Chlorine 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:

Fluorine (F) 2 atoms
Zinc (Zn) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of MTH1 in Complex with 18-Crown-6, PDB code: 6imz:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6imz

Go back to Chlorine Binding Sites List in 6imz
Chlorine binding site 1 out of 4 in the Crystal Structure of MTH1 in Complex with 18-Crown-6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl205

b:64.2
occ:0.50
CL A:VGH205 0.0 64.2 0.5
CL2 A:VGH205 0.2 64.2 0.5
C13 A:VGH205 1.7 51.0 0.5
C18 A:VGH205 1.7 51.0 0.5
C12 A:VGH205 2.7 49.7 0.5
C3 A:VGH205 2.7 49.7 0.5
C17 A:VGH205 2.8 47.6 0.5
C17 A:VGH205 2.8 47.6 0.5
F A:VGH205 2.9 54.1 0.5
O27 A:VGH205 3.1 48.2 1.0
C21 A:VGH205 3.2 50.0 1.0
C1 A:VGH205 3.3 48.0 1.0
CE2 A:PHE27 3.4 49.6 1.0
C4 A:VGH205 3.4 47.8 1.0
C15 A:VGH205 3.7 46.8 1.0
CD2 A:PHE27 3.8 48.6 1.0
C2 A:VGH205 4.0 46.1 0.5
C2 A:VGH205 4.0 46.1 0.5
C18 A:VGH205 4.0 47.5 0.5
C13 A:VGH205 4.0 47.5 0.5
CZ2 A:TRP117 4.3 45.8 1.0
C6 A:VGH205 4.4 45.2 1.0
C3 A:VGH205 4.5 46.1 0.5
C12 A:VGH205 4.5 46.1 0.5
O A:HOH301 4.6 41.9 1.0
CZ A:PHE27 4.6 50.7 1.0
CE2 A:TRP117 4.7 45.3 1.0
C14 A:VGH205 4.7 45.1 1.0
NE1 A:TRP117 4.7 44.5 1.0
C16 A:VGH205 4.9 47.0 1.0

Chlorine binding site 2 out of 4 in 6imz

Go back to Chlorine Binding Sites List in 6imz
Chlorine binding site 2 out of 4 in the Crystal Structure of MTH1 in Complex with 18-Crown-6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl205

b:51.1
occ:0.50
CL A:VGH205 0.0 51.1 0.5
CL2 A:VGH205 0.2 51.0 0.5
C13 A:VGH205 1.7 47.5 0.5
C18 A:VGH205 1.7 47.5 0.5
C17 A:VGH205 2.7 47.6 0.5
C17 A:VGH205 2.7 47.6 0.5
C12 A:VGH205 2.7 46.1 0.5
C3 A:VGH205 2.7 46.1 0.5
C21 A:VGH205 2.9 50.0 1.0
F A:VGH205 2.9 42.4 0.5
CD2 A:LEU9 3.6 30.5 1.0
C1 A:VGH205 3.8 48.0 1.0
CD1 A:LEU9 3.8 34.4 1.0
O27 A:VGH205 3.9 48.2 1.0
N22 A:VGH205 4.0 40.3 1.0
C2 A:VGH205 4.0 46.1 0.5
C18 A:VGH205 4.0 51.0 0.5
C2 A:VGH205 4.0 46.1 0.5
C13 A:VGH205 4.0 51.0 0.5
CE2 A:PHE72 4.0 37.8 1.0
C15 A:VGH205 4.2 46.8 1.0
CG A:LEU9 4.2 35.4 1.0
CG1 A:VAL83 4.2 27.8 1.0
C19 A:VGH205 4.2 48.7 1.0
CB A:LEU9 4.4 27.5 1.0
C3 A:VGH205 4.5 49.7 0.5
C12 A:VGH205 4.5 49.7 0.5
CZ A:PHE72 4.6 34.1 1.0
CG2 A:VAL83 4.8 24.4 1.0

Chlorine binding site 3 out of 4 in 6imz

Go back to Chlorine Binding Sites List in 6imz
Chlorine binding site 3 out of 4 in the Crystal Structure of MTH1 in Complex with 18-Crown-6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of MTH1 in Complex with 18-Crown-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:51.0
occ:0.50
CL2 A:VGH205 0.0 51.0 0.5
CL A:VGH205 0.2 51.1 0.5
C18 A:VGH205 1.7 47.5 0.5
C13 A:VGH205 1.7 47.5 0.5
C17 A:VGH205 2.7 47.6 0.5
C17 A:VGH205 2.7 47.6 0.5
C12 A:VGH205 2.7 46.1 0.5
C3 A:VGH205 2.7 46.1 0.5
C21 A:VGH205 2.8 50.0 1.0
F A:VGH205 2.9 42.4 0.5
CD2 A:LEU9 3.7 30.5 1.0
C1 A:VGH205 3.8 48.0 1.0
N22 A:VGH205 3.9 40.3 1.0
O27 A:VGH205 3.9 48.2 1.0
CE2 A:PHE72 3.9 37.8 1.0
C18 A:VGH205 4.0 51.0 0.5
C13 A:VGH205 4.0 51.0 0.5
C2 A:VGH205 4.0 46.1 0.5
C2 A:VGH205 4.0 46.1 0.5
CD1 A:LEU9 4.0 34.4 1.0
C15 A:VGH205 4.1 46.8 1.0
C19 A:VGH205 4.1 48.7 1.0
CG1 A:VAL83 4.2 27.8 1.0
CG A:LEU9 4.3 35.4 1.0
C3 A:VGH205 4.5 49.7 0.5
C12 A:VGH205 4.5 49.7 0.5
CZ A:PHE72 4.5 34.1 1.0
CB A:LEU9 4.6 27.5 1.0
CG2 A:VAL83 4.7 24.4 1.0
N23 A:VGH205 4.9 41.8 1.0
C4 A:VGH205 4.9 47.8 1.0
CD2 A:PHE72 4.9 43.3 1.0

Chlorine binding site 4 out of 4 in 6imz

Go back to Chlorine Binding Sites List in 6imz
Chlorine binding site 4 out of 4 in the Crystal Structure of MTH1 in Complex with 18-Crown-6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of MTH1 in Complex with 18-Crown-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:64.2
occ:0.50
CL2 A:VGH205 0.0 64.2 0.5
CL A:VGH205 0.2 64.2 0.5
C18 A:VGH205 1.7 51.0 0.5
C13 A:VGH205 1.7 51.0 0.5
C12 A:VGH205 2.7 49.7 0.5
C3 A:VGH205 2.7 49.7 0.5
C17 A:VGH205 2.8 47.6 0.5
C17 A:VGH205 2.8 47.6 0.5
F A:VGH205 2.9 54.1 0.5
O27 A:VGH205 3.1 48.2 1.0
C21 A:VGH205 3.2 50.0 1.0
C4 A:VGH205 3.3 47.8 1.0
CE2 A:PHE27 3.3 49.6 1.0
C1 A:VGH205 3.4 48.0 1.0
C15 A:VGH205 3.6 46.8 1.0
CD2 A:PHE27 3.8 48.6 1.0
C2 A:VGH205 4.0 46.1 0.5
C2 A:VGH205 4.0 46.1 0.5
C18 A:VGH205 4.0 47.5 0.5
C13 A:VGH205 4.0 47.5 0.5
CZ2 A:TRP117 4.2 45.8 1.0
C6 A:VGH205 4.2 45.2 1.0
C14 A:VGH205 4.5 45.1 1.0
C12 A:VGH205 4.5 46.1 0.5
C3 A:VGH205 4.5 46.1 0.5
CZ A:PHE27 4.5 50.7 1.0
CE2 A:TRP117 4.6 45.3 1.0
O A:HOH301 4.6 41.9 1.0
NE1 A:TRP117 4.7 44.5 1.0
C16 A:VGH205 4.8 47.0 1.0
CH2 A:TRP117 4.9 41.9 1.0
C19 A:VGH205 5.0 48.7 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: Sat Dec 12 13:10:24 2020

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