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Fluorine in PDB 2wb4: Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp

Enzymatic activity of Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp

All present enzymatic activity of Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp:
2.7.7.65;

Protein crystallography data

The structure of Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp, PDB code: 2wb4 was solved by P.Wassmann, T.Schirmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.00 / 2.80
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 123.560, 127.430, 88.130, 90.00, 90.00, 90.00
R / Rfree (%) 23.906 / 26.816

Other elements in 2wb4:

The structure of Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp (pdb code 2wb4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp, PDB code: 2wb4:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 2wb4

Go back to Fluorine Binding Sites List in 2wb4
Fluorine binding site 1 out of 6 in the Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:13.5
occ:1.00
 F1 A:BEF501 0.0 13.5 1.0
BE A:BEF501 1.5 19.9 1.0
F2 A:BEF501 2.5 14.4 1.0
F3 A:BEF501 2.5 23.3 1.0
OD1 A:ASP53 2.5 15.5 1.0
NZ A:LYS105 2.7 14.1 1.0
N A:ALA84 2.8 11.9 1.0
CA A:THR83 3.4 11.2 1.0
CE A:LYS105 3.4 13.4 1.0
CG A:ASP53 3.5 11.6 1.0
C A:THR83 3.5 11.9 1.0
CB A:ALA84 3.6 12.4 1.0
O A:HOH2002 3.6 4.0 1.0
CA A:ALA84 3.8 12.6 1.0
CD A:LYS105 3.8 11.3 1.0
OD2 A:ASP53 3.9 8.3 1.0
OG1 A:THR83 3.9 13.0 1.0
CE A:MET55 4.1 13.8 1.0
O A:ILE82 4.2 13.7 1.0
CB A:THR83 4.2 12.0 1.0
N A:THR83 4.4 10.8 1.0
MG A:MG502 4.5 15.2 1.0
O A:THR83 4.7 11.0 1.0
C A:ILE82 4.7 11.8 1.0
N A:VAL54 4.8 11.1 1.0
CB A:ASP53 4.8 11.4 1.0
CG A:LYS105 4.8 11.4 1.0
OD2 A:ASP9 4.9 17.5 1.0
C A:ALA84 5.0 13.2 1.0
N A:MET55 5.0 11.2 1.0
N A:LEU85 5.0 12.9 1.0

Fluorine binding site 2 out of 6 in 2wb4

Go back to Fluorine Binding Sites List in 2wb4
Fluorine binding site 2 out of 6 in the Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:14.4
occ:1.00
 F2 A:BEF501 0.0 14.4 1.0
BE A:BEF501 1.5 19.9 1.0
OD2 A:ASP53 2.1 8.3 1.0
MG A:MG502 2.2 15.2 1.0
F1 A:BEF501 2.5 13.5 1.0
F3 A:BEF501 2.5 23.3 1.0
OD1 A:ASP53 2.5 15.5 1.0
CG A:ASP53 2.6 11.6 1.0
O A:HOH2002 2.7 4.0 1.0
O A:MET55 2.9 11.9 1.0
N A:MET55 3.6 11.2 1.0
CB A:MET55 3.6 12.3 1.0
C A:MET55 3.8 12.0 1.0
CE A:MET55 3.8 13.8 1.0
CA A:MET55 3.8 11.7 1.0
NZ A:LYS105 4.0 14.1 1.0
OD1 A:ASP10 4.1 14.4 1.0
CB A:ASP53 4.1 11.4 1.0
N A:VAL54 4.4 11.1 1.0
CG A:MET55 4.5 15.0 1.0
C A:VAL54 4.7 10.9 1.0
OD2 A:ASP9 4.9 17.5 1.0
CA A:ASP53 4.9 11.3 1.0
OD1 A:ASP9 4.9 12.7 1.0
SD A:MET55 5.0 20.0 1.0

Fluorine binding site 3 out of 6 in 2wb4

Go back to Fluorine Binding Sites List in 2wb4
Fluorine binding site 3 out of 6 in the Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:23.3
occ:1.00
 F3 A:BEF501 0.0 23.3 1.0
BE A:BEF501 1.5 19.9 1.0
F1 A:BEF501 2.5 13.5 1.0
F2 A:BEF501 2.5 14.4 1.0
OD1 A:ASP53 2.5 15.5 1.0
N A:MET55 2.7 11.2 1.0
N A:VAL54 2.9 11.1 1.0
OG1 A:THR83 3.0 13.0 1.0
CG A:ASP53 3.2 11.6 1.0
CA A:VAL54 3.4 10.8 1.0
CB A:VAL54 3.4 10.3 1.0
C A:VAL54 3.5 10.9 1.0
OD2 A:ASP53 3.6 8.3 1.0
CB A:THR83 3.6 12.0 1.0
CB A:MET55 3.7 12.3 1.0
CA A:MET55 3.7 11.7 1.0
CA A:THR83 3.8 11.2 1.0
CE A:MET55 3.8 13.8 1.0
CG A:MET55 3.8 15.0 1.0
N A:ALA84 4.0 11.9 1.0
C A:ASP53 4.0 10.9 1.0
O A:MET55 4.2 11.9 1.0
CA A:ASP53 4.3 11.3 1.0
CB A:ASP53 4.3 11.4 1.0
O A:ILE82 4.4 13.7 1.0
CG2 A:VAL54 4.4 9.0 1.0
CG1 A:VAL54 4.4 10.6 1.0
C A:MET55 4.4 12.0 1.0
C A:THR83 4.4 11.9 1.0
CD2 A:LEU85 4.5 13.1 1.0
MG A:MG502 4.5 15.2 1.0
SD A:MET55 4.6 20.0 1.0
O A:VAL54 4.7 11.5 1.0
O A:HOH2002 4.8 4.0 1.0
NZ A:LYS105 4.8 14.1 1.0
N A:THR83 4.9 10.8 1.0

Fluorine binding site 4 out of 6 in 2wb4

Go back to Fluorine Binding Sites List in 2wb4
Fluorine binding site 4 out of 6 in the Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:6.3
occ:1.00
 F1 B:BEF501 0.0 6.3 1.0
BE B:BEF501 1.5 7.6 1.0
F3 B:BEF501 2.4 5.7 1.0
F2 B:BEF501 2.5 3.1 1.0
OD1 B:ASP53 2.5 15.2 1.0
NZ B:LYS105 2.7 13.9 1.0
N B:ALA84 2.8 11.6 1.0
CE B:LYS105 3.4 13.8 1.0
CA B:THR83 3.4 11.1 1.0
CG B:ASP53 3.5 12.0 1.0
C B:THR83 3.5 12.1 1.0
CB B:ALA84 3.6 12.1 1.0
CA B:ALA84 3.8 12.3 1.0
OD2 B:ASP53 3.9 8.7 1.0
CD B:LYS105 3.9 11.5 1.0
OG1 B:THR83 3.9 12.4 1.0
O B:HOH2001 3.9 4.6 1.0
CE B:MET55 4.1 13.3 1.0
CB B:THR83 4.2 11.5 1.0
O B:ILE82 4.2 13.5 1.0
MG B:MG502 4.3 12.7 1.0
N B:THR83 4.5 10.8 1.0
O B:THR83 4.7 11.5 1.0
N B:VAL54 4.8 10.4 1.0
C B:ILE82 4.8 11.6 1.0
CB B:ASP53 4.9 11.3 1.0
CG B:LYS105 4.9 11.6 1.0
N B:MET55 4.9 10.9 1.0
OD2 B:ASP9 4.9 17.4 1.0
C B:ALA84 4.9 13.0 1.0
N B:LEU85 5.0 12.9 1.0

Fluorine binding site 5 out of 6 in 2wb4

Go back to Fluorine Binding Sites List in 2wb4
Fluorine binding site 5 out of 6 in the Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:3.1
occ:1.00
 F2 B:BEF501 0.0 3.1 1.0
BE B:BEF501 1.5 7.6 1.0
MG B:MG502 2.1 12.7 1.0
OD2 B:ASP53 2.1 8.7 1.0
F3 B:BEF501 2.3 5.7 1.0
F1 B:BEF501 2.5 6.3 1.0
OD1 B:ASP53 2.5 15.2 1.0
CG B:ASP53 2.6 12.0 1.0
O B:HOH2001 2.7 4.6 1.0
O B:MET55 2.8 10.8 1.0
N B:MET55 3.4 10.9 1.0
CB B:MET55 3.4 12.4 1.0
O B:HOH2002 3.6 24.3 1.0
C B:MET55 3.6 11.8 1.0
CA B:MET55 3.6 11.5 1.0
CE B:MET55 3.8 13.3 1.0
OD1 B:ASP10 4.1 14.7 1.0
CB B:ASP53 4.1 11.3 1.0
NZ B:LYS105 4.1 13.9 1.0
N B:VAL54 4.3 10.4 1.0
CG B:MET55 4.4 14.9 1.0
C B:VAL54 4.5 10.7 1.0
CA B:ASP53 4.9 11.3 1.0
N B:MET56 4.9 11.6 1.0
SD B:MET55 4.9 18.4 1.0
CA B:VAL54 4.9 10.7 1.0
C B:ASP53 5.0 10.5 1.0
OD2 B:ASP9 5.0 17.4 1.0

Fluorine binding site 6 out of 6 in 2wb4

Go back to Fluorine Binding Sites List in 2wb4
Fluorine binding site 6 out of 6 in the Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:5.7
occ:1.00
 F3 B:BEF501 0.0 5.7 1.0
BE B:BEF501 1.5 7.6 1.0
F2 B:BEF501 2.3 3.1 1.0
F1 B:BEF501 2.4 6.3 1.0
OD1 B:ASP53 2.5 15.2 1.0
N B:MET55 2.7 10.9 1.0
N B:VAL54 2.9 10.4 1.0
OG1 B:THR83 3.0 12.4 1.0
CG B:ASP53 3.2 12.0 1.0
CA B:VAL54 3.4 10.7 1.0
CB B:VAL54 3.4 9.8 1.0
C B:VAL54 3.5 10.7 1.0
OD2 B:ASP53 3.6 8.7 1.0
CB B:THR83 3.6 11.5 1.0
CB B:MET55 3.7 12.4 1.0
CA B:THR83 3.7 11.1 1.0
CA B:MET55 3.7 11.5 1.0
CG B:MET55 3.9 14.9 1.0
CE B:MET55 3.9 13.3 1.0
N B:ALA84 3.9 11.6 1.0
C B:ASP53 4.0 10.5 1.0
O B:MET55 4.2 10.8 1.0
CA B:ASP53 4.3 11.3 1.0
CB B:ASP53 4.3 11.3 1.0
C B:THR83 4.3 12.1 1.0
CG2 B:VAL54 4.3 8.9 1.0
O B:ILE82 4.4 13.5 1.0
MG B:MG502 4.4 12.7 1.0
C B:MET55 4.4 11.8 1.0
CG1 B:VAL54 4.5 10.2 1.0
SD B:MET55 4.7 18.4 1.0
CD2 B:LEU85 4.7 13.3 1.0
O B:VAL54 4.7 11.0 1.0
NZ B:LYS105 4.8 13.9 1.0
N B:THR83 4.9 10.8 1.0
O B:HOH2001 4.9 4.6 1.0

Reference:

P.Wassmann, C.Massa, F.Zaehringer, T.Schirmer. Crystal Structure of Activated Pled, Identification of Dimerization and Catalysis Relevant Regulatory Mechanisms To Be Published.
Page generated: Mon Jul 14 14:37:34 2025

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