Atomistry » Fluorine » PDB 4ncj-4o16 » 4nv0
Atomistry »
  Fluorine »
    PDB 4ncj-4o16 »
      4nv0 »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy