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Sodium in PDB 3t8j: Structural Analysis of Thermostable S. Solfataricus Pyrimidine- Specific Nucleoside Hydrolase

Enzymatic activity of Structural Analysis of Thermostable S. Solfataricus Pyrimidine- Specific Nucleoside Hydrolase

All present enzymatic activity of Structural Analysis of Thermostable S. Solfataricus Pyrimidine- Specific Nucleoside Hydrolase:
3.2.2.1;

Protein crystallography data

The structure of Structural Analysis of Thermostable S. Solfataricus Pyrimidine- Specific Nucleoside Hydrolase, PDB code: 3t8j was solved by C.Minici, G.Cacciapuoti, E.De Leo, M.Porcelli, M.Degano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.00 / 1.60
Space group P 64 2 2
Cell size a, b, c (Å), α, β, γ (°) 194.940, 194.940, 42.860, 90.00, 90.00, 120.00
R / Rfree (%) 15.6 / 17

Sodium Binding Sites:

The binding sites of Sodium atom in the Structural Analysis of Thermostable S. Solfataricus Pyrimidine- Specific Nucleoside Hydrolase (pdb code 3t8j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structural Analysis of Thermostable S. Solfataricus Pyrimidine- Specific Nucleoside Hydrolase, PDB code: 3t8j:

Sodium binding site 1 out of 1 in 3t8j

Go back to Sodium Binding Sites List in 3t8j
Sodium binding site 1 out of 1 in the Structural Analysis of Thermostable S. Solfataricus Pyrimidine- Specific Nucleoside Hydrolase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural Analysis of Thermostable S. Solfataricus Pyrimidine- Specific Nucleoside Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:24.4
occ:1.00
 O A:ILE121 2.3 20.4 1.0
OD2 A:ASP9 2.3 22.1 1.0
OD1 A:ASP14 2.3 25.2 1.0
O A:HOH468 2.4 21.7 1.0
OG A:SER122 2.5 20.6 1.0
C A:ILE121 3.1 19.5 1.0
CG A:ASP14 3.2 24.1 1.0
OD2 A:ASP14 3.4 23.6 1.0
CB A:SER122 3.4 19.9 1.0
CG A:ASP9 3.5 20.7 1.0
CA A:SER122 3.5 18.5 1.0
N A:SER122 3.6 18.3 1.0
O A:HOH325 3.7 17.1 1.0
N A:ASP9 3.8 20.3 1.0
OD2 A:ASP238 3.8 29.8 1.0
CG1 A:ILE121 4.0 20.0 1.0
CB A:ILE121 4.1 20.2 1.0
CA A:ILE121 4.2 19.3 1.0
OD1 A:ASP9 4.3 20.2 1.0
O A:HOH370 4.3 20.4 1.0
CG A:ASP238 4.3 24.1 1.0
CD1 A:ILE121 4.3 23.6 1.0
OD1 A:ASP238 4.4 23.2 1.0
CA A:CYS8 4.5 20.5 1.0
O A:ASP9 4.5 22.4 1.0
O A:ASP7 4.5 21.0 1.0
ND2 A:ASN37 4.5 25.4 1.0
CA A:ASP9 4.5 20.6 1.0
CB A:ASP9 4.6 19.4 1.0
CB A:ASP14 4.6 21.4 1.0
C A:CYS8 4.6 20.3 1.0
C A:ASP9 4.7 21.6 1.0
OD1 A:ASN164 4.8 19.5 1.0
ND2 A:ASN164 4.9 19.3 1.0

Reference:

C.Minici, G.Cacciapuoti, E.De Leo, M.Porcelli, M.Degano. New Determinants in the Catalytic Mechanism of Nucleoside Hydrolases From the Structures of Two Isozymes From Sulfolobus Solfataricus. Biochemistry V. 51 4590 2012.
ISSN: ISSN 0006-2960
PubMed: 22551416
DOI: 10.1021/BI300209G
Page generated: Mon Oct 7 13:13:49 2024

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