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Fluorine in PDB 8tk3: Human VH1-Related Dual-Specificity Phosphatase (Vhr) Having Oxidized Catalytic Cysteine and Complexed with 6-(Difluoromethyl)Pyrimidin-4- Ol at Two Allosteric Sites

Enzymatic activity of Human VH1-Related Dual-Specificity Phosphatase (Vhr) Having Oxidized Catalytic Cysteine and Complexed with 6-(Difluoromethyl)Pyrimidin-4- Ol at Two Allosteric Sites

All present enzymatic activity of Human VH1-Related Dual-Specificity Phosphatase (Vhr) Having Oxidized Catalytic Cysteine and Complexed with 6-(Difluoromethyl)Pyrimidin-4- Ol at Two Allosteric Sites:
3.1.3.16; 3.1.3.48;

Protein crystallography data

The structure of Human VH1-Related Dual-Specificity Phosphatase (Vhr) Having Oxidized Catalytic Cysteine and Complexed with 6-(Difluoromethyl)Pyrimidin-4- Ol at Two Allosteric Sites, PDB code: 8tk3 was solved by A.E.Aleshin, J.Wu, L.J.Lambert, N.D.P.Cosford, L.Tautz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.25 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 34.133, 52.467, 100.493, 90, 90, 90
R / Rfree (%) 18.6 / 25.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human VH1-Related Dual-Specificity Phosphatase (Vhr) Having Oxidized Catalytic Cysteine and Complexed with 6-(Difluoromethyl)Pyrimidin-4- Ol at Two Allosteric Sites (pdb code 8tk3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Human VH1-Related Dual-Specificity Phosphatase (Vhr) Having Oxidized Catalytic Cysteine and Complexed with 6-(Difluoromethyl)Pyrimidin-4- Ol at Two Allosteric Sites, PDB code: 8tk3:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 8tk3

Go back to Fluorine Binding Sites List in 8tk3
Fluorine binding site 1 out of 4 in the Human VH1-Related Dual-Specificity Phosphatase (Vhr) Having Oxidized Catalytic Cysteine and Complexed with 6-(Difluoromethyl)Pyrimidin-4- Ol at Two Allosteric Sites


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human VH1-Related Dual-Specificity Phosphatase (Vhr) Having Oxidized Catalytic Cysteine and Complexed with 6-(Difluoromethyl)Pyrimidin-4- Ol at Two Allosteric Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:69.1
occ:1.00
 F1 A:I2X201 0.0 69.1 1.0
C4 A:I2X201 1.3 78.0 1.0
H3 A:I2X201 2.0 78.0 1.0
F2 A:I2X201 2.1 78.0 1.0
C3 A:I2X201 2.4 81.2 1.0
O A:HOH383 2.7 49.2 1.0
C2 A:I2X201 3.2 74.5 1.0
N1 A:I2X201 3.3 88.4 1.0
H2 A:I2X201 3.3 74.5 1.0
NH1 A:ARG155 3.4 25.8 1.0
O A:HOH304 3.5 50.6 1.0
O A:HOH381 3.5 36.4 1.0
CZ A:ARG155 4.4 28.8 1.0
NH2 A:ARG155 4.4 27.8 1.0
C5 A:I2X201 4.5 86.2 1.0
C1 A:I2X201 4.5 69.4 1.0
OE2 A:GLU159 4.5 38.9 1.0
O A:GLN156 4.5 29.8 1.0
CG A:GLU159 4.6 28.1 1.0
O A:ARG155 4.7 26.1 1.0
CD A:GLU159 4.8 29.4 1.0

Fluorine binding site 2 out of 4 in 8tk3

Go back to Fluorine Binding Sites List in 8tk3
Fluorine binding site 2 out of 4 in the Human VH1-Related Dual-Specificity Phosphatase (Vhr) Having Oxidized Catalytic Cysteine and Complexed with 6-(Difluoromethyl)Pyrimidin-4- Ol at Two Allosteric Sites


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human VH1-Related Dual-Specificity Phosphatase (Vhr) Having Oxidized Catalytic Cysteine and Complexed with 6-(Difluoromethyl)Pyrimidin-4- Ol at Two Allosteric Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:78.0
occ:1.00
 F2 A:I2X201 0.0 78.0 1.0
C4 A:I2X201 1.3 78.0 1.0
H3 A:I2X201 2.0 78.0 1.0
F1 A:I2X201 2.1 69.1 1.0
C3 A:I2X201 2.4 81.2 1.0
N1 A:I2X201 2.7 88.4 1.0
O A:GLN156 2.8 29.8 1.0
O A:HOH304 3.0 50.6 1.0
C2 A:I2X201 3.6 74.5 1.0
C A:GLN156 3.7 29.4 1.0
CA A:GLN156 4.0 31.6 1.0
C5 A:I2X201 4.0 86.2 1.0
H2 A:I2X201 4.0 74.5 1.0
NH1 A:ARG155 4.2 25.8 1.0
O A:ARG155 4.2 26.1 1.0
H4 A:I2X201 4.6 86.2 1.0
O A:HOH383 4.6 49.2 1.0
CG A:GLN156 4.7 47.1 1.0
C1 A:I2X201 4.7 69.4 1.0
N A:ASN157 4.8 24.1 1.0
N2 A:I2X201 4.9 70.6 1.0
CB A:GLN156 4.9 37.5 1.0
N A:GLN156 5.0 31.9 1.0
C A:ARG155 5.0 29.0 1.0

Fluorine binding site 3 out of 4 in 8tk3

Go back to Fluorine Binding Sites List in 8tk3
Fluorine binding site 3 out of 4 in the Human VH1-Related Dual-Specificity Phosphatase (Vhr) Having Oxidized Catalytic Cysteine and Complexed with 6-(Difluoromethyl)Pyrimidin-4- Ol at Two Allosteric Sites


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human VH1-Related Dual-Specificity Phosphatase (Vhr) Having Oxidized Catalytic Cysteine and Complexed with 6-(Difluoromethyl)Pyrimidin-4- Ol at Two Allosteric Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:72.2
occ:1.00
 F1 A:I2X202 0.0 72.2 1.0
C4 A:I2X202 1.3 71.1 1.0
H3 A:I2X202 1.9 71.1 1.0
F2 A:I2X202 2.1 66.9 1.0
C3 A:I2X202 2.4 73.0 1.0
H2 A:I2X202 2.7 86.0 1.0
C2 A:I2X202 3.0 86.0 1.0
N1 A:I2X202 3.6 74.6 1.0
C1 A:DMS203 3.9 73.0 1.0
CD A:PRO35 4.0 33.0 1.0
C1 A:I2X202 4.4 84.2 1.0
CG A:PRO35 4.5 33.8 1.0
CG1 A:ILE153 4.7 38.3 1.0
C5 A:I2X202 4.7 73.2 1.0
CG2 A:THR34 4.8 36.9 1.0
CD1 A:ILE153 4.9 44.0 1.0

Fluorine binding site 4 out of 4 in 8tk3

Go back to Fluorine Binding Sites List in 8tk3
Fluorine binding site 4 out of 4 in the Human VH1-Related Dual-Specificity Phosphatase (Vhr) Having Oxidized Catalytic Cysteine and Complexed with 6-(Difluoromethyl)Pyrimidin-4- Ol at Two Allosteric Sites


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human VH1-Related Dual-Specificity Phosphatase (Vhr) Having Oxidized Catalytic Cysteine and Complexed with 6-(Difluoromethyl)Pyrimidin-4- Ol at Two Allosteric Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:66.9
occ:1.00
 F2 A:I2X202 0.0 66.9 1.0
C4 A:I2X202 1.3 71.1 1.0
H3 A:I2X202 2.0 71.1 1.0
F1 A:I2X202 2.1 72.2 1.0
C3 A:I2X202 2.3 73.0 1.0
N1 A:I2X202 2.8 74.6 1.0
C2 A:I2X202 3.4 86.0 1.0
H2 A:I2X202 3.7 86.0 1.0
CG1 A:ILE153 3.9 38.3 1.0
CE A:MET145 4.1 37.6 1.0
CG2 A:THR34 4.1 36.9 1.0
C5 A:I2X202 4.1 73.2 1.0
SD A:MET145 4.2 37.1 1.0
CG2 A:ILE153 4.4 36.9 1.0
CB A:ILE153 4.5 36.3 1.0
C1 A:I2X202 4.6 84.2 1.0
CD1 A:ILE153 4.7 44.0 1.0
H4 A:I2X202 4.8 73.2 1.0
N2 A:I2X202 4.9 73.7 1.0
CB A:THR34 4.9 37.4 1.0

Reference:

A.E.Aleshin, J.Wu, L.J.Lambert, N.D.P.Cosford, L.Tautz. Human VH1-Related Dual-Specificity Phosphatase (Vhr) Having Oxidized Catalytic Cysteine and Complexed with 6-(Difluoromethyl)Pyrimidin-4-Ol at Two Allosteric Sites To Be Published.
Page generated: Sat Sep 28 20:32:23 2024

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