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Sodium in PDB 5cvk: Structure of XOO1075, A Peptide Deformyase From Xanthomonas Oryzae Pv. Oryze, in Complex with Fragment 493

Enzymatic activity of Structure of XOO1075, A Peptide Deformyase From Xanthomonas Oryzae Pv. Oryze, in Complex with Fragment 493

All present enzymatic activity of Structure of XOO1075, A Peptide Deformyase From Xanthomonas Oryzae Pv. Oryze, in Complex with Fragment 493:
3.5.1.88;

Protein crystallography data

The structure of Structure of XOO1075, A Peptide Deformyase From Xanthomonas Oryzae Pv. Oryze, in Complex with Fragment 493, PDB code: 5cvk was solved by H.P.T.Ngo, L.W.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.95 / 2.10
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 59.002, 59.002, 264.653, 90.00, 90.00, 120.00
R / Rfree (%) 17.6 / 22.4

Other elements in 5cvk:

The structure of Structure of XOO1075, A Peptide Deformyase From Xanthomonas Oryzae Pv. Oryze, in Complex with Fragment 493 also contains other interesting chemical elements:

Cadmium (Cd) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of XOO1075, A Peptide Deformyase From Xanthomonas Oryzae Pv. Oryze, in Complex with Fragment 493 (pdb code 5cvk). 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 Structure of XOO1075, A Peptide Deformyase From Xanthomonas Oryzae Pv. Oryze, in Complex with Fragment 493, PDB code: 5cvk:

Sodium binding site 1 out of 1 in 5cvk

Go back to Sodium Binding Sites List in 5cvk
Sodium binding site 1 out of 1 in the Structure of XOO1075, A Peptide Deformyase From Xanthomonas Oryzae Pv. Oryze, in Complex with Fragment 493


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of XOO1075, A Peptide Deformyase From Xanthomonas Oryzae Pv. Oryze, in Complex with Fragment 493 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na207

b:35.7
occ:1.00
O A:HOH389 2.3 34.8 1.0
O A:LEU14 2.3 22.4 1.0
O A:HOH447 2.5 31.6 1.0
O A:HOH465 3.3 36.0 1.0
C A:LEU14 3.5 22.9 1.0
CB A:LEU14 4.1 20.0 1.0
CA A:LEU14 4.2 20.4 1.0
O A:GLY148 4.4 20.7 1.0
N A:ARG15 4.6 23.2 1.0
CA A:GLY148 4.8 19.0 1.0
O A:VAL147 4.8 21.7 1.0
CA A:ARG15 4.9 21.9 1.0

Reference:

H.P.T.Ngo, L.W.Kang. Structure of XOO1075, A Peptide Deformyase From Xanthomonas Oryzae Pv.Oryze, in Complex with Fragment 493 To Be Published.
Page generated: Mon Oct 7 20:24:59 2024

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