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Magnesium in PDB 2g08: X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Product- Transition Complex Analog with Aluminum Fluoride

Enzymatic activity of X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Product- Transition Complex Analog with Aluminum Fluoride

All present enzymatic activity of X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Product- Transition Complex Analog with Aluminum Fluoride:
3.1.1.5;

Protein crystallography data

The structure of X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Product- Transition Complex Analog with Aluminum Fluoride, PDB code: 2g08 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) 67.52 / 2.35
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 135.044, 135.044, 39.049, 90.00, 90.00, 120.00
R / Rfree (%) 19 / 26

Other elements in 2g08:

The structure of X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Product- Transition Complex Analog with Aluminum Fluoride also contains other interesting chemical elements:

Fluorine (F) 6 atoms
Aluminium (Al) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Product- Transition Complex Analog with Aluminum Fluoride (pdb code 2g08). 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, Product- Transition Complex Analog with Aluminum Fluoride, PDB code: 2g08:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2g08

Go back to Magnesium Binding Sites List in 2g08
Magnesium binding site 1 out of 2 in the X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Product- Transition Complex Analog with Aluminum 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, Product- Transition Complex Analog with Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg500

b:35.1
occ:1.00
 O A:HOH503 2.0 25.6 1.0
F2 A:AF3501 2.0 35.8 1.0
OD1 A:ASP238 2.0 40.1 1.0
O A:ASP51 2.0 41.6 1.0
OD2 A:ASP49 2.1 39.9 1.0
O A:HOH619 2.2 24.2 1.0
CG A:ASP238 3.0 40.2 1.0
CG A:ASP49 3.0 39.1 1.0
C A:ASP51 3.2 41.2 1.0
OD1 A:ASP49 3.4 38.4 1.0
OD2 A:ASP238 3.4 38.5 1.0
AL A:AF3501 3.4 35.7 1.0
CA A:ASP51 3.9 40.9 1.0
O A:HOH664 3.9 24.8 1.0
CB A:ASP51 3.9 40.8 1.0
N A:ASP51 3.9 39.5 1.0
OG1 A:THR53 4.0 46.2 1.0
O A:HOH507 4.0 42.8 1.0
OD2 A:ASP242 4.2 39.8 1.0
CB A:MSE52 4.2 42.4 1.0
O A:HOH502 4.2 32.1 1.0
N A:MSE52 4.3 41.7 1.0
F1 A:AF3501 4.3 32.3 1.0
CB A:ASP49 4.3 37.4 1.0
CB A:ASP238 4.4 41.0 1.0
O A:HOH716 4.4 42.7 1.0
F3 A:AF3501 4.5 35.4 1.0
N A:THR53 4.5 41.8 1.0
CG A:MSE52 4.5 43.0 1.0
C A:PHE50 4.5 39.5 1.0
CA A:MSE52 4.6 42.1 1.0
C A:MSE52 4.6 41.8 1.0
N A:ASP238 4.7 41.2 1.0
CB A:THR53 4.8 42.1 1.0
O A:PHE50 4.8 40.4 1.0
N A:PHE50 4.9 40.0 1.0

Magnesium binding site 2 out of 2 in 2g08

Go back to Magnesium Binding Sites List in 2g08
Magnesium binding site 2 out of 2 in the X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Product- Transition Complex Analog with Aluminum 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, Product- Transition Complex Analog with Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg600

b:34.9
occ:1.00
 F1 B:AF3601 2.0 37.9 1.0
OD1 B:ASP238 2.0 40.8 1.0
O B:ASP51 2.0 41.8 1.0
O B:HOH603 2.1 32.0 1.0
OD2 B:ASP49 2.1 41.8 1.0
O B:HOH602 2.3 23.6 1.0
CG B:ASP49 3.1 40.0 1.0
CG B:ASP238 3.1 40.4 1.0
C B:ASP51 3.2 41.2 1.0
AL B:AF3601 3.4 38.8 1.0
OD1 B:ASP49 3.4 39.9 1.0
OD2 B:ASP238 3.5 39.8 1.0
CA B:ASP51 3.8 40.8 1.0
CB B:ASP51 3.9 40.4 1.0
N B:ASP51 3.9 39.5 1.0
OG1 B:THR53 4.0 44.5 1.0
O B:HOH679 4.1 31.3 1.0
O B:HOH831 4.2 33.1 1.0
CB B:MSE52 4.2 42.8 1.0
OD2 B:ASP242 4.2 39.8 1.0
N B:MSE52 4.3 41.8 1.0
CB B:ASP49 4.4 37.7 1.0
F2 B:AF3601 4.4 34.9 1.0
CB B:ASP238 4.4 41.0 1.0
F3 B:AF3601 4.4 38.8 1.0
N B:THR53 4.4 41.9 1.0
CG B:MSE52 4.5 43.2 1.0
C B:PHE50 4.5 39.5 1.0
CA B:MSE52 4.6 42.2 1.0
O B:HOH721 4.6 41.7 1.0
C B:MSE52 4.6 41.8 1.0
N B:ASP238 4.7 41.1 1.0
CB B:THR53 4.8 42.1 1.0
O B:PHE50 4.8 40.3 1.0
N B:PHE50 4.9 39.8 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: Tue Aug 13 23:20:34 2024

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