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Fluorine in PDB 2b8w: Crystal-Structure of the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gmp/ALF4

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 Gmp/ALF4, PDB code: 2b8w 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) 29.75 / 2.22
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 149.617, 101.927, 54.121, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 23.3

Other elements in 2b8w:

The structure of Crystal-Structure of the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gmp/ALF4 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 Gmp/ALF4 (pdb code 2b8w). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 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 Gmp/ALF4, PDB code: 2b8w:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 2b8w

Go back to Fluorine Binding Sites List in 2b8w
Fluorine binding site 1 out of 8 in the Crystal-Structure of the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gmp/ALF4


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 Gmp/ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F594

b:24.1
occ:1.00
 F1 A:ALF594 0.0 24.1 1.0
AL A:ALF594 1.8 25.6 1.0
F4 A:ALF594 2.5 26.4 1.0
F3 A:ALF594 2.5 23.0 1.0
O2P A:5GP593 2.6 20.3 1.0
O A:HOH602 2.6 29.7 1.0
NZ A:LYS51 2.8 19.7 1.0
CA A:GLY100 2.9 25.1 1.0
N A:GLY100 3.0 26.7 1.0
CA A:TYR47 3.1 20.5 1.0
CB A:TYR47 3.3 21.4 1.0
N A:ARG48 3.5 20.7 1.0
O3P A:5GP593 3.6 17.8 1.0
F2 A:ALF594 3.6 28.2 1.0
P A:5GP593 3.6 21.5 1.0
CE A:LYS51 3.7 18.7 1.0
C A:TYR47 3.8 23.7 1.0
O A:HOH607 3.9 43.5 1.0
C A:GLY100 4.1 25.4 1.0
C A:GLU99 4.2 24.9 1.0
N A:TYR47 4.2 24.2 1.0
MG A:MG595 4.3 24.4 1.0
O1P A:5GP593 4.3 24.8 1.0
O A:LEU46 4.4 24.1 1.0
O A:HOH633 4.4 27.2 1.0
O A:THR98 4.5 24.7 1.0
O A:GLY100 4.6 21.8 1.0
C A:LEU46 4.7 22.6 1.0
CA A:ARG48 4.7 19.7 1.0
CG A:TYR47 4.7 19.5 1.0
CA A:GLU99 4.9 25.2 1.0
O5' A:5GP593 4.9 21.0 1.0
NE A:ARG48 5.0 20.6 1.0
N A:LEU101 5.0 24.7 1.0

Fluorine binding site 2 out of 8 in 2b8w

Go back to Fluorine Binding Sites List in 2b8w
Fluorine binding site 2 out of 8 in the Crystal-Structure of the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gmp/ALF4


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 Gmp/ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F594

b:28.2
occ:1.00
 F2 A:ALF594 0.0 28.2 1.0
AL A:ALF594 1.8 25.6 1.0
F3 A:ALF594 2.5 23.0 1.0
F4 A:ALF594 2.5 26.4 1.0
O2P A:5GP593 2.6 20.3 1.0
NH2 A:ARG48 2.7 21.6 1.0
O A:HOH602 2.8 29.7 1.0
N A:HIS74 2.8 25.4 1.0
N A:THR75 3.0 23.1 1.0
O A:HOH647 3.2 30.6 1.0
CB A:HIS74 3.2 23.5 1.0
MG A:MG595 3.3 24.4 1.0
CA A:HIS74 3.3 25.4 1.0
F1 A:ALF594 3.6 24.1 1.0
CZ A:ARG48 3.6 24.2 1.0
C A:HIS74 3.6 24.4 1.0
OG1 A:THR75 3.7 25.9 1.0
NE A:ARG48 3.7 20.6 1.0
P A:5GP593 3.9 21.5 1.0
C A:SER73 3.9 25.4 1.0
O A:LEU67 4.0 24.2 1.0
CA A:THR75 4.1 21.9 1.0
O1P A:5GP593 4.1 24.8 1.0
CB A:THR75 4.1 26.2 1.0
CA A:SER73 4.2 23.9 1.0
CG A:HIS74 4.5 28.4 1.0
O A:THR75 4.5 21.5 1.0
C5' A:5GP593 4.6 19.1 1.0
O5' A:5GP593 4.6 21.0 1.0
NH1 A:ARG48 4.8 15.8 1.0
O A:HIS74 4.8 25.5 1.0
C A:THR75 4.8 21.8 1.0
CB A:SER73 4.8 24.7 1.0
O A:HOH633 4.9 27.2 1.0

Fluorine binding site 3 out of 8 in 2b8w

Go back to Fluorine Binding Sites List in 2b8w
Fluorine binding site 3 out of 8 in the Crystal-Structure of the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gmp/ALF4


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 Gmp/ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F594

b:23.0
occ:1.00
 F3 A:ALF594 0.0 23.0 1.0
AL A:ALF594 1.8 25.6 1.0
MG A:MG595 2.0 24.4 1.0
F2 A:ALF594 2.5 28.2 1.0
F1 A:ALF594 2.5 24.1 1.0
O A:HOH602 2.6 29.7 1.0
O A:HOH633 2.6 27.2 1.0
O2P A:5GP593 2.6 20.3 1.0
OG1 A:THR75 2.8 25.9 1.0
CB A:THR75 3.0 26.2 1.0
O1P A:5GP593 3.2 24.8 1.0
P A:5GP593 3.3 21.5 1.0
O A:HOH647 3.5 30.6 1.0
F4 A:ALF594 3.6 26.4 1.0
N A:THR75 3.6 23.1 1.0
O A:THR98 3.7 24.7 1.0
CA A:THR75 3.9 21.9 1.0
N A:GLY100 4.0 26.7 1.0
O3P A:5GP593 4.0 17.8 1.0
OG A:SER52 4.1 23.1 1.0
NZ A:LYS51 4.1 19.7 1.0
CG2 A:THR75 4.2 22.8 1.0
O A:THR75 4.2 21.5 1.0
CE A:LYS51 4.3 18.7 1.0
C A:THR75 4.5 21.8 1.0
CA A:GLY100 4.7 25.1 1.0
CA A:GLU99 4.7 25.2 1.0
C A:THR98 4.7 25.6 1.0
O5' A:5GP593 4.8 21.0 1.0
C A:GLU99 4.8 24.9 1.0
NH2 A:ARG48 4.8 21.6 1.0
C A:HIS74 4.8 24.4 1.0
N A:HIS74 4.9 25.4 1.0

Fluorine binding site 4 out of 8 in 2b8w

Go back to Fluorine Binding Sites List in 2b8w
Fluorine binding site 4 out of 8 in the Crystal-Structure of the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gmp/ALF4


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 Gmp/ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F594

b:26.4
occ:1.00
 F4 A:ALF594 0.0 26.4 1.0
AL A:ALF594 1.8 25.6 1.0
O2P A:5GP593 2.5 20.3 1.0
F1 A:ALF594 2.5 24.1 1.0
F2 A:ALF594 2.5 28.2 1.0
NE A:ARG48 2.7 20.6 1.0
O A:HOH602 2.8 29.7 1.0
N A:ARG48 3.0 20.7 1.0
CB A:TYR47 3.3 21.4 1.0
NH2 A:ARG48 3.5 21.6 1.0
CZ A:ARG48 3.5 24.2 1.0
CA A:SER73 3.5 23.9 1.0
F3 A:ALF594 3.6 23.0 1.0
CD A:ARG48 3.6 16.6 1.0
CA A:TYR47 3.7 20.5 1.0
CG A:ARG48 3.7 19.2 1.0
C A:TYR47 3.7 23.7 1.0
N A:HIS74 3.8 25.4 1.0
CA A:ARG48 3.8 19.7 1.0
CB A:SER73 3.9 24.7 1.0
O A:HOH607 4.0 43.5 1.0
CG A:TYR47 4.0 19.5 1.0
CD1 A:TYR47 4.1 19.3 1.0
P A:5GP593 4.1 21.5 1.0
C A:SER73 4.2 25.4 1.0
CB A:ARG48 4.4 19.5 1.0
N A:SER73 4.6 17.5 1.0
O3P A:5GP593 4.7 17.8 1.0
O5' A:5GP593 4.8 21.0 1.0
NH1 A:ARG48 4.8 15.8 1.0
O A:GLN72 4.8 20.3 1.0
N A:GLY100 4.9 26.7 1.0
O A:TYR47 4.9 23.0 1.0
CA A:GLY100 4.9 25.1 1.0
CA A:HIS74 5.0 25.4 1.0
NZ A:LYS51 5.0 19.7 1.0

Fluorine binding site 5 out of 8 in 2b8w

Go back to Fluorine Binding Sites List in 2b8w
Fluorine binding site 5 out of 8 in the Crystal-Structure of the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gmp/ALF4


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 Gmp/ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F594

b:25.2
occ:1.00
 F1 B:ALF594 0.0 25.2 1.0
AL B:ALF594 1.8 26.8 1.0
O2P B:5GP593 2.5 21.1 1.0
F4 B:ALF594 2.5 23.8 1.0
F3 B:ALF594 2.5 23.6 1.0
NE B:ARG48 2.7 24.0 1.0
O B:HOH599 2.7 32.4 1.0
N B:ARG48 3.0 21.5 1.0
CB B:TYR47 3.4 22.5 1.0
NH2 B:ARG48 3.5 15.3 1.0
CZ B:ARG48 3.5 21.2 1.0
CA B:SER73 3.5 24.1 1.0
F2 B:ALF594 3.6 28.2 1.0
CD B:ARG48 3.6 21.2 1.0
CG B:ARG48 3.7 18.1 1.0
CA B:TYR47 3.7 22.5 1.0
N B:HIS74 3.8 24.6 1.0
C B:TYR47 3.8 21.7 1.0
CA B:ARG48 3.9 18.4 1.0
O B:HOH663 3.9 50.1 1.0
CD1 B:TYR47 4.0 21.6 1.0
CB B:SER73 4.0 26.6 1.0
CG B:TYR47 4.1 22.1 1.0
P B:5GP593 4.1 22.5 1.0
C B:SER73 4.2 24.5 1.0
CB B:ARG48 4.4 19.4 1.0
N B:SER73 4.5 21.1 1.0
O3P B:5GP593 4.7 20.6 1.0
O B:GLN72 4.7 19.8 1.0
O5' B:5GP593 4.8 19.1 1.0
NH1 B:ARG48 4.8 14.9 1.0
N B:GLY100 4.9 22.9 1.0
CA B:GLY100 4.9 21.6 1.0
N B:THR75 4.9 23.0 1.0
C B:GLN72 4.9 20.7 1.0
CA B:HIS74 5.0 25.6 1.0
O B:TYR47 5.0 22.1 1.0
O1P B:5GP593 5.0 26.5 1.0

Fluorine binding site 6 out of 8 in 2b8w

Go back to Fluorine Binding Sites List in 2b8w
Fluorine binding site 6 out of 8 in the Crystal-Structure of the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gmp/ALF4


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 Gmp/ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F594

b:28.2
occ:1.00
 F2 B:ALF594 0.0 28.2 1.0
AL B:ALF594 1.8 26.8 1.0
MG B:MG595 2.0 24.7 1.0
F3 B:ALF594 2.5 23.6 1.0
F4 B:ALF594 2.5 23.8 1.0
O B:HOH599 2.5 32.4 1.0
O2P B:5GP593 2.7 21.1 1.0
OG1 B:THR75 2.8 22.7 1.0
O B:HOH649 2.8 29.9 1.0
CB B:THR75 2.9 20.9 1.0
O1P B:5GP593 3.2 26.5 1.0
O B:HOH671 3.3 35.6 1.0
P B:5GP593 3.4 22.5 1.0
N B:THR75 3.5 23.0 1.0
F1 B:ALF594 3.6 25.2 1.0
CA B:THR75 3.7 21.6 1.0
O B:THR98 3.7 22.7 1.0
N B:GLY100 4.0 22.9 1.0
OG B:SER52 4.1 27.4 1.0
O B:THR75 4.1 25.1 1.0
CG2 B:THR75 4.1 17.1 1.0
O3P B:5GP593 4.1 20.6 1.0
NZ B:LYS51 4.2 21.2 1.0
C B:THR75 4.4 24.0 1.0
CE B:LYS51 4.6 20.7 1.0
C B:HIS74 4.7 24.8 1.0
CA B:GLU99 4.7 23.6 1.0
CA B:GLY100 4.8 21.6 1.0
N B:HIS74 4.8 24.6 1.0
C B:THR98 4.8 25.9 1.0
O5' B:5GP593 4.8 19.1 1.0
NH2 B:ARG48 4.8 15.3 1.0
C B:GLU99 4.8 25.5 1.0

Fluorine binding site 7 out of 8 in 2b8w

Go back to Fluorine Binding Sites List in 2b8w
Fluorine binding site 7 out of 8 in the Crystal-Structure of the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gmp/ALF4


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 the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gmp/ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F594

b:23.6
occ:1.00
 F3 B:ALF594 0.0 23.6 1.0
AL B:ALF594 1.8 26.8 1.0
F1 B:ALF594 2.5 25.2 1.0
F2 B:ALF594 2.5 28.2 1.0
O2P B:5GP593 2.7 21.1 1.0
NH2 B:ARG48 2.7 15.3 1.0
N B:HIS74 2.7 24.6 1.0
O B:HOH599 2.8 32.4 1.0
N B:THR75 2.9 23.0 1.0
O B:HOH671 3.0 35.6 1.0
CB B:HIS74 3.2 22.0 1.0
CA B:HIS74 3.2 25.6 1.0
MG B:MG595 3.4 24.7 1.0
C B:HIS74 3.5 24.8 1.0
F4 B:ALF594 3.6 23.8 1.0
CZ B:ARG48 3.6 21.2 1.0
NE B:ARG48 3.7 24.0 1.0
OG1 B:THR75 3.8 22.7 1.0
C B:SER73 3.8 24.5 1.0
P B:5GP593 3.9 22.5 1.0
O B:LEU67 4.0 22.6 1.0
CA B:THR75 4.0 21.6 1.0
CB B:THR75 4.1 20.9 1.0
CA B:SER73 4.1 24.1 1.0
O1P B:5GP593 4.1 26.5 1.0
CG B:HIS74 4.5 29.6 1.0
O B:THR75 4.6 25.1 1.0
C5' B:5GP593 4.7 22.0 1.0
O5' B:5GP593 4.7 19.1 1.0
O B:HIS74 4.8 23.0 1.0
NH1 B:ARG48 4.8 14.9 1.0
CB B:SER73 4.8 26.6 1.0
C B:THR75 4.8 24.0 1.0
O B:SER73 4.9 26.4 1.0
O B:GLN72 5.0 19.8 1.0

Fluorine binding site 8 out of 8 in 2b8w

Go back to Fluorine Binding Sites List in 2b8w
Fluorine binding site 8 out of 8 in the Crystal-Structure of the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gmp/ALF4


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 the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gmp/ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F594

b:23.8
occ:1.00
 F4 B:ALF594 0.0 23.8 1.0
AL B:ALF594 1.8 26.8 1.0
O2P B:5GP593 2.4 21.1 1.0
F1 B:ALF594 2.5 25.2 1.0
F2 B:ALF594 2.5 28.2 1.0
O B:HOH599 2.5 32.4 1.0
NZ B:LYS51 2.8 21.2 1.0
CA B:GLY100 3.0 21.6 1.0
N B:GLY100 3.0 22.9 1.0
CA B:TYR47 3.2 22.5 1.0
CB B:TYR47 3.4 22.5 1.0
O3P B:5GP593 3.4 20.6 1.0
P B:5GP593 3.5 22.5 1.0
N B:ARG48 3.5 21.5 1.0
F3 B:ALF594 3.6 23.6 1.0
CE B:LYS51 3.8 20.7 1.0
C B:TYR47 3.9 21.7 1.0
O B:HOH663 3.9 50.1 1.0
O1P B:5GP593 4.2 26.5 1.0
MG B:MG595 4.2 24.7 1.0
C B:GLU99 4.3 25.5 1.0
C B:GLY100 4.3 22.8 1.0
N B:TYR47 4.3 22.4 1.0
O B:LEU46 4.4 24.4 1.0
O B:HOH649 4.4 29.9 1.0
O B:THR98 4.6 22.7 1.0
CA B:ARG48 4.7 18.4 1.0
C B:LEU46 4.8 24.5 1.0
O B:GLY100 4.8 20.2 1.0
O5' B:5GP593 4.8 19.1 1.0
CG B:TYR47 4.8 22.1 1.0
CA B:GLU99 4.9 23.6 1.0
NE B:ARG48 5.0 24.0 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 13:49:56 2024

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