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Magnesium 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:

Fluorine (F) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Cytosolic 5'-Nucleotidase Iiib (Cn-Iiib) Bound to 7-Methylguanosine, PDB code: 4nv0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4nv0

Go back to Magnesium Binding Sites List in 4nv0
Magnesium binding site 1 out of 4 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 Magnesium with other atoms in the Mg 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:Mg402

b:12.9
occ:1.00
 F3 A:MGF404 1.9 11.9 1.0
OD1 A:ASP245 2.0 16.2 1.0
OD2 A:ASP55 2.1 12.9 1.0
O A:ASP57 2.1 9.8 1.0
O A:HOH627 2.1 12.8 1.0
O A:HOH626 2.2 15.1 1.0
CG A:ASP55 3.0 11.5 1.0
CG A:ASP245 3.1 15.9 1.0
C A:ASP57 3.3 11.1 1.0
OD2 A:ASP245 3.4 18.9 1.0
OD1 A:ASP55 3.4 11.6 1.0
MG A:MGF404 3.6 22.3 1.0
CA A:ASP57 4.0 10.5 1.0
CB A:ASP57 4.1 9.4 1.0
N A:ASP57 4.1 8.4 1.0
OG1 A:THR59 4.1 9.3 1.0
OD2 A:ASP249 4.2 12.1 1.0
OG A:SER246 4.2 21.3 1.0
O A:HOH605 4.3 29.5 1.0
O A:HOH523 4.3 25.0 1.0
CB A:ASP55 4.3 8.8 1.0
N A:TYR58 4.3 9.7 1.0
CB A:ASP245 4.4 12.0 1.0
CB A:TYR58 4.5 11.6 1.0
F1 A:MGF404 4.6 17.7 1.0
N A:THR59 4.6 8.1 1.0
CA A:TYR58 4.7 10.5 1.0
C A:TYR58 4.7 8.6 1.0
N A:ASP245 4.7 9.1 1.0
C A:PHE56 4.8 8.4 1.0
CD2 A:TYR58 4.8 17.4 1.0
F2 A:MGF404 4.8 13.5 1.0

Magnesium binding site 2 out of 4 in 4nv0

Go back to Magnesium Binding Sites List in 4nv0
Magnesium binding site 2 out of 4 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 Magnesium with other atoms in the Mg 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:Mg404

b:22.3
occ:1.00
 MG A:MGF404 0.0 22.3 1.0
F2 A:MGF404 1.9 13.5 1.0
F1 A:MGF404 1.9 17.7 1.0
F3 A:MGF404 1.9 11.9 1.0
OD1 A:ASP55 2.3 11.6 1.0
O A:HOH540 2.4 23.0 1.0
CG A:ASP55 3.2 11.5 1.0
O A:HOH523 3.4 25.0 1.0
OD2 A:ASP55 3.5 12.9 1.0
MG A:MG402 3.6 12.9 1.0
N A:ASP57 3.8 8.4 1.0
NZ A:LYS219 3.8 12.4 0.6
OG A:SER171 3.8 10.1 1.0
NZ A:LYS219 3.8 12.9 0.4
O A:HOH626 3.9 15.1 1.0
N A:ALA172 4.0 8.8 1.0
CB A:ASP57 4.1 9.4 1.0
N A:PHE56 4.1 10.2 1.0
OD2 A:ASP57 4.1 13.1 1.0
CA A:SER171 4.2 11.3 1.0
O5' A:MG7403 4.2 23.9 0.4
O5' A:MG7403 4.3 22.7 0.6
CB A:SER171 4.4 10.7 1.0
CA A:ASP57 4.4 10.5 1.0
O A:ASP57 4.5 9.8 1.0
CB A:ASP55 4.5 8.8 1.0
CG A:ASP57 4.6 14.3 1.0
C A:SER171 4.6 8.6 1.0
O A:HOH776 4.6 37.8 1.0
C5' A:MG7403 4.6 21.9 0.4
C5' A:MG7403 4.6 23.5 0.6
C A:PHE56 4.7 8.4 1.0
O A:HOH605 4.8 29.5 1.0
N A:GLY173 4.8 10.0 1.0
CA A:PHE56 4.8 9.7 1.0
CA A:ASP55 4.8 9.0 1.0
O A:PHE170 4.8 11.2 1.0
CE A:LYS219 4.8 14.2 0.4
O A:HOH627 4.9 12.8 1.0
C A:ASP55 4.9 10.3 1.0
CE A:LYS219 5.0 11.4 0.6
C A:ASP57 5.0 11.1 1.0

Magnesium binding site 3 out of 4 in 4nv0

Go back to Magnesium Binding Sites List in 4nv0
Magnesium binding site 3 out of 4 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 Magnesium with other atoms in the Mg 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
B:Mg401

b:11.3
occ:1.00
 F1 B:MGF403 1.9 10.8 1.0
OD2 B:ASP55 2.0 9.4 1.0
O B:ASP57 2.1 10.6 1.0
O B:HOH644 2.1 10.3 1.0
OD1 B:ASP245 2.2 13.7 1.0
O B:HOH645 2.2 10.8 1.0
CG B:ASP55 3.0 10.5 1.0
CG B:ASP245 3.2 15.4 1.0
C B:ASP57 3.2 8.8 1.0
OD1 B:ASP55 3.4 10.5 1.0
OD2 B:ASP245 3.5 14.8 1.0
MG B:MGF403 3.5 11.6 1.0
CA B:ASP57 4.0 8.6 1.0
CB B:ASP57 4.1 10.2 1.0
OD2 B:ASP249 4.1 11.9 1.0
OG1 B:THR59 4.1 8.4 1.0
N B:ASP57 4.1 9.2 1.0
OG B:SER246 4.2 13.8 1.0
O B:HOH506 4.2 15.9 1.0
CB B:ASP55 4.3 7.7 1.0
N B:TYR58 4.3 10.3 1.0
O B:HOH574 4.3 22.7 1.0
CB B:TYR58 4.4 13.1 1.0
CB B:ASP245 4.5 13.4 1.0
F3 B:MGF403 4.5 10.4 1.0
N B:THR59 4.6 8.3 1.0
CA B:TYR58 4.6 11.2 1.0
C B:TYR58 4.7 11.6 1.0
N B:ASP245 4.7 11.5 1.0
CD2 B:TYR58 4.7 15.0 1.0
F2 B:MGF403 4.7 11.5 1.0
C B:PHE56 4.8 9.6 1.0
O B:HOH502 4.9 11.3 1.0

Magnesium binding site 4 out of 4 in 4nv0

Go back to Magnesium Binding Sites List in 4nv0
Magnesium binding site 4 out of 4 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 Magnesium with other atoms in the Mg 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:Mg403

b:11.6
occ:1.00
 MG B:MGF403 0.0 11.6 1.0
F2 B:MGF403 1.9 11.5 1.0
F1 B:MGF403 1.9 10.8 1.0
F3 B:MGF403 1.9 10.4 1.0
OD1 B:ASP55 2.2 10.5 1.0
O B:HOH502 2.3 11.3 1.0
CG B:ASP55 3.1 10.5 1.0
OD2 B:ASP55 3.4 9.4 1.0
O B:HOH506 3.4 15.9 1.0
MG B:MG401 3.5 11.3 1.0
N B:ASP57 3.8 9.2 1.0
OG B:SER171 3.8 10.7 1.0
NZ B:LYS219 3.8 10.0 1.0
O B:HOH645 3.8 10.8 1.0
N B:ALA172 3.9 9.6 1.0
CB B:ASP57 4.0 10.2 1.0
N B:PHE56 4.1 8.3 1.0
OD2 B:ASP57 4.1 13.0 1.0
O5' B:MG7402 4.1 15.2 1.0
CA B:SER171 4.1 9.3 1.0
CB B:SER171 4.3 12.2 1.0
CA B:ASP57 4.4 8.6 1.0
O B:ASP57 4.4 10.6 1.0
C5' B:MG7402 4.4 13.8 1.0
CB B:ASP55 4.4 7.7 1.0
CG B:ASP57 4.5 12.1 1.0
C B:SER171 4.5 11.3 1.0
C B:PHE56 4.6 9.6 1.0
N B:GLY173 4.6 11.6 1.0
CA B:PHE56 4.8 10.2 1.0
CB B:ALA172 4.8 11.9 1.0
CA B:ALA172 4.8 8.5 1.0
CA B:ASP55 4.8 7.3 1.0
O B:HOH521 4.8 16.0 1.0
O B:HOH644 4.8 10.3 1.0
C B:ASP57 4.9 8.8 1.0
O B:PHE170 4.9 10.0 1.0
C B:ASP55 4.9 9.1 1.0
CE B:LYS219 5.0 15.5 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: Mon Aug 19 23:46:45 2024

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