Fluorine in PDB 6zxc: Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State

Protein crystallography data

The structure of Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State, PDB code: 6zxc was solved by R.D.Teixeira, T.Schirmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.80
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 132.812, 247.368, 41.539, 90, 90, 90
R / Rfree (%) 23.7 / 28.8

Other elements in 6zxc:

The structure of Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State also contains other interesting chemical elements:

Magnesium (Mg) 12 atoms

Fluorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Fluorine atom in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State (pdb code 6zxc). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State, PDB code: 6zxc:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 6zxc

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Fluorine binding site 1 out of 12 in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F56

b:53.2
occ:1.00
 F1 A:BFD56 0.0 53.2 1.0
BE A:BFD56 1.7 50.2 1.0
F3 A:BFD56 2.5 57.0 1.0
NZ A:LYS108 2.6 52.9 1.0
N A:GLY87 2.9 43.4 1.0
OD1 A:BFD56 2.9 47.0 1.0
F2 A:BFD56 3.0 51.0 1.0
CE A:LYS108 3.4 50.8 1.0
CD A:LYS108 3.5 50.5 1.0
C A:THR86 3.7 44.2 1.0
CA A:GLY87 3.7 44.6 1.0
CA A:THR86 3.7 43.7 1.0
MG A:MG300 3.8 128.5 1.0
CG A:BFD56 4.1 45.8 1.0
OD2 A:BFD56 4.2 46.9 1.0
CB A:THR86 4.4 45.7 1.0
CG A:LYS108 4.7 48.5 1.0
OE1 A:GLU12 4.8 53.3 1.0
O A:VAL85 4.8 43.0 1.0
O A:THR86 4.9 42.1 1.0
N A:THR86 4.9 41.8 1.0
C A:GLY87 4.9 44.9 1.0

Fluorine binding site 2 out of 12 in 6zxc

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Fluorine binding site 2 out of 12 in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F56

b:51.0
occ:1.00
 F2 A:BFD56 0.0 51.0 1.0
BE A:BFD56 1.7 50.2 1.0
F3 A:BFD56 2.7 57.0 1.0
OD1 A:BFD56 2.8 47.0 1.0
N A:GLU58 2.9 49.9 1.0
F1 A:BFD56 3.0 53.2 1.0
CB A:TRP57 3.2 49.0 1.0
N A:TRP57 3.2 46.1 1.0
CA A:TRP57 3.5 48.0 1.0
CB A:THR86 3.5 45.7 1.0
C A:TRP57 3.6 49.6 1.0
CG A:GLU58 3.7 59.1 1.0
CB A:GLU58 3.8 57.2 1.0
CA A:GLU58 3.9 53.4 1.0
CG A:BFD56 3.9 45.8 1.0
N A:GLY87 4.0 43.4 1.0
CA A:THR86 4.0 43.7 1.0
CG2 A:THR86 4.0 46.5 1.0
CD2 A:HIS88 4.0 49.0 1.0
OD2 A:BFD56 4.3 46.9 1.0
CG A:TRP57 4.4 52.5 1.0
C A:BFD56 4.4 44.6 1.0
O A:GLU58 4.5 53.1 1.0
OG1 A:THR86 4.5 46.6 1.0
C A:THR86 4.5 44.2 1.0
MG A:MG300 4.5 128.5 1.0
C A:GLU58 4.6 52.0 1.0
NE2 A:HIS88 4.7 50.9 1.0
CA A:BFD56 4.8 42.8 1.0
CG A:HIS88 4.8 48.3 1.0
N A:HIS88 4.9 44.2 1.0
O A:TRP57 4.9 49.6 1.0
CB A:BFD56 4.9 44.0 1.0
NZ A:LYS108 5.0 52.9 1.0
CA A:GLY87 5.0 44.6 1.0

Fluorine binding site 3 out of 12 in 6zxc

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Fluorine binding site 3 out of 12 in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F56

b:57.0
occ:1.00
 F3 A:BFD56 0.0 57.0 1.0
BE A:BFD56 1.8 50.2 1.0
MG A:MG300 2.0 128.5 1.0
F1 A:BFD56 2.5 53.2 1.0
OD2 A:BFD56 2.6 46.9 1.0
OD1 A:BFD56 2.6 47.0 1.0
F2 A:BFD56 2.7 51.0 1.0
O A:GLU58 2.8 53.1 1.0
CG A:BFD56 3.0 45.8 1.0
CB A:GLU58 3.6 57.2 1.0
N A:GLU58 3.6 49.9 1.0
C A:GLU58 3.7 52.0 1.0
OD1 A:ASP13 3.8 51.9 1.0
CA A:GLU58 3.8 53.4 1.0
NZ A:LYS108 3.9 52.9 1.0
CG A:GLU58 4.3 59.1 1.0
CB A:BFD56 4.5 44.0 1.0
N A:TRP57 4.6 46.1 1.0
CG A:ASP13 4.7 53.5 1.0
OE2 A:GLU12 4.7 52.5 1.0
OD2 A:ASP13 4.7 53.3 1.0
C A:TRP57 4.7 49.6 1.0
OE1 A:GLU12 4.8 53.3 1.0
N A:LEU59 5.0 49.4 1.0

Fluorine binding site 4 out of 12 in 6zxc

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Fluorine binding site 4 out of 12 in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F56

b:53.7
occ:1.00
 F1 B:BFD56 0.0 53.7 1.0
BE B:BFD56 1.7 46.6 1.0
F3 B:BFD56 2.6 46.0 1.0
NZ B:LYS108 2.6 44.5 1.0
N B:GLY87 2.8 45.0 1.0
F2 B:BFD56 2.8 47.6 1.0
OD1 B:BFD56 2.9 44.2 1.0
CE B:LYS108 3.3 43.7 1.0
CD B:LYS108 3.4 43.2 1.0
C B:THR86 3.6 44.8 1.0
CA B:THR86 3.6 43.1 1.0
CA B:GLY87 3.7 46.4 1.0
CG B:BFD56 4.0 44.4 1.0
MG B:MG300 4.2 48.1 1.0
OD2 B:BFD56 4.3 49.5 1.0
CB B:THR86 4.3 43.0 1.0
CG B:LYS108 4.6 41.8 1.0
O B:VAL85 4.7 37.6 1.0
O B:THR86 4.8 44.7 1.0
OE1 B:GLU12 4.8 45.3 1.0
N B:THR86 4.8 39.5 1.0
C B:GLY87 4.9 47.3 1.0

Fluorine binding site 5 out of 12 in 6zxc

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Fluorine binding site 5 out of 12 in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F56

b:47.6
occ:1.00
 F2 B:BFD56 0.0 47.6 1.0
BE B:BFD56 1.7 46.6 1.0
F3 B:BFD56 2.6 46.0 1.0
OD1 B:BFD56 2.8 44.2 1.0
F1 B:BFD56 2.8 53.7 1.0
N B:GLU58 2.9 44.1 1.0
CB B:TRP57 3.1 42.7 1.0
N B:TRP57 3.3 39.7 1.0
CA B:TRP57 3.5 41.8 1.0
CB B:THR86 3.5 43.0 1.0
C B:TRP57 3.6 42.5 1.0
CB B:GLU58 3.8 50.7 1.0
CG B:BFD56 3.9 44.4 1.0
CA B:GLU58 3.9 48.1 1.0
N B:GLY87 3.9 45.0 1.0
CA B:THR86 3.9 43.1 1.0
CG B:GLU58 4.2 53.3 1.0
CG B:TRP57 4.2 44.5 1.0
OD2 B:BFD56 4.3 49.5 1.0
OG1 B:THR86 4.4 43.4 1.0
CD2 B:HIS88 4.4 54.7 1.0
CG2 B:THR86 4.4 43.1 1.0
C B:BFD56 4.4 38.7 1.0
O B:GLU58 4.5 46.5 1.0
C B:THR86 4.5 44.8 1.0
MG B:MG300 4.6 48.1 1.0
C B:GLU58 4.6 48.0 1.0
O B:TRP57 4.8 43.3 1.0
CA B:BFD56 4.8 39.0 1.0
CD1 B:TRP57 4.8 47.9 1.0
NZ B:LYS108 4.9 44.5 1.0
N B:HIS88 4.9 46.5 1.0
CB B:BFD56 4.9 41.1 1.0
CA B:GLY87 4.9 46.4 1.0

Fluorine binding site 6 out of 12 in 6zxc

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Fluorine binding site 6 out of 12 in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F56

b:46.0
occ:1.00
 F3 B:BFD56 0.0 46.0 1.0
BE B:BFD56 1.8 46.6 1.0
MG B:MG300 2.0 48.1 1.0
F1 B:BFD56 2.6 53.7 1.0
OD2 B:BFD56 2.6 49.5 1.0
F2 B:BFD56 2.6 47.6 1.0
OD1 B:BFD56 2.6 44.2 1.0
O B:GLU58 2.9 46.5 1.0
CG B:BFD56 3.0 44.4 1.0
CB B:GLU58 3.5 50.7 1.0
N B:GLU58 3.5 44.1 1.0
C B:GLU58 3.7 48.0 1.0
CA B:GLU58 3.7 48.1 1.0
OD1 B:ASP13 3.9 46.7 1.0
NZ B:LYS108 3.9 44.5 1.0
CB B:BFD56 4.5 41.1 1.0
N B:TRP57 4.5 39.7 1.0
CG B:GLU58 4.6 53.3 1.0
C B:TRP57 4.6 42.5 1.0
OE2 B:GLU12 4.6 47.8 1.0
OD2 B:ASP13 4.7 46.9 1.0
CG B:ASP13 4.7 46.1 1.0
OE1 B:GLU12 4.9 45.3 1.0
N B:LEU59 4.9 48.2 1.0

Fluorine binding site 7 out of 12 in 6zxc

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Fluorine binding site 7 out of 12 in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F56

b:73.7
occ:1.00
 F1 C:BFD56 0.0 73.7 1.0
BE C:BFD56 1.7 70.4 1.0
F3 C:BFD56 2.6 68.6 1.0
NZ C:LYS108 2.6 61.1 1.0
N C:GLY87 2.9 62.8 1.0
F2 C:BFD56 2.9 80.7 1.0
OD1 C:BFD56 3.0 64.7 1.0
CE C:LYS108 3.3 59.1 1.0
CD C:LYS108 3.6 58.8 1.0
C C:THR86 3.7 62.0 1.0
CA C:GLY87 3.7 64.9 1.0
CA C:THR86 3.8 63.5 1.0
MG C:MG300 3.8 50.4 1.0
CG C:BFD56 4.1 65.5 1.0
OD2 C:BFD56 4.3 69.0 1.0
CB C:THR86 4.4 67.4 1.0
CG C:LYS108 4.7 59.6 1.0
O C:THR86 4.8 63.2 1.0
OE1 C:GLU12 4.8 64.4 1.0
C C:GLY87 4.9 66.3 1.0
O C:VAL85 4.9 64.9 1.0
N C:THR86 5.0 62.8 1.0

Fluorine binding site 8 out of 12 in 6zxc

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Fluorine binding site 8 out of 12 in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F56

b:80.7
occ:1.00
 F2 C:BFD56 0.0 80.7 1.0
BE C:BFD56 1.7 70.4 1.0
F3 C:BFD56 2.6 68.6 1.0
N C:GLU58 2.9 71.3 1.0
OD1 C:BFD56 2.9 64.7 1.0
F1 C:BFD56 2.9 73.7 1.0
CB C:TRP57 3.1 75.5 1.0
N C:TRP57 3.3 67.5 1.0
CA C:TRP57 3.5 71.8 1.0
CB C:THR86 3.5 67.4 1.0
C C:TRP57 3.6 73.1 1.0
CB C:GLU58 3.8 72.1 1.0
CA C:GLU58 3.9 71.3 1.0
CG C:BFD56 3.9 65.5 1.0
N C:GLY87 4.0 62.8 1.0
CG C:GLU58 4.0 75.7 1.0
CA C:THR86 4.0 63.5 1.0
CD2 C:HIS88 4.1 75.4 1.0
CG C:TRP57 4.3 81.7 1.0
OD2 C:BFD56 4.3 69.0 1.0
CG2 C:THR86 4.3 67.7 1.0
MG C:MG300 4.4 50.4 1.0
OG1 C:THR86 4.4 71.3 1.0
O C:GLU58 4.5 68.8 1.0
C C:BFD56 4.5 66.2 1.0
C C:THR86 4.5 62.0 1.0
NE2 C:HIS88 4.5 77.8 1.0
C C:GLU58 4.6 69.7 1.0
CG C:HIS88 4.8 74.5 1.0
N C:HIS88 4.8 68.4 1.0
O C:TRP57 4.9 75.7 1.0
CD1 C:TRP57 4.9 85.6 1.0
CA C:BFD56 4.9 65.1 1.0
NZ C:LYS108 5.0 61.1 1.0

Fluorine binding site 9 out of 12 in 6zxc

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Fluorine binding site 9 out of 12 in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F56

b:68.6
occ:1.00
 F3 C:BFD56 0.0 68.6 1.0
BE C:BFD56 1.8 70.4 1.0
MG C:MG300 1.8 50.4 1.0
F1 C:BFD56 2.6 73.7 1.0
OD2 C:BFD56 2.6 69.0 1.0
F2 C:BFD56 2.6 80.7 1.0
OD1 C:BFD56 2.7 64.7 1.0
O C:GLU58 2.8 68.8 1.0
CG C:BFD56 3.0 65.5 1.0
N C:GLU58 3.5 71.3 1.0
CB C:GLU58 3.6 72.1 1.0
C C:GLU58 3.7 69.7 1.0
CA C:GLU58 3.7 71.3 1.0
OD1 C:ASP13 3.9 67.1 1.0
NZ C:LYS108 3.9 61.1 1.0
N C:TRP57 4.5 67.5 1.0
CB C:BFD56 4.5 64.3 1.0
CG C:GLU58 4.6 75.7 1.0
C C:TRP57 4.7 73.1 1.0
OD2 C:ASP13 4.7 72.0 1.0
CG C:ASP13 4.7 67.9 1.0
OE2 C:GLU12 4.8 63.6 1.0
OE1 C:GLU12 4.9 64.4 1.0
N C:LEU59 4.9 69.2 1.0

Fluorine binding site 10 out of 12 in 6zxc

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Fluorine binding site 10 out of 12 in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F56

b:74.3
occ:1.00
 F1 D:BFD56 0.0 74.3 1.0
BE D:BFD56 1.7 74.0 1.0
F3 D:BFD56 2.5 78.1 1.0
N D:GLY87 2.9 73.8 1.0
F2 D:BFD56 2.9 73.4 1.0
OD1 D:BFD56 3.0 73.3 1.0
CE D:LYS108 3.3 74.5 1.0
NZ D:LYS108 3.6 76.1 1.0
CD D:LYS108 3.6 74.9 1.0
CA D:GLY87 3.7 77.2 1.0
C D:THR86 3.7 70.3 1.0
CA D:THR86 3.8 69.2 1.0
OG1 D:THR86 3.8 78.2 1.0
MG D:MG300 3.9 72.0 1.0
CG D:BFD56 4.1 77.4 1.0
OD2 D:BFD56 4.3 83.7 1.0
CB D:THR86 4.4 71.7 1.0
C D:GLY87 4.8 79.4 1.0
OE1 D:GLU12 4.8 82.1 1.0
O D:THR86 4.9 69.9 1.0
O D:VAL85 4.9 65.8 1.0
N D:HIS88 5.0 81.1 1.0
CG D:LYS108 5.0 73.9 1.0
N D:THR86 5.0 66.6 1.0

Reference:

R.D.Teixeira, T.Schirmer. Dgcr Structure in Activated State To Be Published.
Page generated: Sat Apr 3 15:05:45 2021

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