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Fluorine in PDB 3kvv: Trapping of An Oxocarbenium Ion Intermediate in Up Crystals

Enzymatic activity of Trapping of An Oxocarbenium Ion Intermediate in Up Crystals

All present enzymatic activity of Trapping of An Oxocarbenium Ion Intermediate in Up Crystals:
2.4.2.3;

Protein crystallography data

The structure of Trapping of An Oxocarbenium Ion Intermediate in Up Crystals, PDB code: 3kvv was solved by D.Paul, S.O'leary, K.Rajashankar, W.Bu, A.Toms, E.Settembre, J.Sanders, T.P.Begley, S.E.Ealick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.52 / 1.80
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 92.864, 92.864, 145.016, 90.00, 90.00, 120.00
R / Rfree (%) 17.3 / 20.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Trapping of An Oxocarbenium Ion Intermediate in Up Crystals (pdb code 3kvv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Trapping of An Oxocarbenium Ion Intermediate in Up Crystals, PDB code: 3kvv:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3kvv

Go back to Fluorine Binding Sites List in 3kvv
Fluorine binding site 1 out of 6 in the Trapping of An Oxocarbenium Ion Intermediate in Up Crystals


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Trapping of An Oxocarbenium Ion Intermediate in Up Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F254

b:22.6
occ:1.00
 F5 A:URF254 0.0 22.6 1.0
C5 A:URF254 1.4 21.9 1.0
C4 A:URF254 2.4 20.4 1.0
C6 A:URF254 2.4 19.2 1.0
O4 A:URF254 2.7 22.9 1.0
CG1 A:VAL221 3.0 19.6 1.0
CG1 A:ILE220 3.4 18.9 1.0
N A:GLY96 3.5 19.6 1.0
C A:THR95 3.5 20.1 1.0
CD1 A:ILE220 3.6 25.1 1.0
O A:THR95 3.6 16.6 1.0
N3 A:URF254 3.7 19.9 1.0
N1 A:URF254 3.7 19.2 1.0
CA A:GLY96 3.8 18.8 1.0
CB A:VAL221 4.1 24.5 1.0
C2 A:URF254 4.2 19.4 1.0
CA A:THR95 4.3 19.6 1.0
N A:VAL221 4.5 21.5 1.0
NH2 A:ARG168 4.5 16.1 1.0
N A:THR95 4.6 20.2 1.0
CE1 A:PHE162 4.7 19.9 1.0
O A:HOH317 4.8 25.8 1.0
CB A:ILE220 4.8 20.9 1.0
CA A:VAL221 4.9 20.9 1.0
C A:ILE220 4.9 22.4 1.0
CZ A:PHE162 5.0 15.5 1.0

Fluorine binding site 2 out of 6 in 3kvv

Go back to Fluorine Binding Sites List in 3kvv
Fluorine binding site 2 out of 6 in the Trapping of An Oxocarbenium Ion Intermediate in Up Crystals


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Trapping of An Oxocarbenium Ion Intermediate in Up Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F254

b:23.9
occ:1.00
 F5 B:URF254 0.0 23.9 1.0
C5 B:URF254 1.4 21.0 1.0
C4 B:URF254 2.4 19.6 1.0
C6 B:URF254 2.4 18.9 1.0
O4 B:URF254 2.7 18.1 1.0
CG1 B:VAL221 3.2 26.8 1.0
CG1 B:ILE220 3.4 20.4 1.0
N B:GLY96 3.6 17.0 1.0
CD1 B:ILE220 3.6 20.1 1.0
C B:THR95 3.6 18.7 1.0
O B:THR95 3.6 17.6 1.0
N3 B:URF254 3.7 19.0 1.0
N1 B:URF254 3.7 19.6 1.0
CA B:GLY96 3.8 17.9 1.0
CB B:VAL221 4.1 25.9 1.0
C2 B:URF254 4.2 20.2 1.0
CA B:THR95 4.4 19.8 1.0
N B:VAL221 4.5 22.5 1.0
N B:THR95 4.6 20.5 1.0
NH2 B:ARG168 4.7 20.0 1.0
CE1 B:PHE162 4.8 18.8 1.0
CB B:ILE220 4.8 21.0 1.0
CZ A:PHE7 4.8 35.0 1.0
O B:HOH324 4.8 24.8 1.0
CA B:VAL221 4.9 26.1 1.0
C B:ILE220 4.9 22.8 1.0

Fluorine binding site 3 out of 6 in 3kvv

Go back to Fluorine Binding Sites List in 3kvv
Fluorine binding site 3 out of 6 in the Trapping of An Oxocarbenium Ion Intermediate in Up Crystals


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Trapping of An Oxocarbenium Ion Intermediate in Up Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F254

b:22.2
occ:1.00
 F5 C:URF254 0.0 22.2 1.0
C5 C:URF254 1.4 22.6 1.0
C6 C:URF254 2.4 22.9 1.0
C4 C:URF254 2.4 22.7 1.0
O4 C:URF254 2.7 22.3 1.0
CG1 C:VAL221 2.9 31.9 1.0
N C:GLY96 3.6 22.5 1.0
CG1 C:ILE220 3.6 31.0 1.0
N1 C:URF254 3.7 23.3 1.0
N3 C:URF254 3.7 22.5 1.0
C C:THR95 3.7 20.5 1.0
CA C:GLY96 3.8 24.6 1.0
O C:THR95 3.8 23.2 1.0
CD1 C:ILE220 3.8 29.8 1.0
CB C:VAL221 3.9 31.8 1.0
C2 C:URF254 4.2 22.5 1.0
N C:VAL221 4.3 27.8 1.0
CA C:THR95 4.5 22.7 1.0
NH2 C:ARG168 4.5 19.0 1.0
CE1 C:PHE162 4.6 18.4 1.0
CZ D:PHE7 4.7 40.3 1.0
CA C:VAL221 4.7 25.5 1.0
CZ C:PHE162 4.8 17.3 1.0
O C:HOH462 4.8 28.5 1.0
N C:THR95 4.8 27.4 1.0
C C:ILE220 4.8 28.3 1.0

Fluorine binding site 4 out of 6 in 3kvv

Go back to Fluorine Binding Sites List in 3kvv
Fluorine binding site 4 out of 6 in the Trapping of An Oxocarbenium Ion Intermediate in Up Crystals


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Trapping of An Oxocarbenium Ion Intermediate in Up Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F254

b:35.5
occ:1.00
 F5 D:URF254 0.0 35.5 1.0
C5 D:URF254 1.4 36.6 1.0
C6 D:URF254 2.4 35.2 1.0
C4 D:URF254 2.4 36.2 1.0
O4 D:URF254 2.7 38.2 1.0
CG1 D:VAL221 3.1 30.6 1.0
CG1 D:ILE220 3.4 30.5 1.0
CD1 D:ILE220 3.4 30.2 1.0
N D:GLY96 3.5 27.2 1.0
C D:THR95 3.6 22.9 1.0
N1 D:URF254 3.7 35.5 1.0
N3 D:URF254 3.7 34.6 1.0
O D:THR95 3.7 23.9 1.0
CA D:GLY96 3.7 29.8 1.0
CB D:VAL221 4.1 35.5 1.0
C2 D:URF254 4.2 35.0 1.0
CA D:THR95 4.4 26.5 1.0
N D:VAL221 4.5 33.2 1.0
NH2 D:ARG168 4.6 33.9 1.0
CB D:ILE220 4.8 30.2 1.0
N D:THR95 4.8 28.4 1.0
CA D:VAL221 4.9 34.0 1.0
CZ C:PHE7 4.9 42.2 1.0
CE1 D:PHE162 5.0 24.3 1.0

Fluorine binding site 5 out of 6 in 3kvv

Go back to Fluorine Binding Sites List in 3kvv
Fluorine binding site 5 out of 6 in the Trapping of An Oxocarbenium Ion Intermediate in Up Crystals


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Trapping of An Oxocarbenium Ion Intermediate in Up Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F254

b:34.6
occ:1.00
 F5 E:URF254 0.0 34.6 1.0
C5 E:URF254 1.4 33.9 1.0
C6 E:URF254 2.4 33.7 1.0
C4 E:URF254 2.4 34.2 1.0
O4 E:URF254 2.7 32.1 1.0
CG1 E:VAL221 3.2 31.4 1.0
CG1 E:ILE220 3.2 29.2 1.0
CD1 E:ILE220 3.3 37.2 1.0
N E:GLY96 3.5 27.9 1.0
C E:THR95 3.5 30.4 1.0
O E:THR95 3.6 28.1 1.0
N1 E:URF254 3.7 34.5 1.0
N3 E:URF254 3.7 33.3 1.0
CA E:GLY96 3.7 28.5 1.0
C2 E:URF254 4.2 34.1 1.0
CB E:VAL221 4.2 35.7 1.0
CA E:THR95 4.3 30.5 1.0
N E:VAL221 4.4 30.4 1.0
N E:THR95 4.6 29.1 1.0
CB E:ILE220 4.6 33.5 1.0
NH2 E:ARG168 4.7 26.8 1.0
C E:ILE220 4.8 35.6 1.0
CE1 E:PHE162 4.8 25.4 1.0
CA E:VAL221 4.9 29.4 1.0

Fluorine binding site 6 out of 6 in 3kvv

Go back to Fluorine Binding Sites List in 3kvv
Fluorine binding site 6 out of 6 in the Trapping of An Oxocarbenium Ion Intermediate in Up Crystals


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Trapping of An Oxocarbenium Ion Intermediate in Up Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F254

b:25.7
occ:1.00
 F5 F:URF254 0.0 25.7 1.0
C5 F:URF254 1.4 26.8 1.0
C6 F:URF254 2.4 24.6 1.0
C4 F:URF254 2.4 26.5 1.0
O4 F:URF254 2.7 27.2 1.0
CG1 F:ILE220 3.2 31.8 1.0
CG1 F:VAL221 3.3 26.5 1.0
CD1 F:ILE220 3.4 28.3 1.0
N1 F:URF254 3.7 26.2 1.0
N3 F:URF254 3.7 25.8 1.0
N F:GLY96 3.7 27.4 1.0
C F:THR95 3.7 26.5 1.0
O F:THR95 3.8 26.6 1.0
CA F:GLY96 3.9 25.7 1.0
CB F:VAL221 4.1 33.5 1.0
C2 F:URF254 4.2 27.0 1.0
NH2 F:ARG168 4.4 22.0 1.0
CA F:THR95 4.5 28.0 1.0
N F:VAL221 4.5 31.8 1.0
CB F:ILE220 4.7 29.2 1.0
CE1 F:PHE162 4.7 24.9 1.0
O F:HOH563 4.8 31.2 1.0
N F:THR95 4.8 27.3 1.0
C F:ILE220 4.9 35.0 1.0
CA F:VAL221 4.9 30.7 1.0
CZ F:PHE162 5.0 22.7 1.0

Reference:

D.Paul, S.E.O'leary, K.Rajashankar, W.Bu, A.Toms, E.C.Settembre, J.M.Sanders, T.P.Begley, S.E.Ealick. Glycal Formation in Crystals of Uridine Phosphorylase. Biochemistry V. 49 3499 2010.
ISSN: ISSN 0006-2960
PubMed: 20364833
DOI: 10.1021/BI902073B
Page generated: Mon Jul 14 17:37:17 2025

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