Sodium in PDB 5io0: Xanthomonas Campestris Peroxiredoxin Q - Structure F9

The structure of Xanthomonas Campestris Peroxiredoxin Q - Structure F9, PDB code: 5io0 was solved by A.Perkins, D.Parsonage, K.J.Nelson, L.B.Poole, A.Karplus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.62 / 1.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.350, 51.240, 39.950, 90.00, 103.12, 90.00
R / Rfree (%)	13.5 / 17.2

The binding sites of Sodium atom in the Xanthomonas Campestris Peroxiredoxin Q - Structure F9 (pdb code 5io0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Xanthomonas Campestris Peroxiredoxin Q - Structure F9, PDB code: 5io0:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Xanthomonas Campestris Peroxiredoxin Q - Structure F9


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Xanthomonas Campestris Peroxiredoxin Q - Structure F9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:20.4 occ:1.00 O A:HOH440 2.3 44.6 1.0 O A:HOH351 2.3 22.9 1.0 OG A:SER18 2.4 16.3 1.0 O A:HOH445 2.4 37.2 1.0 O A:HOH447 2.5 31.0 1.0 O A:HOH355 2.5 13.9 1.0 HB2 A:SER18 3.2 16.5 1.0 H A:SER18 3.4 13.0 1.0 CB A:SER18 3.4 13.8 1.0 O A:HOH455 3.9 38.6 1.0 N A:SER18 4.0 10.9 1.0 HB3 A:SER18 4.0 16.5 1.0 O A:SER95 4.1 12.0 1.0 CA A:SER18 4.3 11.4 1.0 O A:HOH320 4.4 15.2 1.0 O A:HOH307 4.4 28.2 1.0 O A:PRO16 4.4 14.9 1.0 O A:HOH501 4.4 53.2 1.0 H A:GLY97 4.7 13.1 1.0 O A:HOH324 4.7 29.8 1.0 HA A:LEU17 4.7 11.8 1.0 HA A:SER18 4.8 13.7 1.0

Sodium binding site 2 out of 2 in the Xanthomonas Campestris Peroxiredoxin Q - Structure F9


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Xanthomonas Campestris Peroxiredoxin Q - Structure F9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:22.7 occ:1.00 HD23 A:LEU128 2.8 17.6 0.6 O A:HOH413 2.8 20.5 1.0 O A:SER129 2.9 11.4 1.0 O A:HIS33 2.9 11.3 1.0 O A:HIS30 3.2 14.0 1.0 HA A:PRO130 3.4 15.6 1.0 HB3 A:HIS30 3.4 16.9 1.0 HG A:LEU128 3.5 16.8 0.6 HB2 A:LEU35 3.5 15.1 1.0 CD2 A:LEU128 3.5 14.6 0.6 HB3 A:LEU35 3.6 15.1 1.0 HB3 A:LEU128 3.7 11.1 0.5 HD21 A:LEU128 3.7 17.6 0.6 C A:HIS30 3.8 13.1 1.0 HB2 A:HIS30 3.8 16.9 1.0 HA A:ALA31 3.8 17.7 1.0 C A:SER129 3.8 10.9 1.0 H A:GLY132 3.9 17.4 1.0 HB3 A:LEU128 3.9 16.0 0.6 CG A:LEU128 4.0 14.0 0.6 HA2 A:GLY132 4.0 19.2 1.0 O A:LEU128 4.0 10.5 0.6 CB A:HIS30 4.0 14.1 1.0 CB A:LEU35 4.0 12.6 1.0 H A:HIS33 4.1 16.1 1.0 CA A:PRO130 4.1 13.0 1.0 C A:HIS33 4.1 11.3 1.0 H A:LEU35 4.3 11.7 1.0 HA A:TRP34 4.3 12.1 1.0 HB2 A:LEU128 4.3 11.1 0.5 HD22 A:LEU128 4.3 17.6 0.6 N A:ALA31 4.3 14.0 1.0 C A:PRO130 4.4 13.9 1.0 HD22 A:LEU35 4.4 18.0 1.0 N A:PRO130 4.4 12.1 1.0 N A:LEU35 4.4 9.8 1.0 CB A:LEU128 4.4 13.3 0.6 CB A:LEU128 4.4 9.3 0.5 C A:LEU128 4.4 10.9 0.6 O A:PRO130 4.5 14.6 1.0 N A:GLY132 4.5 14.5 1.0 CA A:ALA31 4.5 14.8 1.0 O A:LEU128 4.5 10.1 0.5 H A:GLY32 4.5 17.1 1.0 CA A:HIS30 4.5 13.9 1.0 HD23 A:LEU35 4.5 18.0 1.0 C A:LEU128 4.7 9.7 0.5 C A:TRP34 4.7 10.1 1.0 CA A:GLY132 4.7 16.0 1.0 HD23 A:LEU128 4.7 12.2 0.5 O A:LEU27 4.8 13.6 1.0 N A:HIS33 4.8 13.4 1.0 CD2 A:LEU35 4.8 15.0 1.0 CA A:TRP34 4.8 10.1 1.0 N A:SER129 4.9 9.9 1.0 CA A:LEU35 4.9 9.6 1.0 HD2 A:HIS33 4.9 18.2 1.0 N A:GLY32 4.9 14.2 1.0 N A:TRP34 4.9 11.3 1.0 H A:ALA31 5.0 16.8 1.0 CA A:SER129 5.0 10.2 1.0

A.Perkins, D.Parsonage, K.J.Nelson, O.M.Ogba, P.H.Cheong, L.B.Poole, P.A.Karplus. Peroxiredoxin Catalysis at Atomic Resolution. Structure V. 24 1668 2016.
ISSN: ISSN 0969-2126
PubMed: 27594682
DOI: 10.1016/J.STR.2016.07.012