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Magnesium in PDB 2g07: X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Phospho- Enzyme Intermediate Analog with Beryllium Fluoride

Enzymatic activity of X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Phospho- Enzyme Intermediate Analog with Beryllium Fluoride

All present enzymatic activity of X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Phospho- Enzyme Intermediate Analog with Beryllium Fluoride:
3.1.1.5;

Protein crystallography data

The structure of X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Phospho- Enzyme Intermediate Analog with Beryllium Fluoride, PDB code: 2g07 was solved by E.Bitto, C.A.Bingman, G.E.Wesenberg, G.N.Phillips Jr., Center Foreukaryotic Structural Genomics (Cesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 67.42 / 2.30
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 134.834, 134.834, 38.945, 90.00, 90.00, 120.00
R / Rfree (%) 18 / 25.9

Other elements in 2g07:

The structure of X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Phospho- Enzyme Intermediate Analog with Beryllium Fluoride also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Phospho- Enzyme Intermediate Analog with Beryllium Fluoride (pdb code 2g07). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Phospho- Enzyme Intermediate Analog with Beryllium Fluoride, PDB code: 2g07:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2g07

Go back to Magnesium Binding Sites List in 2g07
Magnesium binding site 1 out of 2 in the X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Phospho- Enzyme Intermediate Analog with Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Phospho- Enzyme Intermediate Analog with Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:29.0
occ:1.00
 F1 A:BFD49 2.0 37.5 1.0
O A:HOH666 2.0 16.4 1.0
O A:ASP51 2.2 34.8 1.0
OD2 A:BFD49 2.2 39.5 1.0
OD1 A:ASP238 2.2 35.4 1.0
O A:HOH846 2.2 26.8 1.0
CG A:BFD49 3.0 34.8 1.0
BE A:BFD49 3.1 38.5 1.0
CG A:ASP238 3.2 35.8 1.0
C A:ASP51 3.3 35.2 1.0
OD1 A:BFD49 3.3 36.6 1.0
OD2 A:ASP238 3.5 33.6 1.0
O A:HOH676 3.8 24.9 1.0
F3 A:BFD49 3.9 38.3 1.0
CA A:ASP51 4.0 34.7 1.0
CB A:ASP51 4.0 33.2 1.0
N A:ASP51 4.0 33.5 1.0
OD2 A:ASP242 4.1 32.1 1.0
F2 A:BFD49 4.1 38.9 1.0
O A:HOH874 4.2 32.0 1.0
OG1 A:THR53 4.2 39.0 1.0
CB A:MSE52 4.3 36.5 1.0
O A:HOH742 4.3 27.0 1.0
CB A:BFD49 4.4 34.6 1.0
N A:MSE52 4.4 35.2 1.0
CB A:ASP238 4.6 35.5 1.0
CG A:MSE52 4.6 38.7 1.0
C A:PHE50 4.7 34.0 1.0
N A:THR53 4.7 35.4 1.0
CA A:MSE52 4.7 35.8 1.0
O A:HOH681 4.8 29.9 1.0
C A:MSE52 4.9 35.4 1.0
N A:ASP238 4.9 36.2 1.0
OD1 A:ASP242 4.9 36.0 1.0
CG A:ASP242 5.0 32.1 1.0

Magnesium binding site 2 out of 2 in 2g07

Go back to Magnesium Binding Sites List in 2g07
Magnesium binding site 2 out of 2 in the X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Phospho- Enzyme Intermediate Analog with Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Phospho- Enzyme Intermediate Analog with Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:33.8
occ:1.00
 O B:HOH863 1.9 28.9 1.0
F2 B:BFD49 2.0 36.9 1.0
O B:HOH669 2.1 23.8 1.0
OD2 B:BFD49 2.1 39.6 1.0
OD1 B:ASP238 2.2 39.3 1.0
O B:ASP51 2.2 35.7 1.0
CG B:BFD49 3.1 35.5 1.0
BE B:BFD49 3.1 36.1 1.0
CG B:ASP238 3.2 35.6 1.0
C B:ASP51 3.3 35.1 1.0
OD1 B:BFD49 3.5 34.3 1.0
OD2 B:ASP238 3.5 36.3 1.0
CB B:ASP51 3.9 33.7 1.0
O B:HOH674 3.9 21.4 1.0
CA B:ASP51 4.0 34.5 1.0
F1 B:BFD49 4.1 30.5 1.0
N B:ASP51 4.1 33.5 1.0
F3 B:BFD49 4.2 33.1 1.0
OD2 B:ASP242 4.2 33.3 1.0
CB B:MSE52 4.3 36.4 1.0
OG1 B:THR53 4.3 37.7 1.0
CB B:BFD49 4.4 32.7 1.0
O B:HOH735 4.4 29.9 1.0
N B:MSE52 4.4 34.8 1.0
CB B:ASP238 4.6 35.3 1.0
CG B:MSE52 4.6 36.5 1.0
CA B:MSE52 4.7 35.5 1.0
N B:THR53 4.7 35.1 1.0
C B:PHE50 4.8 34.0 1.0
O B:HOH720 4.8 40.9 1.0
C B:MSE52 4.9 35.1 1.0
N B:ASP238 4.9 36.4 1.0

Reference:

E.Bitto, C.A.Bingman, G.E.Wesenberg, J.G.Mccoy, G.N.Phillips. Structure of Pyrimidine 5'-Nucleotidase Type 1. Insight Into Mechanism of Action and Inhibition During Lead Poisoning. J.Biol.Chem. V. 281 20521 2006.
ISSN: ISSN 0021-9258
PubMed: 16672222
DOI: 10.1074/JBC.M602000200
Page generated: Mon Dec 14 07:23:49 2020

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