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Magnesium in PDB 3onn: Crystal Structure of 5'-Nucleotidase SDT1 From Saccharomyces Cerevisiae

Protein crystallography data

The structure of Crystal Structure of 5'-Nucleotidase SDT1 From Saccharomyces Cerevisiae, PDB code: 3onn was solved by M.K.Teng, L.W.Niu, N.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.77 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.720, 77.550, 82.160, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 25

Other elements in 3onn:

The structure of Crystal Structure of 5'-Nucleotidase SDT1 From Saccharomyces Cerevisiae also contains other interesting chemical elements:

Iodine (I) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of 5'-Nucleotidase SDT1 From Saccharomyces Cerevisiae (pdb code 3onn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of 5'-Nucleotidase SDT1 From Saccharomyces Cerevisiae, PDB code: 3onn:

Magnesium binding site 1 out of 1 in 3onn

Go back to Magnesium Binding Sites List in 3onn
Magnesium binding site 1 out of 1 in the Crystal Structure of 5'-Nucleotidase SDT1 From Saccharomyces Cerevisiae


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 5'-Nucleotidase SDT1 From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg276

b:5.0
occ:1.00
OD1 A:ASP203 2.3 13.6 1.0
O1 A:PO4264 2.4 11.7 1.0
OD2 A:ASP36 2.4 13.6 1.0
O A:ASP38 2.5 9.2 1.0
O A:HOH453 2.5 11.7 1.0
O A:HOH452 2.6 12.8 1.0
OD1 A:ASP36 2.6 9.9 1.0
CG A:ASP36 2.8 12.3 1.0
CG A:ASP203 3.4 15.8 1.0
C A:ASP38 3.6 9.9 1.0
P A:PO4264 3.6 15.8 1.0
OD1 A:ASP202 3.9 12.1 1.0
OD2 A:ASP203 3.9 14.9 1.0
O3 A:PO4264 4.0 12.1 1.0
O A:HOH379 4.1 26.7 1.0
O4 A:PO4264 4.1 12.0 1.0
N A:ASP38 4.1 11.6 1.0
CA A:ASP38 4.2 11.9 1.0
O A:HOH378 4.2 29.5 1.0
CB A:ASP38 4.2 12.0 1.0
O A:HOH277 4.3 12.7 1.0
CB A:ASP36 4.3 11.6 1.0
N A:ASP203 4.5 11.2 1.0
CG A:ASP202 4.5 12.8 1.0
ND2 A:ASN39 4.6 20.9 1.0
CB A:ASN39 4.6 12.1 1.0
CB A:ASP203 4.7 13.2 1.0
N A:ASN39 4.7 10.2 1.0
OD2 A:ASP202 4.7 12.2 1.0
C A:ILE37 4.8 9.1 1.0
N A:ILE37 4.8 8.4 1.0
O2 A:PO4264 4.8 13.2 1.0
NZ A:LYS177 4.9 9.9 1.0
C A:ASN39 5.0 13.6 1.0
CA A:ASN39 5.0 12.0 1.0

Reference:

N.Shi, M.K.Teng, L.W.Niu. Crystal Structure of the First Pyrimidine 5'-Nucleotidase SDT1 From Saccharomyces Cerevisiae To Be Published.
Page generated: Mon Dec 14 08:36:30 2020

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