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Zinc in PDB 6aa3: Crystal Structure of MTH1 in Apo Form (Cocktail No. 1)

Enzymatic activity of Crystal Structure of MTH1 in Apo Form (Cocktail No. 1)

All present enzymatic activity of Crystal Structure of MTH1 in Apo Form (Cocktail No. 1):
3.6.1.55; 3.6.1.56;

Protein crystallography data

The structure of Crystal Structure of MTH1 in Apo Form (Cocktail No. 1), PDB code: 6aa3 was solved by T.Yokoyama, R.Kitakami, M.Mizuguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.49 / 2.00
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 66.948, 66.948, 141.114, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 25.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of MTH1 in Apo Form (Cocktail No. 1) (pdb code 6aa3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of MTH1 in Apo Form (Cocktail No. 1), PDB code: 6aa3:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6aa3

Go back to Zinc Binding Sites List in 6aa3
Zinc binding site 1 out of 3 in the Crystal Structure of MTH1 in Apo Form (Cocktail No. 1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of MTH1 in Apo Form (Cocktail No. 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:33.9
occ:1.00
OD2 A:ASP82 1.9 36.0 1.0
NE2 A:HIS161 2.0 36.9 1.0
ND1 A:HIS159 2.0 38.6 1.0
NE2 A:HIS84 2.1 37.1 1.0
CG A:ASP82 2.7 35.9 1.0
CE1 A:HIS161 2.8 36.4 1.0
OD1 A:ASP82 2.9 34.7 1.0
CE1 A:HIS159 2.9 40.2 1.0
CE1 A:HIS84 3.0 39.2 1.0
CG A:HIS159 3.1 41.2 1.0
CD2 A:HIS161 3.1 34.8 1.0
CD2 A:HIS84 3.2 34.6 1.0
CB A:HIS159 3.5 36.8 1.0
CD1 A:LEU6 3.9 36.8 1.0
ND1 A:HIS161 4.0 34.0 1.0
NE2 A:HIS159 4.1 44.7 1.0
ND1 A:HIS84 4.1 36.0 1.0
CB A:ASP82 4.1 37.0 1.0
CG A:HIS161 4.2 35.9 1.0
CD2 A:HIS159 4.2 42.8 1.0
CG A:HIS84 4.2 32.1 1.0
OE1 A:GLN69 4.6 46.4 1.0
CD1 A:ILE45 4.8 41.3 1.0
O A:HOH304 4.8 41.9 1.0

Zinc binding site 2 out of 3 in 6aa3

Go back to Zinc Binding Sites List in 6aa3
Zinc binding site 2 out of 3 in the Crystal Structure of MTH1 in Apo Form (Cocktail No. 1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of MTH1 in Apo Form (Cocktail No. 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:38.6
occ:1.00
NE2 A:HIS164 1.9 35.9 1.0
OE1 A:GLU41 2.1 35.4 1.0
OE2 A:GLU41 2.7 43.4 1.0
CD A:GLU41 2.8 42.7 1.0
CE1 A:HIS164 2.8 40.5 1.0
CD2 A:HIS164 3.0 37.0 1.0
ND1 A:HIS164 4.0 38.2 1.0
CG A:HIS164 4.1 37.0 1.0
CG A:GLU41 4.3 41.9 1.0
CB A:HIS163 4.4 34.0 1.0
O A:HOH305 4.6 42.6 1.0
O3 A:SO4204 5.0 38.6 0.5

Zinc binding site 3 out of 3 in 6aa3

Go back to Zinc Binding Sites List in 6aa3
Zinc binding site 3 out of 3 in the Crystal Structure of MTH1 in Apo Form (Cocktail No. 1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of MTH1 in Apo Form (Cocktail No. 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:77.8
occ:1.00
SG A:CYS87 2.1 47.3 1.0
ND1 A:HIS65 2.6 46.1 1.0
CB A:CYS87 3.1 36.4 1.0
C A:CYS87 3.3 36.3 1.0
CE1 A:HIS65 3.4 46.2 1.0
O A:CYS87 3.5 36.6 1.0
N A:THR88 3.6 36.3 1.0
CG A:HIS65 3.6 46.7 1.0
CA A:CYS87 3.8 34.2 1.0
CB A:HIS65 4.0 41.2 1.0
CA A:THR88 4.1 39.1 1.0
C A:THR88 4.4 42.0 1.0
N A:CYS87 4.5 32.4 1.0
N A:ASP89 4.5 42.9 1.0
NE2 A:HIS65 4.6 47.7 1.0
NZ A:LYS130 4.7 57.5 1.0
CD2 A:HIS65 4.7 49.4 1.0
CG1 A:VAL67 4.9 48.3 1.0
O A:THR88 4.9 41.4 1.0

Reference:

T.Yokoyama, R.Kitakami, M.Mizuguchi. Discovery of A New Class of MTH1 Inhibitor By X-Ray Crystallographic Screening. Eur J Med Chem V. 167 153 2019.
ISSN: ISSN 1768-3254
PubMed: 30771603
DOI: 10.1016/J.EJMECH.2019.02.011
Page generated: Wed Dec 16 11:29:20 2020

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