Fluorine in PDB 6imz: Crystal Structure of MTH1 in Complex with 18-Crown-6

Enzymatic activity of Crystal Structure of MTH1 in Complex with 18-Crown-6

All present enzymatic activity of Crystal Structure of MTH1 in Complex with 18-Crown-6:
3.6.1.55; 3.6.1.56;

Protein crystallography data

The structure of Crystal Structure of MTH1 in Complex with 18-Crown-6, PDB code: 6imz was solved by T.Yokoyama, Y.Kosaka, K.Matsumoto, R.Kitakami, Y.Nabeshima, M.Mizuguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.02 / 2.10
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 66.434, 66.434, 140.182, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 22.8

Other elements in 6imz:

The structure of Crystal Structure of MTH1 in Complex with 18-Crown-6 also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Zinc (Zn) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of MTH1 in Complex with 18-Crown-6 (pdb code 6imz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of MTH1 in Complex with 18-Crown-6, PDB code: 6imz:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 6imz

Go back to Fluorine Binding Sites List in 6imz
Fluorine binding site 1 out of 2 in the Crystal Structure of MTH1 in Complex with 18-Crown-6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of MTH1 in Complex with 18-Crown-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F205

b:42.4
occ:0.50
F A:VGH205 0.0 42.4 0.5
C12 A:VGH205 1.4 46.1 0.5
C3 A:VGH205 1.4 46.1 0.5
C13 A:VGH205 2.4 47.5 0.5
C18 A:VGH205 2.4 47.5 0.5
C2 A:VGH205 2.4 46.1 0.5
C2 A:VGH205 2.4 46.1 0.5
CL A:VGH205 2.9 51.1 0.5
CL2 A:VGH205 2.9 51.0 0.5
CE A:MET81 3.1 45.7 1.0
CG2 A:VAL83 3.2 24.4 1.0
CB A:TYR7 3.4 27.0 1.0
CG A:TYR7 3.5 30.3 1.0
C17 A:VGH205 3.7 47.6 0.5
C3 A:VGH205 3.7 49.7 0.5
C17 A:VGH205 3.7 47.6 0.5
C12 A:VGH205 3.7 49.7 0.5
CG1 A:VAL83 3.7 27.8 1.0
CD2 A:TYR7 3.7 32.4 1.0
CB A:VAL83 4.1 23.1 1.0
C18 A:VGH205 4.2 51.0 0.5
C13 A:VGH205 4.2 51.0 0.5
CD1 A:TYR7 4.3 32.5 1.0
CE2 A:PHE72 4.5 37.8 1.0
CE2 A:TYR7 4.6 34.3 1.0
O A:THR8 4.7 28.4 1.0
C21 A:VGH205 4.7 50.0 1.0
CD2 A:PHE72 4.8 43.3 1.0
F A:VGH205 4.8 54.1 0.5
SD A:MET81 4.8 36.5 1.0
CA A:TYR7 4.8 29.4 1.0
CA A:VAL83 4.9 24.1 1.0

Fluorine binding site 2 out of 2 in 6imz

Go back to Fluorine Binding Sites List in 6imz
Fluorine binding site 2 out of 2 in the Crystal Structure of MTH1 in Complex with 18-Crown-6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of MTH1 in Complex with 18-Crown-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F205

b:54.1
occ:0.50
F A:VGH205 0.0 54.1 0.5
C12 A:VGH205 1.4 49.7 0.5
C3 A:VGH205 1.4 49.7 0.5
C13 A:VGH205 2.4 51.0 0.5
C18 A:VGH205 2.4 51.0 0.5
C2 A:VGH205 2.4 46.1 0.5
C2 A:VGH205 2.4 46.1 0.5
CL A:VGH205 2.9 64.2 0.5
CL2 A:VGH205 2.9 64.2 0.5
C3 A:VGH205 3.6 46.1 0.5
C17 A:VGH205 3.6 47.6 0.5
C17 A:VGH205 3.6 47.6 0.5
C12 A:VGH205 3.6 46.1 0.5
CE2 A:TYR7 4.0 34.3 1.0
C6 A:VGH205 4.1 45.2 1.0
C18 A:VGH205 4.1 47.5 0.5
C13 A:VGH205 4.1 47.5 0.5
CE2 A:PHE27 4.4 49.6 1.0
CD2 A:TYR7 4.5 32.4 1.0
C4 A:VGH205 4.6 47.8 1.0
CZ A:TYR7 4.7 39.9 1.0
CD2 A:PHE27 4.7 48.6 1.0
F A:VGH205 4.8 42.4 0.5
OH A:TYR7 4.8 40.1 1.0
N24 A:VGH205 4.8 44.9 1.0
C21 A:VGH205 4.8 50.0 1.0
CE A:MET81 4.9 45.7 1.0

Reference:

T.Yokoyama, Y.Kosaka, K.Matsumoto, R.Kitakami, Y.Nabeshima, M.Mizuguchi. Crown Ethers As Transthyretin Amyloidogenesis Inhibitor To Be Published.
Page generated: Sun Dec 13 12:54:09 2020

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