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Fluorine in PDB 5m12: Structure of GH36 Alpha-Galactosidase From Thermotoga Maritima in Complex with Intact Cyclopropyl-Carbasugar.

Enzymatic activity of Structure of GH36 Alpha-Galactosidase From Thermotoga Maritima in Complex with Intact Cyclopropyl-Carbasugar.

All present enzymatic activity of Structure of GH36 Alpha-Galactosidase From Thermotoga Maritima in Complex with Intact Cyclopropyl-Carbasugar.:
3.2.1.22;

Protein crystallography data

The structure of Structure of GH36 Alpha-Galactosidase From Thermotoga Maritima in Complex with Intact Cyclopropyl-Carbasugar., PDB code: 5m12 was solved by R.Pengelly, T.Gloster, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.69 / 1.53
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.150, 96.040, 98.120, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 22.2

Other elements in 5m12:

The structure of Structure of GH36 Alpha-Galactosidase From Thermotoga Maritima in Complex with Intact Cyclopropyl-Carbasugar. also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of GH36 Alpha-Galactosidase From Thermotoga Maritima in Complex with Intact Cyclopropyl-Carbasugar. (pdb code 5m12). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Structure of GH36 Alpha-Galactosidase From Thermotoga Maritima in Complex with Intact Cyclopropyl-Carbasugar., PDB code: 5m12:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5m12

Go back to Fluorine Binding Sites List in 5m12
Fluorine binding site 1 out of 2 in the Structure of GH36 Alpha-Galactosidase From Thermotoga Maritima in Complex with Intact Cyclopropyl-Carbasugar.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of GH36 Alpha-Galactosidase From Thermotoga Maritima in Complex with Intact Cyclopropyl-Carbasugar. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F604

b:63.0
occ:1.00
 FAE A:7D0604 0.0 63.0 1.0
CAP A:7D0604 1.3 64.4 1.0
CAN A:7D0604 2.4 53.7 1.0
CAO A:7D0604 2.4 53.6 1.0
CH2 A:TRP85 3.1 25.2 1.0
CZ2 A:TRP85 3.3 22.1 1.0
OD1 A:ASN290 3.3 19.1 1.0
ND2 A:ASN290 3.5 18.8 1.0
CG A:ASN290 3.6 17.1 1.0
CAM A:7D0604 3.6 40.7 1.0
CAS A:7D0604 3.7 50.9 1.0
CZ A:PHE328 4.0 16.2 1.0
CE2 A:PHE328 4.1 18.2 1.0
CZ3 A:TRP85 4.1 24.1 1.0
CAR A:7D0604 4.2 41.8 1.0
CE2 A:TRP85 4.5 24.7 1.0
CB A:ASN290 4.6 16.6 1.0
OAL A:7D0604 4.7 30.0 1.0
FAF A:7D0604 4.9 53.0 1.0

Fluorine binding site 2 out of 2 in 5m12

Go back to Fluorine Binding Sites List in 5m12
Fluorine binding site 2 out of 2 in the Structure of GH36 Alpha-Galactosidase From Thermotoga Maritima in Complex with Intact Cyclopropyl-Carbasugar.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of GH36 Alpha-Galactosidase From Thermotoga Maritima in Complex with Intact Cyclopropyl-Carbasugar. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F604

b:53.0
occ:1.00
 FAF A:7D0604 0.0 53.0 1.0
CAS A:7D0604 1.5 50.9 1.0
CAO A:7D0604 2.5 53.6 1.0
CAR A:7D0604 2.5 41.8 1.0
CE3 A:TRP65 3.0 20.7 1.0
CD2 A:TRP65 3.3 18.0 1.0
O A:HOH903 3.3 25.0 1.0
CZ3 A:TRP65 3.5 21.3 1.0
CG A:TRP65 3.7 16.3 1.0
CAP A:7D0604 3.8 64.4 1.0
CAM A:7D0604 3.8 40.7 1.0
CB A:TRP65 4.0 16.8 1.0
CE2 A:TRP65 4.1 19.3 1.0
O A:GLY400 4.1 44.8 1.0
CH2 A:TRP65 4.3 21.2 1.0
CAN A:7D0604 4.3 53.7 1.0
CZ2 A:TRP65 4.5 19.9 1.0
CD1 A:TRP65 4.6 16.1 1.0
O A:HOH1036 4.7 36.0 1.0
NE1 A:TRP65 4.8 19.8 1.0
FAE A:7D0604 4.9 63.0 1.0
OAL A:7D0604 4.9 30.0 1.0

Reference:

C.Adamson, R.J.Pengelly, S.Shamsi Kazem Abadi, S.Chakladar, J.Draper, R.Britton, T.M.Gloster, A.J.Bennet. Structural Snapshots For Mechanism-Based Inactivation of A Glycoside Hydrolase By Cyclopropyl Carbasugars. Angew.Chem.Int.Ed.Engl. V. 55 14978 2016.
ISSN: ESSN 1521-3773
PubMed: 27783466
DOI: 10.1002/ANIE.201607431
Page generated: Tue Jul 15 05:10:40 2025

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