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Fluorine in PDB 2b92: Crystal-Structure of the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gdp/ALF3

Protein crystallography data

The structure of Crystal-Structure of the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gdp/ALF3, PDB code: 2b92 was solved by A.Ghosh, G.J.K.Praefcke, L.Renault, A.Wittinghofer, C.Herrmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 148.820, 103.921, 55.485, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 25

Other elements in 2b92:

The structure of Crystal-Structure of the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gdp/ALF3 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Aluminium (Al) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal-Structure of the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gdp/ALF3 (pdb code 2b92). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal-Structure of the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gdp/ALF3, PDB code: 2b92:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 2b92

Go back to Fluorine Binding Sites List in 2b92
Fluorine binding site 1 out of 6 in the Crystal-Structure of the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gdp/ALF3


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 the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gdp/ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F594

b:39.0
occ:1.00
 F1 A:AF3594 0.0 39.0 1.0
AL A:AF3594 1.8 32.3 1.0
MG A:MG595 1.9 40.1 1.0
OG1 A:THR75 2.6 51.7 1.0
CB A:THR75 2.7 52.2 1.0
N A:THR75 2.8 53.5 1.0
O3B A:GDP593 2.8 46.7 1.0
O2B A:GDP593 2.9 56.8 1.0
F3 A:AF3594 3.1 38.5 1.0
F2 A:AF3594 3.2 37.8 1.0
CA A:THR75 3.3 52.3 1.0
O A:HOH602 3.4 77.1 1.0
PB A:GDP593 3.5 48.0 1.0
C A:HIS74 3.9 54.4 1.0
O A:THR75 3.9 52.6 1.0
OG A:SER52 4.0 37.5 1.0
O2A A:GDP593 4.0 52.3 1.0
N A:HIS74 4.0 54.7 1.0
CB A:HIS74 4.1 54.8 1.0
CG2 A:THR75 4.1 50.4 1.0
C A:THR75 4.1 52.8 1.0
CA A:HIS74 4.2 54.6 1.0
NH2 A:ARG48 4.4 46.6 1.0
O1B A:GDP593 4.5 51.9 1.0
O3A A:GDP593 4.5 53.7 1.0
O A:THR98 4.6 42.3 1.0
PA A:GDP593 4.9 55.1 1.0
N A:GLY100 5.0 41.1 1.0
O A:LEU67 5.0 55.4 1.0

Fluorine binding site 2 out of 6 in 2b92

Go back to Fluorine Binding Sites List in 2b92
Fluorine binding site 2 out of 6 in the Crystal-Structure of the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gdp/ALF3


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 the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gdp/ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F594

b:37.8
occ:1.00
 F2 A:AF3594 0.0 37.8 1.0
AL A:AF3594 1.8 32.3 1.0
O A:HOH602 2.5 77.1 1.0
O3B A:GDP593 2.5 46.7 1.0
N A:GLY100 3.0 41.1 1.0
NZ A:LYS51 3.0 29.8 1.0
CA A:GLY100 3.0 40.4 1.0
F1 A:AF3594 3.2 39.0 1.0
F3 A:AF3594 3.2 38.5 1.0
PB A:GDP593 3.3 48.0 1.0
O1B A:GDP593 3.4 51.9 1.0
CA A:TYR47 3.5 38.1 1.0
CE A:LYS51 3.6 29.7 1.0
CB A:TYR47 3.6 37.8 1.0
N A:ARG48 3.7 38.5 1.0
O2B A:GDP593 3.8 56.8 1.0
C A:TYR47 4.1 38.5 1.0
MG A:MG595 4.1 40.1 1.0
C A:GLU99 4.2 41.4 1.0
C A:GLY100 4.2 39.7 1.0
O A:THR98 4.3 42.3 1.0
N A:TYR47 4.5 36.8 1.0
O A:GLY100 4.6 39.6 1.0
O A:LEU46 4.6 34.6 1.0
CA A:GLU99 4.7 42.4 1.0
O3A A:GDP593 4.8 53.7 1.0
C A:LEU46 4.9 35.4 1.0
CA A:ARG48 4.9 38.4 1.0

Fluorine binding site 3 out of 6 in 2b92

Go back to Fluorine Binding Sites List in 2b92
Fluorine binding site 3 out of 6 in the Crystal-Structure of the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gdp/ALF3


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 the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gdp/ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F594

b:38.5
occ:1.00
 F3 A:AF3594 0.0 38.5 1.0
AL A:AF3594 1.8 32.3 1.0
NE A:ARG48 2.5 44.5 1.0
O3B A:GDP593 2.6 46.7 1.0
O A:HOH602 2.7 77.1 1.0
NH2 A:ARG48 2.9 46.6 1.0
N A:HIS74 3.0 54.7 1.0
CZ A:ARG48 3.1 45.8 1.0
F1 A:AF3594 3.1 39.0 1.0
F2 A:AF3594 3.2 37.8 1.0
CA A:SER73 3.2 54.2 1.0
C A:SER73 3.5 54.4 1.0
CD A:ARG48 3.6 41.6 1.0
CB A:SER73 3.7 54.1 1.0
N A:ARG48 3.8 38.5 1.0
PB A:GDP593 4.0 48.0 1.0
CA A:HIS74 4.1 54.6 1.0
CB A:HIS74 4.1 54.8 1.0
CG A:ARG48 4.2 39.8 1.0
NH1 A:ARG48 4.3 46.0 1.0
O A:GLN72 4.3 52.2 1.0
CA A:ARG48 4.3 38.4 1.0
N A:SER73 4.4 53.1 1.0
CB A:TYR47 4.4 37.8 1.0
N A:THR75 4.4 53.5 1.0
O2B A:GDP593 4.5 56.8 1.0
O3A A:GDP593 4.6 53.7 1.0
MG A:MG595 4.7 40.1 1.0
O A:SER73 4.7 54.8 1.0
C A:TYR47 4.7 38.5 1.0
C A:HIS74 4.8 54.4 1.0
O2A A:GDP593 4.8 52.3 1.0
C A:GLN72 4.8 52.4 1.0
CA A:TYR47 4.8 38.1 1.0
CB A:ARG48 4.8 38.4 1.0
OG A:SER73 4.8 55.4 1.0
CD1 A:TYR47 4.9 38.9 1.0
O1B A:GDP593 4.9 51.9 1.0

Fluorine binding site 4 out of 6 in 2b92

Go back to Fluorine Binding Sites List in 2b92
Fluorine binding site 4 out of 6 in the Crystal-Structure of the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gdp/ALF3


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 the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gdp/ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F594

b:37.5
occ:1.00
 F1 B:AF3594 0.0 37.5 1.0
AL B:AF3594 1.8 30.4 1.0
NE B:ARG48 2.5 44.7 1.0
O3B B:GDP593 2.6 47.3 1.0
O B:HOH599 2.7 64.2 1.0
NH2 B:ARG48 3.0 47.9 1.0
CZ B:ARG48 3.1 45.9 1.0
F3 B:AF3594 3.1 34.6 1.0
F2 B:AF3594 3.2 36.5 1.0
N B:HIS74 3.2 55.3 1.0
CA B:SER73 3.2 54.3 1.0
N B:ARG48 3.5 39.0 1.0
CD B:ARG48 3.5 41.4 1.0
CB B:SER73 3.6 54.3 1.0
C B:SER73 3.7 54.8 1.0
CG B:ARG48 3.8 40.2 1.0
CB B:TYR47 4.0 38.1 1.0
PB B:GDP593 4.0 47.9 1.0
CA B:ARG48 4.1 38.8 1.0
CA B:HIS74 4.3 55.3 1.0
CD1 B:TYR47 4.3 39.0 1.0
CB B:HIS74 4.3 55.3 1.0
O B:GLN72 4.4 51.7 1.0
N B:SER73 4.4 52.9 1.0
C B:TYR47 4.4 39.1 1.0
CA B:TYR47 4.4 38.6 1.0
NH1 B:ARG48 4.4 47.0 1.0
CB B:ARG48 4.6 38.6 1.0
O2B B:GDP593 4.6 48.8 1.0
CG B:TYR47 4.6 39.2 1.0
N B:THR75 4.6 54.4 1.0
O3A B:GDP593 4.7 55.8 1.0
C B:GLN72 4.8 51.9 1.0
MG B:MG595 4.9 43.6 1.0
O1B B:GDP593 4.9 53.2 1.0
OG B:SER73 4.9 56.0 1.0
O B:SER73 4.9 55.2 1.0
C B:HIS74 5.0 55.3 1.0

Fluorine binding site 5 out of 6 in 2b92

Go back to Fluorine Binding Sites List in 2b92
Fluorine binding site 5 out of 6 in the Crystal-Structure of the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gdp/ALF3


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 the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gdp/ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F594

b:36.5
occ:1.00
 F2 B:AF3594 0.0 36.5 1.0
AL B:AF3594 1.8 30.4 1.0
O B:HOH599 2.6 64.2 1.0
O3B B:GDP593 2.6 47.3 1.0
NZ B:LYS51 2.8 29.5 1.0
N B:GLY100 2.9 41.6 1.0
CA B:GLY100 3.0 40.9 1.0
F1 B:AF3594 3.2 37.5 1.0
F3 B:AF3594 3.2 34.6 1.0
PB B:GDP593 3.3 47.9 1.0
CE B:LYS51 3.3 29.4 1.0
O1B B:GDP593 3.4 53.2 1.0
CA B:TYR47 3.6 38.6 1.0
O2B B:GDP593 3.6 48.8 1.0
MG B:MG595 3.7 43.6 1.0
CB B:TYR47 3.7 38.1 1.0
N B:ARG48 3.8 39.0 1.0
C B:GLU99 4.1 41.9 1.0
O B:THR98 4.2 42.9 1.0
C B:TYR47 4.3 39.1 1.0
C B:GLY100 4.4 40.1 1.0
N B:TYR47 4.6 37.4 1.0
CA B:GLU99 4.7 42.9 1.0
O B:LEU46 4.7 34.9 1.0
CD B:LYS51 4.8 29.5 1.0
O3A B:GDP593 4.8 55.8 1.0
O B:GLY100 4.8 40.1 1.0
CB B:THR75 4.9 53.0 1.0
O B:THR75 5.0 53.4 1.0
C B:LEU46 5.0 36.0 1.0

Fluorine binding site 6 out of 6 in 2b92

Go back to Fluorine Binding Sites List in 2b92
Fluorine binding site 6 out of 6 in the Crystal-Structure of the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gdp/ALF3


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 the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gdp/ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F594

b:34.6
occ:1.00
 F3 B:AF3594 0.0 34.6 1.0
AL B:AF3594 1.8 30.4 1.0
MG B:MG595 2.1 43.6 1.0
OG1 B:THR75 2.6 52.4 1.0
N B:THR75 2.7 54.4 1.0
O3B B:GDP593 2.9 47.3 1.0
CB B:THR75 2.9 53.0 1.0
O2B B:GDP593 2.9 48.8 1.0
F1 B:AF3594 3.1 37.5 1.0
F2 B:AF3594 3.2 36.5 1.0
O B:HOH599 3.2 64.2 1.0
CA B:THR75 3.3 53.3 1.0
PB B:GDP593 3.5 47.9 1.0
CB B:HIS74 3.7 55.3 1.0
C B:HIS74 3.7 55.3 1.0
N B:HIS74 3.7 55.3 1.0
CA B:HIS74 3.8 55.3 1.0
OG B:SER52 3.8 36.9 1.0
O2A B:GDP593 3.9 55.8 1.0
NH2 B:ARG48 3.9 47.9 1.0
O B:THR75 4.1 53.4 1.0
C B:THR75 4.2 53.7 1.0
CG2 B:THR75 4.4 51.4 1.0
O3A B:GDP593 4.5 55.8 1.0
O1B B:GDP593 4.6 53.2 1.0
CG B:HIS74 4.7 54.4 1.0
O B:LEU67 4.8 55.5 1.0
O B:HIS74 4.8 55.6 1.0
PA B:GDP593 4.9 55.4 1.0
CZ B:ARG48 4.9 45.9 1.0
C B:SER73 4.9 54.8 1.0

Reference:

A.Ghosh, G.J.Praefcke, L.Renault, A.Wittinghofer, C.Herrmann. How Guanylate-Binding Proteins Achieve Assembly-Stimulated Processive Cleavage of Gtp to Gmp. Nature V. 440 101 2006.
ISSN: ISSN 0028-0836
PubMed: 16511497
DOI: 10.1038/NATURE04510
Page generated: Wed Jul 31 13:50:45 2024

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