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Fluorine in PDB 4nv0: Crystal Structure of Cytosolic 5'-Nucleotidase Iiib (Cn-Iiib) Bound to 7-Methylguanosine

Enzymatic activity of Crystal Structure of Cytosolic 5'-Nucleotidase Iiib (Cn-Iiib) Bound to 7-Methylguanosine

All present enzymatic activity of Crystal Structure of Cytosolic 5'-Nucleotidase Iiib (Cn-Iiib) Bound to 7-Methylguanosine:
3.1.3.5;

Protein crystallography data

The structure of Crystal Structure of Cytosolic 5'-Nucleotidase Iiib (Cn-Iiib) Bound to 7-Methylguanosine, PDB code: 4nv0 was solved by T.Monecke, P.Neumann, R.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.19 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.670, 99.110, 74.120, 90.00, 90.99, 90.00
R / Rfree (%) 15.9 / 19.4

Other elements in 4nv0:

The structure of Crystal Structure of Cytosolic 5'-Nucleotidase Iiib (Cn-Iiib) Bound to 7-Methylguanosine also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Cytosolic 5'-Nucleotidase Iiib (Cn-Iiib) Bound to 7-Methylguanosine (pdb code 4nv0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Cytosolic 5'-Nucleotidase Iiib (Cn-Iiib) Bound to 7-Methylguanosine, PDB code: 4nv0:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4nv0

Go back to Fluorine Binding Sites List in 4nv0
Fluorine binding site 1 out of 6 in the Crystal Structure of Cytosolic 5'-Nucleotidase Iiib (Cn-Iiib) Bound to 7-Methylguanosine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Cytosolic 5'-Nucleotidase Iiib (Cn-Iiib) Bound to 7-Methylguanosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:17.7
occ:1.00
 F1 A:MGF404 0.0 17.7 1.0
MG A:MGF404 1.9 22.3 1.0
N A:ASP57 2.7 8.4 1.0
OG A:SER171 2.7 10.1 1.0
O A:HOH540 2.9 23.0 1.0
OD1 A:ASP55 2.9 11.6 1.0
N A:PHE56 2.9 10.2 1.0
F3 A:MGF404 3.2 11.9 1.0
CB A:PHE56 3.2 8.0 1.0
CB A:SER171 3.3 10.7 1.0
CA A:PHE56 3.3 9.7 1.0
F2 A:MGF404 3.3 13.5 1.0
C A:PHE56 3.5 8.4 1.0
OD2 A:ASP57 3.5 13.1 1.0
CG A:ASP55 3.6 11.5 1.0
CA A:SER171 3.7 11.3 1.0
CB A:ASP57 3.8 9.4 1.0
CA A:ASP57 3.8 10.5 1.0
CG A:ASP57 3.9 14.3 1.0
OD2 A:ASP55 4.0 12.9 1.0
C A:ASP55 4.1 10.3 1.0
CG A:PHE56 4.3 9.8 1.0
CD2 A:PHE56 4.4 11.7 1.0
N A:ALA172 4.4 8.8 1.0
CA A:ASP55 4.5 9.0 1.0
C A:SER171 4.5 8.6 1.0
MG A:MG402 4.6 12.9 1.0
O A:PHE170 4.6 11.2 1.0
CB A:ASP55 4.7 8.8 1.0
O A:PHE56 4.7 9.0 1.0
O A:ASP57 4.7 9.8 1.0
NZ A:LYS219 4.7 12.4 0.6
C A:ASP57 4.8 11.1 1.0
NZ A:LYS219 4.8 12.9 0.4
N A:GLY173 4.8 10.0 1.0
N A:SER171 4.8 10.9 1.0
O5' A:MG7403 4.9 23.9 0.4
OD1 A:ASP57 4.9 13.1 1.0

Fluorine binding site 2 out of 6 in 4nv0

Go back to Fluorine Binding Sites List in 4nv0
Fluorine binding site 2 out of 6 in the Crystal Structure of Cytosolic 5'-Nucleotidase Iiib (Cn-Iiib) Bound to 7-Methylguanosine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Cytosolic 5'-Nucleotidase Iiib (Cn-Iiib) Bound to 7-Methylguanosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:13.5
occ:1.00
 F2 A:MGF404 0.0 13.5 1.0
MG A:MGF404 1.9 22.3 1.0
O A:HOH523 2.5 25.0 1.0
N A:ALA172 2.8 8.8 1.0
NZ A:LYS219 2.9 12.9 0.4
NZ A:LYS219 2.9 12.4 0.6
O A:HOH540 3.0 23.0 1.0
OD1 A:ASP55 3.0 11.6 1.0
F1 A:MGF404 3.3 17.7 1.0
F3 A:MGF404 3.3 11.9 1.0
CE A:LYS219 3.4 14.2 0.4
CB A:ALA172 3.5 12.5 1.0
CE A:LYS219 3.6 11.4 0.6
CD A:LYS219 3.7 9.3 0.6
CA A:SER171 3.7 11.3 1.0
CA A:ALA172 3.7 11.8 1.0
C A:SER171 3.7 8.6 1.0
O A:HOH776 3.8 37.8 1.0
CD A:LYS219 3.9 12.8 0.4
OG A:SER171 4.2 10.1 1.0
CG A:ASP55 4.2 11.5 1.0
O5' A:MG7403 4.2 22.7 0.6
O A:HOH626 4.3 15.1 1.0
N A:GLY173 4.4 10.0 1.0
C A:ALA172 4.4 10.3 1.0
O A:PHE170 4.4 11.2 1.0
OD1 A:ASP249 4.5 16.0 1.0
CB A:SER171 4.5 10.7 1.0
O A:HOH543 4.6 24.2 1.0
C5' A:MG7403 4.6 21.9 0.4
O5' A:MG7403 4.7 23.9 0.4
O A:HOH605 4.8 29.5 1.0
OD2 A:ASP55 4.8 12.9 1.0
MG A:MG402 4.8 12.9 1.0
N A:SER171 4.8 10.9 1.0
O A:SER171 4.9 9.5 1.0
CG A:LYS219 5.0 13.9 0.6
C5' A:MG7403 5.0 23.5 0.6

Fluorine binding site 3 out of 6 in 4nv0

Go back to Fluorine Binding Sites List in 4nv0
Fluorine binding site 3 out of 6 in the Crystal Structure of Cytosolic 5'-Nucleotidase Iiib (Cn-Iiib) Bound to 7-Methylguanosine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Cytosolic 5'-Nucleotidase Iiib (Cn-Iiib) Bound to 7-Methylguanosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:11.9
occ:1.00
 F3 A:MGF404 0.0 11.9 1.0
MG A:MG402 1.9 12.9 1.0
MG A:MGF404 1.9 22.3 1.0
OD2 A:ASP55 2.9 12.9 1.0
O A:HOH627 2.9 12.8 1.0
O A:ASP57 2.9 9.8 1.0
O A:HOH626 3.0 15.1 1.0
OD1 A:ASP55 3.0 11.6 1.0
F1 A:MGF404 3.2 17.7 1.0
O A:HOH540 3.2 23.0 1.0
CB A:ASP57 3.2 9.4 1.0
CG A:ASP55 3.3 11.5 1.0
F2 A:MGF404 3.3 13.5 1.0
O A:HOH523 3.5 25.0 1.0
N A:ASP57 3.6 8.4 1.0
CA A:ASP57 3.7 10.5 1.0
O A:HOH605 3.7 29.5 1.0
C A:ASP57 3.7 11.1 1.0
OD1 A:ASP245 4.0 16.2 1.0
CG A:ASP57 4.3 14.3 1.0
OD2 A:ASP57 4.3 13.1 1.0
C5' A:MG7403 4.3 23.5 0.6
O5' A:MG7403 4.3 23.9 0.4
O A:HOH776 4.6 37.8 1.0
O5' A:MG7403 4.6 22.7 0.6
C A:PHE56 4.6 8.4 1.0
C5' A:MG7403 4.7 21.9 0.4
CB A:ASP55 4.8 8.8 1.0
N A:PHE56 4.8 10.2 1.0
CG A:ASP245 5.0 15.9 1.0
N A:TYR58 5.0 9.7 1.0

Fluorine binding site 4 out of 6 in 4nv0

Go back to Fluorine Binding Sites List in 4nv0
Fluorine binding site 4 out of 6 in the Crystal Structure of Cytosolic 5'-Nucleotidase Iiib (Cn-Iiib) Bound to 7-Methylguanosine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Cytosolic 5'-Nucleotidase Iiib (Cn-Iiib) Bound to 7-Methylguanosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:10.8
occ:1.00
 F1 B:MGF403 0.0 10.8 1.0
MG B:MGF403 1.9 11.6 1.0
MG B:MG401 1.9 11.3 1.0
O B:HOH645 2.8 10.8 1.0
OD2 B:ASP55 2.8 9.4 1.0
O B:HOH644 2.9 10.3 1.0
OD1 B:ASP55 3.0 10.5 1.0
O B:ASP57 3.0 10.6 1.0
O B:HOH502 3.0 11.3 1.0
F3 B:MGF403 3.3 10.4 1.0
CB B:ASP57 3.3 10.2 1.0
CG B:ASP55 3.3 10.5 1.0
F2 B:MGF403 3.3 11.5 1.0
O B:HOH506 3.4 15.9 1.0
N B:ASP57 3.7 9.2 1.0
CA B:ASP57 3.7 8.6 1.0
C5' B:MG7402 3.7 13.8 1.0
C B:ASP57 3.7 8.8 1.0
O5' B:MG7402 3.9 15.2 1.0
OD1 B:ASP245 4.1 13.7 1.0
O B:HOH574 4.1 22.7 1.0
O B:HOH521 4.3 16.0 1.0
OD2 B:ASP57 4.3 13.0 1.0
CG B:ASP57 4.3 12.1 1.0
C B:PHE56 4.7 9.6 1.0
CB B:ASP55 4.8 7.7 1.0
N B:PHE56 4.9 8.3 1.0
NZ B:LYS219 5.0 10.0 1.0

Fluorine binding site 5 out of 6 in 4nv0

Go back to Fluorine Binding Sites List in 4nv0
Fluorine binding site 5 out of 6 in the Crystal Structure of Cytosolic 5'-Nucleotidase Iiib (Cn-Iiib) Bound to 7-Methylguanosine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Cytosolic 5'-Nucleotidase Iiib (Cn-Iiib) Bound to 7-Methylguanosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:11.5
occ:1.00
 F2 B:MGF403 0.0 11.5 1.0
MG B:MGF403 1.9 11.6 1.0
O B:HOH506 2.6 15.9 1.0
NZ B:LYS219 2.7 10.0 1.0
N B:ALA172 2.7 9.6 1.0
OD1 B:ASP55 2.8 10.5 1.0
O B:HOH502 3.0 11.3 1.0
F1 B:MGF403 3.3 10.8 1.0
F3 B:MGF403 3.3 10.4 1.0
CB B:ALA172 3.4 11.9 1.0
CE B:LYS219 3.5 15.5 1.0
CD B:LYS219 3.6 15.7 1.0
CA B:SER171 3.6 9.3 1.0
CA B:ALA172 3.6 8.5 1.0
C B:SER171 3.6 11.3 1.0
CG B:ASP55 4.0 10.5 1.0
OG B:SER171 4.2 10.7 1.0
O B:HOH645 4.2 10.8 1.0
O B:PHE170 4.3 10.0 1.0
O5' B:MG7402 4.4 15.2 1.0
OD1 B:ASP249 4.4 13.4 1.0
C B:ALA172 4.4 10.6 1.0
CB B:SER171 4.4 12.2 1.0
N B:GLY173 4.4 11.6 1.0
O B:HOH521 4.5 16.0 1.0
OD2 B:ASP55 4.6 9.4 1.0
O B:HOH503 4.6 13.9 1.0
N B:SER171 4.7 7.9 1.0
MG B:MG401 4.7 11.3 1.0
O B:SER171 4.8 10.9 1.0
CG B:LYS219 4.9 11.2 1.0
C B:PHE170 4.9 6.7 1.0

Fluorine binding site 6 out of 6 in 4nv0

Go back to Fluorine Binding Sites List in 4nv0
Fluorine binding site 6 out of 6 in the Crystal Structure of Cytosolic 5'-Nucleotidase Iiib (Cn-Iiib) Bound to 7-Methylguanosine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Cytosolic 5'-Nucleotidase Iiib (Cn-Iiib) Bound to 7-Methylguanosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:10.4
occ:1.00
 F3 B:MGF403 0.0 10.4 1.0
MG B:MGF403 1.9 11.6 1.0
OG B:SER171 2.6 10.7 1.0
N B:ASP57 2.7 9.2 1.0
O B:HOH502 2.8 11.3 1.0
N B:PHE56 2.9 8.3 1.0
OD1 B:ASP55 2.9 10.5 1.0
CB B:SER171 3.1 12.2 1.0
CB B:PHE56 3.2 8.8 1.0
F1 B:MGF403 3.3 10.8 1.0
CA B:PHE56 3.3 10.2 1.0
F2 B:MGF403 3.3 11.5 1.0
C B:PHE56 3.4 9.6 1.0
OD2 B:ASP57 3.5 13.0 1.0
CG B:ASP55 3.6 10.5 1.0
CA B:SER171 3.6 9.3 1.0
CB B:ASP57 3.7 10.2 1.0
CA B:ASP57 3.8 8.6 1.0
CG B:ASP57 3.9 12.1 1.0
OD2 B:ASP55 3.9 9.4 1.0
C B:ASP55 4.1 9.1 1.0
N B:ALA172 4.3 9.6 1.0
CG B:PHE56 4.3 7.5 1.0
C B:SER171 4.4 11.3 1.0
CD2 B:PHE56 4.4 11.8 1.0
CA B:ASP55 4.5 7.3 1.0
MG B:MG401 4.5 11.3 1.0
N B:GLY173 4.6 11.6 1.0
O B:PHE56 4.6 9.3 1.0
CB B:ASP55 4.6 7.7 1.0
O B:PHE170 4.6 10.0 1.0
O B:ASP57 4.7 10.6 1.0
C B:ASP57 4.7 8.8 1.0
NZ B:LYS219 4.8 10.0 1.0
N B:SER171 4.8 7.9 1.0
OD1 B:ASP57 4.9 11.6 1.0

Reference:

T.Monecke, J.Buschmann, P.Neumann, E.Wahle, R.Ficner. Crystal Structures of the Novel Cytosolic 5'-Nucleotidase Iiib Explain Its Preference For M7GMP Plos One V. 9 90915 2014.
ISSN: ESSN 1932-6203
PubMed: 24603684
DOI: 10.1371/JOURNAL.PONE.0090915
Page generated: Thu Aug 1 04:23:34 2024

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