Atomistry » Fluorine » PDB 2vh0-2wbk » 2wb4
Atomistry »
  Fluorine »
    PDB 2vh0-2wbk »
      2wb4 »

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

Last articles

Mg in 7JM6
Mg in 7JM7
Mg in 7JLV
Mg in 7JMK
Mg in 7JL3
Mg in 7JL2
Mg in 7JLE
Mg in 7JLH
Mg in 7JKK
Mg in 7JL1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy