Fluorine in PDB 5w8b: Carbonic Anhydrase II in Complex with Activating Histamine Pyridinium Derivative

Enzymatic activity of Carbonic Anhydrase II in Complex with Activating Histamine Pyridinium Derivative

All present enzymatic activity of Carbonic Anhydrase II in Complex with Activating Histamine Pyridinium Derivative:
4.2.1.1;

Protein crystallography data

The structure of Carbonic Anhydrase II in Complex with Activating Histamine Pyridinium Derivative, PDB code: 5w8b was solved by A.Bhatt, M.Ilies, R.Mckenna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.00 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.268, 41.252, 72.096, 90.00, 104.10, 90.00
R / Rfree (%) 15.6 / 18.3

Other elements in 5w8b:

The structure of Carbonic Anhydrase II in Complex with Activating Histamine Pyridinium Derivative also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Carbonic Anhydrase II in Complex with Activating Histamine Pyridinium Derivative (pdb code 5w8b). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Carbonic Anhydrase II in Complex with Activating Histamine Pyridinium Derivative, PDB code: 5w8b:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5w8b

Go back to Fluorine Binding Sites List in 5w8b
Fluorine binding site 1 out of 6 in the Carbonic Anhydrase II in Complex with Activating Histamine Pyridinium Derivative


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Carbonic Anhydrase II in Complex with Activating Histamine Pyridinium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:15.2
occ:1.00
 F1 A:A9J302 0.0 15.2 1.0
P1 A:A9J302 1.6 14.4 1.0
F6 A:A9J302 2.3 15.0 1.0
F5 A:A9J302 2.3 16.5 1.0
F4 A:A9J302 2.3 13.8 1.0
F3 A:A9J302 2.3 15.5 1.0
CG1 A:VAL143 3.2 8.9 1.0
F2 A:A9J302 3.2 18.2 1.0
CG2 A:VAL143 3.2 9.7 1.0
CH2 A:TRP209 3.4 9.1 1.0
ND1 A:HIS119 3.6 8.6 1.0
CB A:HIS119 3.7 7.0 1.0
CZ2 A:TRP209 3.7 9.3 1.0
CB A:VAL143 3.7 10.6 1.0
CG A:HIS119 3.7 6.8 1.0
CG2 A:VAL121 3.7 8.7 1.0
HAS A:A57304 4.0 37.2 0.5
ZN A:ZN301 4.0 9.2 1.0
HAP A:A57304 4.1 35.3 0.5
CE1 A:HIS94 4.3 9.4 1.0
HAV A:A57304 4.4 34.3 0.5
O A:HOH419 4.4 11.4 1.0
CZ3 A:TRP209 4.4 11.2 1.0
CE1 A:HIS119 4.4 8.9 1.0
NE2 A:HIS94 4.6 8.4 1.0
CD2 A:HIS119 4.6 7.9 1.0
HAN A:A57304 4.7 35.3 0.5
HAR A:A57304 4.7 37.2 0.5
CAP A:A57304 4.8 31.0 0.5
CAN A:A57304 4.8 29.4 0.5
CE2 A:TRP209 4.8 9.4 1.0
CB A:VAL121 4.9 7.1 1.0
CA A:HIS119 4.9 7.7 1.0
NE2 A:HIS119 4.9 7.7 1.0

Fluorine binding site 2 out of 6 in 5w8b

Go back to Fluorine Binding Sites List in 5w8b
Fluorine binding site 2 out of 6 in the Carbonic Anhydrase II in Complex with Activating Histamine Pyridinium Derivative


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Carbonic Anhydrase II in Complex with Activating Histamine Pyridinium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:18.2
occ:1.00
 F2 A:A9J302 0.0 18.2 1.0
P1 A:A9J302 1.6 14.4 1.0
F6 A:A9J302 2.2 15.0 1.0
F3 A:A9J302 2.3 15.5 1.0
F4 A:A9J302 2.3 13.8 1.0
F5 A:A9J302 2.4 16.5 1.0
HAR A:A57304 3.1 37.2 0.5
F1 A:A9J302 3.2 15.2 1.0
N A:THR199 3.2 8.8 1.0
CA A:LEU198 3.3 7.3 1.0
HAN A:A57304 3.3 35.3 0.5
HAP A:A57304 3.3 35.3 0.5
HAD A:A57304 3.3 49.6 0.5
O A:HOH419 3.4 11.4 1.0
HAD A:A57304 3.4 49.8 0.5
CB A:LEU198 3.4 11.8 1.0
O A:HOH540 3.5 12.6 1.0
CD2 A:LEU198 3.6 11.0 1.0
HAS A:A57304 3.6 37.2 0.5
HAV A:A57304 3.7 34.3 0.5
CAN A:A57304 3.7 29.4 0.5
C A:LEU198 3.8 8.6 1.0
HAW A:A57304 3.8 34.3 0.5
CAP A:A57304 3.8 31.0 0.5
CG A:LEU198 4.1 10.7 1.0
CAD A:A57304 4.1 41.3 0.5
CAQ A:A57304 4.1 28.6 0.5
HAQ A:A57304 4.2 51.5 0.5
OG1 A:THR199 4.3 11.8 1.0
CAD A:A57304 4.3 41.5 0.5
CG2 A:THR200 4.4 7.1 1.0
HAN A:A57304 4.4 52.6 0.5
CAC A:A57304 4.4 38.5 0.5
CA A:THR199 4.4 7.0 1.0
CAO A:A57304 4.5 36.0 0.5
HAO A:A57304 4.5 35.3 0.5
ZN A:ZN301 4.5 9.2 1.0
N A:THR200 4.5 14.3 1.0
N A:LEU198 4.6 8.1 1.0
HAT A:A57304 4.6 37.2 0.5
CB A:THR199 4.8 9.4 1.0
O A:SER197 4.9 9.3 1.0
C A:THR199 4.9 12.4 1.0
CB A:THR200 4.9 25.4 1.0
CD1 A:LEU198 4.9 10.8 1.0
O A:LEU198 5.0 9.1 1.0

Fluorine binding site 3 out of 6 in 5w8b

Go back to Fluorine Binding Sites List in 5w8b
Fluorine binding site 3 out of 6 in the Carbonic Anhydrase II in Complex with Activating Histamine Pyridinium Derivative


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Carbonic Anhydrase II in Complex with Activating Histamine Pyridinium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:15.5
occ:1.00
 F3 A:A9J302 0.0 15.5 1.0
P1 A:A9J302 1.6 14.4 1.0
F2 A:A9J302 2.3 18.2 1.0
F1 A:A9J302 2.3 15.2 1.0
F6 A:A9J302 2.3 15.0 1.0
F5 A:A9J302 2.3 16.5 1.0
HAV A:A57304 2.5 34.3 0.5
HAN A:A57304 2.6 35.3 0.5
O A:HOH419 2.7 11.4 1.0
HAP A:A57304 2.7 35.3 0.5
ZN A:ZN301 2.9 9.2 1.0
CE1 A:HIS94 2.9 9.4 1.0
NE2 A:HIS94 3.1 8.4 1.0
CAN A:A57304 3.1 29.4 0.5
O A:HOH540 3.2 12.6 1.0
HAS A:A57304 3.2 37.2 0.5
F4 A:A9J302 3.2 13.8 1.0
CAQ A:A57304 3.4 28.6 0.5
HAW A:A57304 3.4 34.3 0.5
HAO A:A57304 3.5 35.3 0.5
ND1 A:HIS119 3.7 8.6 1.0
HAR A:A57304 3.7 37.2 0.5
CAP A:A57304 3.8 31.0 0.5
HAU A:A57304 4.0 34.3 0.5
CG2 A:VAL121 4.0 8.7 1.0
HAD A:A57304 4.1 49.6 0.5
ND1 A:HIS94 4.2 8.3 1.0
CB A:HIS119 4.2 7.0 1.0
CAO A:A57304 4.2 36.0 0.5
HAD A:A57304 4.3 49.8 0.5
CG A:HIS119 4.3 6.8 1.0
CAC A:A57304 4.4 38.5 0.5
CD2 A:HIS94 4.4 10.4 1.0
OG1 A:THR199 4.6 11.8 1.0
CE1 A:HIS119 4.7 8.9 1.0
CAD A:A57304 4.7 41.3 0.5
HAT A:A57304 4.7 37.2 0.5
NE2 A:HIS96 4.8 7.6 1.0
HAQ A:A57304 4.9 43.3 0.5
N A:THR199 4.9 8.8 1.0
CG A:HIS94 5.0 9.1 1.0

Fluorine binding site 4 out of 6 in 5w8b

Go back to Fluorine Binding Sites List in 5w8b
Fluorine binding site 4 out of 6 in the Carbonic Anhydrase II in Complex with Activating Histamine Pyridinium Derivative


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Carbonic Anhydrase II in Complex with Activating Histamine Pyridinium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:13.8
occ:1.00
 F4 A:A9J302 0.0 13.8 1.0
P1 A:A9J302 1.6 14.4 1.0
F6 A:A9J302 2.2 15.0 1.0
F5 A:A9J302 2.3 16.5 1.0
F1 A:A9J302 2.3 15.2 1.0
F2 A:A9J302 2.3 18.2 1.0
F3 A:A9J302 3.2 15.5 1.0
CZ2 A:TRP209 3.4 9.3 1.0
CA A:LEU198 3.4 7.3 1.0
CG2 A:VAL143 3.6 9.7 1.0
CD2 A:LEU198 3.7 11.0 1.0
CG2 A:VAL207 3.7 10.7 1.0
O A:SER197 3.8 9.3 1.0
CH2 A:TRP209 4.0 9.1 1.0
N A:THR199 4.0 8.8 1.0
N A:LEU198 4.1 8.1 1.0
CB A:LEU198 4.2 11.8 1.0
HAR A:A57304 4.2 37.2 0.5
C A:LEU198 4.2 8.6 1.0
CE2 A:TRP209 4.2 9.4 1.0
HAS A:A57304 4.3 37.2 0.5
C A:SER197 4.3 7.1 1.0
HAP A:A57304 4.5 35.3 0.5
CG1 A:VAL207 4.5 9.1 1.0
CB A:VAL143 4.5 10.6 1.0
CG A:LEU198 4.5 10.7 1.0
NE1 A:TRP209 4.6 10.1 1.0
CB A:VAL207 4.6 10.1 1.0
CG1 A:VAL143 4.7 8.9 1.0
CAP A:A57304 4.7 31.0 0.5
O A:HOH419 4.9 11.4 1.0

Fluorine binding site 5 out of 6 in 5w8b

Go back to Fluorine Binding Sites List in 5w8b
Fluorine binding site 5 out of 6 in the Carbonic Anhydrase II in Complex with Activating Histamine Pyridinium Derivative


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Carbonic Anhydrase II in Complex with Activating Histamine Pyridinium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:16.5
occ:1.00
 F5 A:A9J302 0.0 16.5 1.0
P1 A:A9J302 1.6 14.4 1.0
HAS A:A57304 2.0 37.2 0.5
F4 A:A9J302 2.3 13.8 1.0
F1 A:A9J302 2.3 15.2 1.0
F3 A:A9J302 2.3 15.5 1.0
F2 A:A9J302 2.4 18.2 1.0
HAP A:A57304 2.4 35.3 0.5
HAR A:A57304 2.5 37.2 0.5
CAP A:A57304 2.7 31.0 0.5
HAV A:A57304 3.2 34.3 0.5
F6 A:A9J302 3.2 15.0 1.0
HAT A:A57304 3.2 37.2 0.5
CAN A:A57304 3.3 29.4 0.5
HAN A:A57304 3.4 35.3 0.5
CG2 A:VAL121 3.4 8.7 1.0
CD2 A:LEU198 3.7 11.0 1.0
CG2 A:VAL143 3.8 9.7 1.0
HAO A:A57304 3.8 35.3 0.5
CG1 A:VAL121 3.8 7.8 1.0
CAO A:A57304 3.9 36.0 0.5
CAQ A:A57304 3.9 28.6 0.5
HAD A:A57304 4.0 49.8 0.5
HAW A:A57304 4.1 34.3 0.5
HAD A:A57304 4.1 49.6 0.5
CAC A:A57304 4.2 38.5 0.5
CB A:VAL121 4.3 7.1 1.0
CD1 A:LEU141 4.4 10.9 1.0
HAQ A:A57304 4.4 43.3 0.5
CAD A:A57304 4.5 41.3 0.5
CE1 A:HIS94 4.5 9.4 1.0
HAU A:A57304 4.7 34.3 0.5
O A:HOH540 4.7 12.6 1.0
CAD A:A57304 4.7 41.5 0.5
O A:HOH419 4.8 11.4 1.0
CA A:LEU198 4.8 7.3 1.0
CG1 A:VAL143 4.9 8.9 1.0
CAE A:A57304 4.9 41.2 0.5
CB A:LEU198 4.9 11.8 1.0
CB A:VAL143 5.0 10.6 1.0
CG A:LEU198 5.0 10.7 1.0

Fluorine binding site 6 out of 6 in 5w8b

Go back to Fluorine Binding Sites List in 5w8b
Fluorine binding site 6 out of 6 in the Carbonic Anhydrase II in Complex with Activating Histamine Pyridinium Derivative


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Carbonic Anhydrase II in Complex with Activating Histamine Pyridinium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:15.0
occ:1.00
 F6 A:A9J302 0.0 15.0 1.0
P1 A:A9J302 1.6 14.4 1.0
F2 A:A9J302 2.2 18.2 1.0
F4 A:A9J302 2.2 13.8 1.0
F1 A:A9J302 2.3 15.2 1.0
F3 A:A9J302 2.3 15.5 1.0
O A:HOH419 2.9 11.4 1.0
F5 A:A9J302 3.2 16.5 1.0
OG1 A:THR199 3.3 11.8 1.0
N A:THR199 3.3 8.8 1.0
CZ2 A:TRP209 3.3 9.3 1.0
ZN A:ZN301 3.5 9.2 1.0
CH2 A:TRP209 3.5 9.1 1.0
ND1 A:HIS119 3.5 8.6 1.0
CG2 A:THR199 3.6 8.3 1.0
CB A:THR199 3.8 9.4 1.0
CE1 A:HIS119 3.9 8.9 1.0
CA A:LEU198 4.1 7.3 1.0
CA A:THR199 4.2 7.0 1.0
C A:LEU198 4.2 8.6 1.0
CG A:HIS119 4.4 6.8 1.0
O A:SER197 4.5 9.3 1.0
O A:HOH540 4.5 12.6 1.0
CE2 A:TRP209 4.6 9.4 1.0
HAN A:A57304 4.6 35.3 0.5
HAP A:A57304 4.7 35.3 0.5
NE2 A:HIS94 4.7 8.4 1.0
OE1 A:GLU106 4.8 9.3 1.0
HAV A:A57304 4.8 34.3 0.5
NE2 A:HIS119 4.8 7.7 1.0
CZ3 A:TRP209 4.9 11.2 1.0
CB A:LEU198 4.9 11.8 1.0
HAS A:A57304 4.9 37.2 0.5
CB A:HIS119 4.9 7.0 1.0
CE1 A:HIS94 4.9 9.4 1.0

Reference:

A.Bhatt, U.K.Mondal, C.T.Supuran, M.A.Ilies, R.Mckenna. Crystal Structure of Carbonic Anhydrase II in Complex with An Activating Ligand: Implications in Neuronal Function. Mol. Neurobiol. V. 55 7431 2018.
ISSN: ISSN 1559-1182
PubMed: 29423818
DOI: 10.1007/S12035-017-0854-2
Page generated: Sun Dec 13 12:41:29 2020

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