Sodium in PDB 5imd: Xanthomonas Campestris Peroxiredoxin Q - Structure F4

The structure of Xanthomonas Campestris Peroxiredoxin Q - Structure F4, PDB code: 5imd 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)	21.15 / 1.16
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.660, 51.510, 40.060, 90.00, 104.03, 90.00
R / Rfree (%)	14.4 / 17.2

The binding sites of Sodium atom in the Xanthomonas Campestris Peroxiredoxin Q - Structure F4 (pdb code 5imd). 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 F4, PDB code: 5imd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Xanthomonas Campestris Peroxiredoxin Q - Structure F4


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 F4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:17.6 occ:1.00 O A:HOH441 2.7 13.6 1.0 HD23 A:LEU128 2.9 7.3 0.5 O A:HIS33 2.9 7.6 1.0 O A:SER129 2.9 7.4 1.0 O A:HIS30 3.3 8.7 1.0 HB3 A:HIS30 3.3 9.7 1.0 HG A:LEU128 3.4 7.4 0.5 HA A:PRO130 3.4 10.5 1.0 HB3 A:LEU128 3.6 11.3 0.5 HB3 A:LEU35 3.6 9.5 1.0 CD2 A:LEU128 3.6 6.1 0.5 HB2 A:HIS30 3.7 9.7 1.0 HB2 A:LEU35 3.7 9.5 1.0 HD21 A:LEU128 3.8 7.3 0.5 C A:HIS30 3.8 8.0 1.0 C A:SER129 3.8 7.2 1.0 HB3 A:LEU128 3.9 8.6 0.5 HA A:ALA31 3.9 10.6 1.0 O A:LEU128 3.9 6.4 0.5 CB A:HIS30 3.9 8.1 1.0 CG A:LEU128 4.0 6.2 0.5 H A:GLY132 4.0 11.8 1.0 HA2 A:GLY132 4.0 11.5 1.0 C A:HIS33 4.1 7.6 1.0 H A:HIS33 4.1 10.7 1.0 CA A:PRO130 4.1 8.8 1.0 CB A:LEU35 4.1 8.0 1.0 O A:LEU128 4.2 7.2 0.5 HA A:TRP34 4.3 8.4 1.0 H A:LEU35 4.3 7.6 1.0 O A:HOH436 4.3 8.2 0.3 N A:PRO130 4.4 8.0 1.0 C A:LEU128 4.4 6.7 0.5 CB A:LEU128 4.4 9.4 0.5 HB2 A:LEU128 4.4 11.3 0.5 N A:ALA31 4.4 7.8 1.0 CB A:LEU128 4.4 7.2 0.5 C A:PRO130 4.4 9.4 1.0 HD22 A:LEU128 4.4 7.3 0.5 N A:LEU35 4.4 6.3 1.0 C A:LEU128 4.5 7.2 0.5 O A:PRO130 4.5 9.7 1.0 CA A:HIS30 4.5 7.4 1.0 CA A:ALA31 4.6 8.8 1.0 HD22 A:LEU35 4.6 13.0 1.0 HD23 A:LEU35 4.6 13.0 1.0 N A:GLY132 4.6 9.8 1.0 HD23 A:LEU128 4.6 12.2 0.5 C A:TRP34 4.7 7.3 1.0 H A:GLY32 4.7 9.9 1.0 O A:LEU27 4.7 6.7 1.0 CA A:GLY132 4.8 9.6 1.0 N A:HIS33 4.8 8.9 1.0 CA A:TRP34 4.8 7.0 1.0 N A:SER129 4.8 7.0 1.0 CA A:SER129 4.9 7.5 1.0 N A:TRP34 4.9 7.2 1.0 CD2 A:LEU35 5.0 10.8 1.0 CA A:LEU35 5.0 6.1 1.0 H A:ALA31 5.0 9.4 1.0

Sodium binding site 2 out of 2 in the Xanthomonas Campestris Peroxiredoxin Q - Structure F4


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 F4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:9.6 occ:1.00 HG A:SER44 2.3 14.8 1.0 HD1 A:PHE83 2.7 8.7 1.0 OG A:SER44 3.0 12.3 1.0 HA A:PHE83 3.1 7.1 1.0 HB3 A:LYS86 3.1 10.7 1.0 HG2 A:LYS86 3.2 14.9 1.0 O A:HOH303 3.2 20.4 0.6 HB3 A:SER44 3.3 12.3 1.0 OE1 A:GLN87 3.3 8.7 1.0 CD1 A:PHE83 3.5 7.2 1.0 HG2 A:GLN87 3.6 7.2 1.0 HA A:SER44 3.6 10.3 1.0 CB A:SER44 3.6 10.3 1.0 CG A:LYS86 3.8 12.4 1.0 CB A:LYS86 3.8 8.9 1.0 HG3 A:LYS86 3.9 14.9 1.0 HE1 A:PHE83 4.0 8.9 1.0 CA A:PHE83 4.0 5.9 1.0 HB2 A:LYS86 4.1 10.7 1.0 CA A:SER44 4.2 8.6 1.0 CD A:GLN87 4.2 6.8 1.0 HD21 A:ASN82 4.2 13.1 0.4 CE1 A:PHE83 4.2 7.5 1.0 CG A:GLN87 4.3 6.0 1.0 HD22 A:ASN82 4.4 13.1 0.4 CG A:PHE83 4.4 6.2 1.0 HB2 A:SER44 4.5 12.3 1.0 O A:PHE83 4.5 6.7 1.0 HG3 A:GLN87 4.5 7.2 1.0 O A:HOH366 4.5 28.7 1.0 ND2 A:ASN82 4.5 10.9 0.4 CB A:PHE83 4.6 5.9 1.0 HB2 A:PHE83 4.6 7.1 1.0 O A:ASN82 4.7 7.2 0.6 C A:PHE83 4.8 6.2 1.0 O A:ASN82 4.8 7.2 0.4 N A:PHE83 4.8 6.4 1.0 O A:HOH435 4.9 18.8 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