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Fluorine in PDB 4u2k: X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Anticancer Compound at 2.13 A Resolution

Enzymatic activity of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Anticancer Compound at 2.13 A Resolution

All present enzymatic activity of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Anticancer Compound at 2.13 A Resolution:
2.4.2.3;

Protein crystallography data

The structure of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Anticancer Compound at 2.13 A Resolution, PDB code: 4u2k was solved by I.I.Prokofev, A.A.Lashkov, A.G.Gabdoulkhakov, C.Betzel, A.M.Mikhailov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.77 / 2.13
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 91.280, 91.280, 137.227, 90.00, 90.00, 120.00
R / Rfree (%) 20.9 / 26.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Anticancer Compound at 2.13 A Resolution (pdb code 4u2k). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Anticancer Compound at 2.13 A Resolution, PDB code: 4u2k:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 4u2k

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Fluorine binding site 1 out of 4 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Anticancer Compound at 2.13 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Anticancer Compound at 2.13 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F302

b:18.3
occ:0.76
 F5 B:4WR302 0.0 18.3 0.8
C5 B:4WR302 1.4 24.5 0.8
C4 B:4WR302 2.4 18.3 0.8
C6 B:4WR302 2.4 17.9 0.8
O4 B:4WR302 2.7 34.6 0.8
CG2 B:ILE220 3.2 31.8 1.0
N B:GLY95 3.4 27.6 1.0
CA B:GLY95 3.4 24.0 1.0
N3 B:4WR302 3.6 24.4 0.8
N1 B:4WR302 3.7 19.6 0.8
C B:THR94 3.7 23.1 1.0
O B:THR94 3.9 23.7 1.0
C2 B:4WR302 4.1 22.7 0.8
CG1 B:ILE219 4.2 34.5 1.0
O B:HOH401 4.2 16.0 1.0
CD1 B:ILE219 4.2 29.7 1.0
CA B:THR94 4.4 24.1 1.0
CB B:ILE220 4.5 34.9 1.0
NH2 B:ARG167 4.5 27.8 1.0
C B:GLY95 4.8 26.4 1.0
CAB B:4WR302 4.9 29.0 0.8

Fluorine binding site 2 out of 4 in 4u2k

Go back to Fluorine Binding Sites List in 4u2k
Fluorine binding site 2 out of 4 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Anticancer Compound at 2.13 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Anticancer Compound at 2.13 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F303

b:29.1
occ:0.39
 F5 D:M5F303 0.0 29.1 0.4
F5 D:4WR304 0.5 29.2 0.5
C5 D:M5F303 1.3 27.6 0.4
C5 D:4WR304 1.5 28.1 0.5
C4 D:M5F303 2.3 24.2 0.4
C4 D:4WR304 2.4 24.4 0.5
C6 D:M5F303 2.4 23.8 0.4
O4 D:4WR304 2.6 29.2 0.5
C6 D:4WR304 2.7 23.3 0.5
O4 D:M5F303 2.7 29.9 0.4
C D:THR94 3.2 25.6 1.0
N D:GLY95 3.2 25.5 1.0
O D:THR94 3.4 24.4 1.0
N3 D:M5F303 3.5 24.2 0.4
N1 D:M5F303 3.5 24.2 0.4
CD1 D:ILE219 3.5 31.9 1.0
CG1 D:ILE219 3.6 38.4 1.0
N3 D:4WR304 3.6 23.9 0.5
CA D:GLY95 3.6 26.8 1.0
CG1 D:ILE220 3.7 38.2 1.0
CD1 D:ILE220 3.8 27.8 1.0
CA D:THR94 3.8 22.2 1.0
N1 D:4WR304 3.8 24.7 0.5
C2 D:M5F303 4.0 23.0 0.4
C2 D:4WR304 4.2 22.9 0.5
N D:THR94 4.3 24.6 1.0
O D:THR93 4.7 25.8 0.6
CAB D:M5F303 4.8 24.7 0.4
C D:THR93 4.8 25.2 0.6
OG1 D:THR93 4.8 24.1 0.4
CAL D:M5F303 5.0 24.4 0.4
C D:THR93 5.0 25.2 0.4
N D:ILE220 5.0 32.0 1.0

Fluorine binding site 3 out of 4 in 4u2k

Go back to Fluorine Binding Sites List in 4u2k
Fluorine binding site 3 out of 4 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Anticancer Compound at 2.13 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Anticancer Compound at 2.13 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F304

b:29.2
occ:0.45
 F5 D:4WR304 0.0 29.2 0.5
F5 D:M5F303 0.5 29.1 0.4
C5 D:M5F303 1.2 27.6 0.4
C5 D:4WR304 1.3 28.1 0.5
C6 D:M5F303 2.1 23.8 0.4
C4 D:M5F303 2.3 24.2 0.4
C6 D:4WR304 2.3 23.3 0.5
C4 D:4WR304 2.4 24.4 0.5
O4 D:4WR304 2.8 29.2 0.5
O4 D:M5F303 2.9 29.9 0.4
N1 D:M5F303 3.3 24.2 0.4
CD1 D:ILE219 3.4 31.9 1.0
N3 D:M5F303 3.5 24.2 0.4
C D:THR94 3.5 25.6 1.0
N1 D:4WR304 3.6 24.7 0.5
N D:GLY95 3.6 25.5 1.0
N3 D:4WR304 3.6 23.9 0.5
CG1 D:ILE219 3.7 38.4 1.0
O D:THR94 3.7 24.4 1.0
C2 D:M5F303 3.8 23.0 0.4
CA D:THR94 4.0 22.2 1.0
CD1 D:ILE220 4.0 27.8 1.0
CG1 D:ILE220 4.0 38.2 1.0
C2 D:4WR304 4.1 22.9 0.5
CA D:GLY95 4.1 26.8 1.0
N D:THR94 4.3 24.6 1.0
CAB D:M5F303 4.5 24.7 0.4
OG1 D:THR93 4.5 24.1 0.4
CAL D:M5F303 4.6 24.4 0.4
O D:THR93 4.6 25.8 0.6
C D:THR93 4.7 25.2 0.6
CAB D:4WR304 4.8 24.7 0.5
C D:THR93 4.9 25.2 0.4

Fluorine binding site 4 out of 4 in 4u2k

Go back to Fluorine Binding Sites List in 4u2k
Fluorine binding site 4 out of 4 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Anticancer Compound at 2.13 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Anticancer Compound at 2.13 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F302

b:39.0
occ:0.86
 F5 F:M5F302 0.0 39.0 0.9
C5 F:M5F302 1.3 33.8 0.9
C4 F:M5F302 2.3 24.7 0.9
C6 F:M5F302 2.4 22.4 0.9
O4 F:M5F302 2.7 36.7 0.9
CG2 F:ILE220 3.5 34.9 1.0
N1 F:M5F302 3.5 23.6 0.9
N3 F:M5F302 3.5 26.1 0.9
CD1 F:ILE219 3.7 28.5 1.0
CG1 F:ILE219 3.8 33.0 1.0
N F:GLY95 3.9 27.2 1.0
C2 F:M5F302 4.0 19.2 0.9
C F:THR94 4.1 25.6 1.0
CA F:GLY95 4.2 24.1 1.0
O F:THR94 4.3 19.1 1.0
CE2 F:PHE161 4.5 19.4 1.0
CA F:THR94 4.6 17.7 1.0
CAB F:M5F302 4.8 26.1 0.9
CB F:ILE220 4.8 38.5 1.0
NH2 F:ARG167 4.8 14.5 1.0
O F:HOH415 4.9 14.0 1.0
CZ F:PHE161 5.0 24.5 1.0
CZ E:PHE6 5.0 53.1 1.0
N F:THR94 5.0 19.8 1.0

Reference:

I.I.Prokofev, A.A.Lashkov, A.G.Gabdoulkhakov, C.Betzel, A.M.Mikhailov. X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with New Anticancer Compound at 1.17 A Resolution To Be Published.
Page generated: Sun Dec 13 12:12:53 2020

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