Sodium in PDB 5imf: Xanthomonas Campestris Peroxiredoxin Q - Structure F5

The structure of Xanthomonas Campestris Peroxiredoxin Q - Structure F5, PDB code: 5imf 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)	23.15 / 1.04
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.590, 51.490, 40.020, 90.00, 104.07, 90.00
R / Rfree (%)	13.8 / 16

The binding sites of Sodium atom in the Xanthomonas Campestris Peroxiredoxin Q - Structure F5 (pdb code 5imf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Xanthomonas Campestris Peroxiredoxin Q - Structure F5, PDB code: 5imf:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Xanthomonas Campestris Peroxiredoxin Q - Structure F5


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 F5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:17.5 occ:1.00 O A:HOH444 2.8 14.5 1.0 HD23 A:LEU128 2.8 7.7 0.5 O A:HIS33 2.9 8.3 1.0 O A:SER129 2.9 7.2 1.0 O A:HIS30 3.3 9.6 1.0 HB3 A:HIS30 3.4 11.5 1.0 HA A:PRO130 3.4 10.7 1.0 HG A:LEU128 3.5 7.9 0.5 HB3 A:LEU128 3.6 11.5 0.5 HB3 A:LEU35 3.6 10.8 1.0 CD2 A:LEU128 3.6 6.4 0.5 HB2 A:LEU35 3.6 10.8 1.0 HB2 A:HIS30 3.7 11.5 1.0 HD21 A:LEU128 3.8 7.7 0.5 HB3 A:LEU128 3.8 8.7 0.5 C A:SER129 3.8 7.5 1.0 O A:LEU128 3.8 6.5 0.5 C A:HIS30 3.8 9.4 1.0 HA A:ALA31 3.9 11.5 1.0 CG A:LEU128 4.0 6.6 0.5 CB A:HIS30 4.0 9.6 1.0 H A:GLY132 4.0 12.3 1.0 HA2 A:GLY132 4.0 12.4 1.0 CB A:LEU35 4.1 9.0 1.0 C A:HIS33 4.1 8.2 1.0 H A:HIS33 4.1 11.2 1.0 CA A:PRO130 4.1 8.9 1.0 O A:HOH421 4.2 9.7 0.3 HA A:TRP34 4.3 9.1 1.0 H A:LEU35 4.3 8.3 1.0 O A:LEU128 4.3 7.5 0.5 HB2 A:LEU128 4.3 11.5 0.5 C A:LEU128 4.3 7.0 0.5 CB A:LEU128 4.4 9.6 0.5 CB A:LEU128 4.4 7.3 0.5 N A:PRO130 4.4 8.3 1.0 C A:PRO130 4.4 9.7 1.0 N A:LEU35 4.4 6.9 1.0 N A:ALA31 4.4 9.4 1.0 HD22 A:LEU128 4.4 7.7 0.5 O A:PRO130 4.5 10.3 1.0 HD22 A:LEU35 4.5 14.0 1.0 C A:LEU128 4.5 7.7 0.5 HD23 A:LEU35 4.6 14.0 1.0 CA A:ALA31 4.6 9.6 1.0 CA A:HIS30 4.6 8.8 1.0 N A:GLY132 4.6 10.3 1.0 C A:TRP34 4.6 7.0 1.0 H A:GLY32 4.7 10.9 1.0 HD23 A:LEU128 4.7 13.1 0.5 O A:LEU27 4.7 7.0 1.0 CA A:GLY132 4.8 10.3 1.0 CA A:TRP34 4.8 7.6 1.0 N A:SER129 4.8 7.6 1.0 N A:HIS33 4.8 9.3 1.0 CD2 A:LEU35 4.9 11.7 1.0 CA A:SER129 4.9 7.5 1.0 N A:TRP34 4.9 8.0 1.0 CA A:LEU35 4.9 7.1 1.0

Sodium binding site 2 out of 3 in the Xanthomonas Campestris Peroxiredoxin Q - Structure F5


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 F5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:10.3 occ:1.00 HG A:SER44 2.3 14.9 1.0 HD1 A:PHE83 2.7 8.8 1.0 OG A:SER44 3.0 12.4 1.0 HA A:PHE83 3.1 7.9 1.0 O A:HOH305 3.1 26.4 0.7 HB3 A:LYS86 3.2 11.4 1.0 HB3 A:SER44 3.2 12.2 1.0 HG2 A:LYS86 3.2 16.1 1.0 OE1 A:GLN87 3.3 9.4 1.0 CD1 A:PHE83 3.5 7.3 1.0 CB A:SER44 3.6 10.2 1.0 HG2 A:GLN87 3.6 7.8 1.0 HA A:SER44 3.6 10.9 1.0 CG A:LYS86 3.9 13.4 1.0 CB A:LYS86 3.9 9.5 1.0 HG3 A:LYS86 4.0 16.1 1.0 CA A:PHE83 4.1 6.6 1.0 HE1 A:PHE83 4.1 8.8 1.0 HB2 A:LYS86 4.1 11.4 1.0 HD21 A:ASN82 4.1 14.9 0.3 CA A:SER44 4.1 9.1 1.0 CD A:GLN87 4.2 6.9 1.0 CE1 A:PHE83 4.3 7.3 1.0 CG A:GLN87 4.3 6.5 1.0 HB2 A:SER44 4.4 12.2 1.0 HG3 A:GLN87 4.4 7.8 1.0 HD22 A:ASN82 4.5 14.9 0.3 CG A:PHE83 4.5 6.5 1.0 ND2 A:ASN82 4.5 12.4 0.3 O A:PHE83 4.5 6.7 1.0 O A:HOH361 4.6 29.2 1.0 HB2 A:PHE83 4.6 7.9 1.0 CB A:PHE83 4.6 6.6 1.0 O A:ASN82 4.7 7.8 0.7 O A:HOH438 4.8 21.0 1.0 C A:PHE83 4.8 6.4 1.0 O A:ASN82 4.9 6.8 0.3 N A:PHE83 4.9 6.7 1.0 H A:SER44 5.0 9.3 1.0 N A:SER44 5.0 7.8 1.0

Sodium binding site 3 out of 3 in the Xanthomonas Campestris Peroxiredoxin Q - Structure F5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Xanthomonas Campestris Peroxiredoxin Q - Structure F5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:30.1 occ:0.60 O A:HOH522 1.8 19.4 1.0 O A:ALA137 2.3 6.7 1.0 O A:HOH424 2.4 11.6 1.0 O A:HOH393 2.6 26.1 1.0 O A:HOH466 2.6 9.5 1.0 H A:ALA137 3.3 7.7 1.0 C A:ALA137 3.6 6.1 1.0 HG3 A:GLN136 3.6 9.8 1.0 O A:HOH566 3.8 23.6 1.0 HE21 A:GLN136 3.9 11.7 1.0 N A:ALA137 4.1 6.4 1.0 HA A:TRP138 4.1 7.3 1.0 HB3 A:ALA137 4.1 8.7 1.0 HG2 A:GLN136 4.2 9.8 1.0 CA A:ALA137 4.3 6.2 1.0 CG A:GLN136 4.4 8.1 1.0 O A:HOH489 4.5 19.8 1.0 O A:HOH440 4.5 14.8 1.0 N A:TRP138 4.6 6.0 1.0 NE2 A:GLN136 4.6 9.8 1.0 CB A:ALA137 4.8 7.2 1.0 CA A:TRP138 4.8 6.1 1.0 HA A:GLN136 4.8 7.8 1.0 O A:HOH433 4.9 26.7 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