-Alfx-RANBP1-Rangap Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F2252

b:57.5
occ:1.00
F3 D:AF32252 0.0 57.5 1.0
AL D:AF32252 1.6 57.4 1.0
O3B D:GDP2250 2.7 32.0 1.0
F1 D:AF32252 2.7 57.3 1.0
F2 D:AF32252 2.9 57.7 1.0
NZ D:LYS23 3.1 26.3 1.0
MG D:MG2251 3.2 45.2 1.0
PB D:GDP2250 3.2 32.0 1.0
CA D:GLY19 3.3 32.7 1.0
O2B D:GDP2250 3.3 32.0 1.0
CE D:LYS23 3.4 26.3 1.0
O1B D:GDP2250 3.4 32.0 1.0
N D:GLY68 3.5 44.9 1.0
N D:GLY20 3.7 43.9 1.0
CA D:GLY68 4.1 44.9 1.0
C D:GLY19 4.1 32.7 1.0
N D:GLY19 4.2 32.7 1.0
O D:ASP18 4.3 23.8 1.0
O D:THR66 4.4 23.3 1.0
C D:ALA67 4.5 36.2 1.0
C D:ASP18 4.6 23.8 1.0
CA D:ALA67 4.6 36.2 1.0
O3A D:GDP2250 4.7 32.0 1.0
OE1 D:GLN69 4.8 42.4 1.0
O D:GLY17 4.8 27.6 1.0
OH D:TYR39 4.9 60.1 1.0
CD D:LYS23 4.9 26.3 1.0
CA D:GLY20 5.0 43.9 1.0

Fluorine binding site 7 out of 12 in 1k5g

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Fluorine binding site 7 out of 12 in the Crystal Structure of Ran-Gdp-Alfx-RANBP1-Rangap Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Ran-Gdp-Alfx-RANBP1-Rangap Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F3252

b:57.3
occ:1.00
F1 G:AF33252 0.0 57.3 1.0
AL G:AF33252 1.7 57.4 1.0
N G:THR42 2.5 40.0 1.0
F3 G:AF33252 2.7 57.5 1.0
MG G:MG3251 2.9 44.9 1.0
CB G:THR42 3.0 46.2 1.0
F2 G:AF33252 3.1 57.7 1.0
CA G:THR42 3.1 40.0 1.0
O G:THR42 3.2 40.0 1.0
OG1 G:THR42 3.4 46.2 1.0
C G:THR42 3.4 40.0 1.0
C G:ALA41 3.6 14.8 1.0
CA G:ALA67 3.7 42.5 1.0
CA G:ALA41 3.9 14.8 1.0
CB G:ALA67 4.0 14.2 1.0
O2B G:GDP3250 4.1 35.4 1.0
N G:GLY68 4.1 42.8 1.0
OE1 G:GLN69 4.2 55.0 1.0
O G:THR66 4.3 29.3 1.0
CG2 G:THR42 4.3 46.2 1.0
CB G:ALA41 4.3 63.6 1.0
C G:ALA67 4.5 42.5 1.0
N G:LEU43 4.6 42.1 1.0
O G:ALA41 4.6 14.8 1.0
N G:ALA67 4.7 42.5 1.0
O3B G:GDP3250 4.8 35.4 1.0
C G:THR66 4.9 29.3 1.0
PB G:GDP3250 5.0 35.4 1.0

Fluorine binding site 8 out of 12 in 1k5g

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Fluorine binding site 8 out of 12 in the Crystal Structure of Ran-Gdp-Alfx-RANBP1-Rangap Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Ran-Gdp-Alfx-RANBP1-Rangap Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F3252

b:57.7
occ:1.00
F2 G:AF33252 0.0 57.7 1.0
AL G:AF33252 1.7 57.4 1.0
OH G:TYR39 2.6 25.3 1.0
F3 G:AF33252 2.9 57.5 1.0
F1 G:AF33252 3.1 57.3 1.0
NE2 G:GLN69 3.5 54.8 1.0
CZ G:TYR39 3.5 25.3 1.0
O3B G:GDP3250 3.5 35.4 1.0
CE1 G:TYR39 3.6 25.3 1.0
CA G:GLY19 3.6 27.0 1.0
N G:GLY20 3.7 57.5 1.0
OE1 G:GLN69 3.7 55.0 1.0
CA G:ALA41 3.9 14.8 1.0
CB G:ALA41 4.0 63.6 1.0
CD G:GLN69 4.0 54.7 1.0
C G:GLY19 4.1 27.0 1.0
O2B G:GDP3250 4.4 35.4 1.0
MG G:MG3251 4.4 44.9 1.0
N G:THR42 4.4 40.0 1.0
PB G:GDP3250 4.6 35.4 1.0
CA I:GLY133 4.6 34.4 1.0
CA G:GLY20 4.7 57.5 1.0
C G:ALA41 4.8 14.8 1.0
N G:GLY68 4.8 42.8 1.0
CE2 G:TYR39 4.8 25.3 1.0
N G:ALA41 4.9 14.8 1.0
N G:GLY19 4.9 27.0 1.0
CD1 G:TYR39 4.9 25.3 1.0

Fluorine binding site 9 out of 12 in 1k5g

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Fluorine binding site 9 out of 12 in the Crystal Structure of Ran-Gdp-Alfx-RANBP1-Rangap Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Ran-Gdp-Alfx-RANBP1-Rangap Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F3252

b:57.5
occ:1.00
F3 G:AF33252 0.0 57.5 1.0
AL G:AF33252 1.6 57.4 1.0
O3B G:GDP3250 2.7 35.4 1.0
F1 G:AF33252 2.7 57.3 1.0
MG G:MG3251 2.8 44.9 1.0
F2 G:AF33252 2.9 57.7 1.0
O2B G:GDP3250 3.1 35.4 1.0
PB G:GDP3250 3.1 35.4 1.0
NZ G:LYS23 3.2 26.7 1.0
O1B G:GDP3250 3.3 35.4 1.0
CE G:LYS23 3.3 26.7 1.0
N G:GLY68 3.6 42.8 1.0
CA G:GLY19 3.6 27.0 1.0
N G:GLY20 4.0 57.5 1.0
O G:THR66 4.1 29.3 1.0
CA G:GLY68 4.3 42.8 1.0
C G:GLY19 4.4 27.0 1.0
CA G:ALA67 4.5 42.5 1.0
C G:ALA67 4.5 42.5 1.0
N G:GLY19 4.5 27.0 1.0
O3A G:GDP3250 4.6 35.4 1.0
O G:ASP18 4.6 31.3 1.0
OG1 G:THR42 4.7 46.2 1.0
CD G:LYS23 4.9 26.7 1.0
N G:THR42 4.9 40.0 1.0
CB G:THR42 4.9 46.2 1.0
C G:ASP18 4.9 31.3 1.0
OE1 G:GLN69 5.0 55.0 1.0

Fluorine binding site 10 out of 12 in 1k5g

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Fluorine binding site 10 out of 12 in the Crystal Structure of Ran-Gdp-Alfx-RANBP1-Rangap Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Ran-Gdp-Alfx-RANBP1-Rangap Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:F4252

b:57.3
occ:1.00
F1 J:AF34252 0.0 57.3 1.0
AL J:AF34252 1.7 57.4 1.0
MG J:MG4251 2.3 33.0 1.0
F3 J:AF34252 2.7 57.5 1.0
N J:THR42 2.8 14.9 1.0
CB J:THR42 2.9 20.4 1.0
F2 J:AF34252 3.1 57.7 1.0
OG1 J:THR42 3.2 20.4 1.0
CA J:THR42 3.3 14.9 1.0
O2B J:GDP4250 3.5 29.1 1.0
O J:THR42 3.6 14.9 1.0
C J:THR42 3.8 14.9 1.0
C J:ALA41 3.9 12.5 1.0
CA J:ALA67 3.9 27.0 1.0
O J:THR66 4.0 28.0 1.0
CA J:ALA41 4.1 12.5 1.0
N J:GLY68 4.1 34.3 1.0
CG2 J:THR42 4.3 20.4 1.0
O3B J:GDP4250 4.3 29.1 1.0
CB J:ALA67 4.3 60.3 1.0
PB J:GDP4250 4.4 29.1 1.0
C J:ALA67 4.6 27.0 1.0
OE1 J:GLN69 4.7 45.1 1.0
C J:THR66 4.7 28.0 1.0
N J:ALA67 4.7 27.0 1.0
CB J:ALA41 4.7 19.7 1.0
O1B J:GDP4250 4.9 29.1 1.0
CE J:LYS23 4.9 28.9 1.0
O J:ALA41 5.0 12.5 1.0

Reference:

M.J.Seewald, C.Korner, A.Wittinghofer, I.R.Vetter. Rangap Mediates Gtp Hydrolysis Without An Arginine Finger. Nature V. 415 662 2002.
ISSN: ISSN 0028-0836
PubMed: 11832950
DOI: 10.1038/415662A
Page generated: Sun Dec 13 11:30:37 2020

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