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Sodium in PDB 8vlj: Crystal Structure of the Cacodylate-Bound Yeast Cytosine Deaminase (Closed Form)

Enzymatic activity of Crystal Structure of the Cacodylate-Bound Yeast Cytosine Deaminase (Closed Form)

All present enzymatic activity of Crystal Structure of the Cacodylate-Bound Yeast Cytosine Deaminase (Closed Form):
3.5.4.1;

Protein crystallography data

The structure of Crystal Structure of the Cacodylate-Bound Yeast Cytosine Deaminase (Closed Form), PDB code: 8vlj was solved by M.-E.Picard, J.Grenier, P.C.Despres, A.K.Dube, C.R.Landry, R.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.55 / 1.39
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.108, 55.073, 66.867, 90, 90.5, 90
R / Rfree (%) 14.2 / 16.7

Other elements in 8vlj:

The structure of Crystal Structure of the Cacodylate-Bound Yeast Cytosine Deaminase (Closed Form) also contains other interesting chemical elements:

Arsenic (As) 2 atoms
Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Cacodylate-Bound Yeast Cytosine Deaminase (Closed Form) (pdb code 8vlj). 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 Crystal Structure of the Cacodylate-Bound Yeast Cytosine Deaminase (Closed Form), PDB code: 8vlj:

Sodium binding site 1 out of 1 in 8vlj

Go back to Sodium Binding Sites List in 8vlj
Sodium binding site 1 out of 1 in the Crystal Structure of the Cacodylate-Bound Yeast Cytosine Deaminase (Closed Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Cacodylate-Bound Yeast Cytosine Deaminase (Closed Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na203

b:16.4
occ:1.00
 O B:LYS115 2.3 11.9 1.0
O B:HOH431 2.4 13.2 1.0
O B:HOH445 2.4 30.0 1.0
O B:HOH458 2.6 24.1 1.0
C B:LYS115 3.5 8.7 1.0
N B:LYS115 3.9 7.6 1.0
O B:HOH442 4.0 27.7 1.0
CA B:LYS115 4.1 8.6 1.0
CB B:LYS115 4.2 10.7 1.0
O B:HOH444 4.3 27.4 1.0
N B:SER116 4.5 6.6 1.0
CA B:SER116 4.8 7.1 1.0
O B:HOH322 5.0 22.1 1.0

Reference:

P.C.Despres, A.K.Dube, M.-E.Picard, J.Grenier, R.Shi, C.R.Landry. Compensatory Mutations Potentiate Constructive Neutral Evolution By Gene Duplication Science 2024.
ISSN: ESSN 1095-9203
DOI: 10.1126/SCIENCE.ADO5719
Page generated: Wed Oct 9 14:03:28 2024

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