Sodium in PDB 5ima: Xanthomonas Campestris Peroxiredoxin Q - Structure F2

The structure of Xanthomonas Campestris Peroxiredoxin Q - Structure F2, PDB code: 5ima 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)	29.61 / 1.04
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.600, 51.295, 40.025, 90.00, 103.99, 90.00
R / Rfree (%)	11.6 / 13.5

The binding sites of Sodium atom in the Xanthomonas Campestris Peroxiredoxin Q - Structure F2 (pdb code 5ima). 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 F2, PDB code: 5ima:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Xanthomonas Campestris Peroxiredoxin Q - Structure F2


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 F2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:17.1 occ:1.00 O A:HOH426 2.8 14.5 1.0 O A:SER129 2.9 7.3 1.0 O A:HIS33 2.9 8.4 1.0 HD23 A:LEU128 2.9 9.4 0.5 O A:HIS30 3.3 9.2 1.0 HB3 A:HIS30 3.4 11.7 1.0 HG A:LEU128 3.4 8.6 0.5 HA A:PRO130 3.5 10.1 1.0 HB3 A:LEU128 3.6 10.6 0.5 HB3 A:LEU35 3.6 10.0 1.0 HB2 A:LEU35 3.6 10.0 1.0 CD2 A:LEU128 3.6 7.9 0.5 HB2 A:HIS30 3.7 11.7 1.0 HB3 A:LEU128 3.8 9.5 0.5 C A:SER129 3.8 7.3 1.0 O A:LEU128 3.8 6.2 0.5 HA A:ALA31 3.8 11.2 1.0 HD21 A:LEU128 3.8 9.4 0.5 C A:HIS30 3.9 9.0 1.0 CG A:LEU128 3.9 7.2 0.5 H A:GLY132 4.0 11.4 1.0 CB A:HIS30 4.0 9.7 1.0 HA2 A:GLY132 4.0 12.4 1.0 CB A:LEU35 4.1 8.3 1.0 C A:HIS33 4.1 7.7 1.0 H A:HIS33 4.1 10.4 1.0 CA A:PRO130 4.2 8.4 1.0 O A:HOH433 4.2 8.6 0.3 HA A:TRP34 4.2 8.0 1.0 H A:LEU35 4.2 7.9 1.0 HB2 A:LEU128 4.3 10.6 0.5 O A:LEU128 4.3 6.3 0.5 C A:LEU128 4.3 6.5 0.5 CB A:LEU128 4.3 7.9 0.5 CB A:LEU128 4.4 8.8 0.5 N A:PRO130 4.4 7.9 1.0 N A:LEU35 4.4 6.6 1.0 N A:ALA31 4.4 8.4 1.0 C A:PRO130 4.4 9.0 1.0 HD22 A:LEU128 4.4 9.4 0.5 HD22 A:LEU35 4.5 13.8 1.0 HD23 A:LEU35 4.5 13.8 1.0 C A:LEU128 4.5 6.8 0.5 O A:PRO130 4.5 10.3 1.0 CA A:ALA31 4.6 9.3 1.0 CA A:HIS30 4.6 8.2 1.0 N A:GLY132 4.6 9.5 1.0 C A:TRP34 4.6 6.7 1.0 H A:GLY32 4.7 10.5 1.0 HD23 A:LEU128 4.7 11.2 0.5 O A:LEU27 4.8 6.9 1.0 CA A:GLY132 4.8 10.3 1.0 CA A:TRP34 4.8 6.7 1.0 N A:SER129 4.8 6.8 1.0 N A:HIS33 4.8 8.7 1.0 CD2 A:LEU35 4.9 11.5 1.0 CA A:SER129 4.9 6.9 1.0 N A:TRP34 4.9 7.2 1.0 CA A:LEU35 4.9 6.5 1.0

Sodium binding site 2 out of 3 in the Xanthomonas Campestris Peroxiredoxin Q - Structure F2


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 F2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:10.6 occ:1.00 HG A:SER44 2.3 16.1 1.0 HD1 A:PHE83 2.7 8.8 1.0 OG A:SER44 3.0 13.4 1.0 O A:HOH303 3.1 23.1 0.6 HA A:PHE83 3.1 7.9 1.0 HB3 A:LYS86 3.2 10.0 1.0 HG2 A:LYS86 3.2 15.0 1.0 HB3 A:SER44 3.3 12.5 1.0 OE1 A:GLN87 3.4 9.3 1.0 CD1 A:PHE83 3.5 7.3 1.0 CB A:SER44 3.6 10.4 1.0 HA A:SER44 3.6 10.8 1.0 HG2 A:GLN87 3.6 7.4 1.0 CG A:LYS86 3.8 12.5 1.0 CB A:LYS86 3.9 8.3 1.0 HG3 A:LYS86 4.0 15.0 1.0 HB2 A:LYS86 4.1 10.0 1.0 CA A:PHE83 4.1 6.6 1.0 HE1 A:PHE83 4.1 8.7 1.0 HD21 A:ASN82 4.2 17.2 0.4 CA A:SER44 4.2 9.0 1.0 CD A:GLN87 4.2 6.6 1.0 CE1 A:PHE83 4.3 7.2 1.0 CG A:GLN87 4.3 6.2 1.0 HD22 A:ASN82 4.4 17.2 0.4 CG A:PHE83 4.5 6.1 1.0 HB2 A:SER44 4.5 12.5 1.0 ND2 A:ASN82 4.5 14.4 0.4 O A:HOH346 4.5 27.9 1.0 HG3 A:GLN87 4.5 7.4 1.0 O A:PHE83 4.5 6.5 1.0 HB2 A:PHE83 4.6 8.3 1.0 CB A:PHE83 4.6 6.9 1.0 O A:ASN82 4.7 7.6 0.6 C A:PHE83 4.8 5.8 1.0 O A:HOH446 4.9 20.6 1.0 N A:PHE83 4.9 6.5 1.0 O A:ASN82 4.9 7.0 0.4

Sodium binding site 3 out of 3 in the Xanthomonas Campestris Peroxiredoxin Q - Structure F2


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 F2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:18.1 occ:0.50 O A:HOH514 1.8 19.6 1.0 O A:ALA137 2.3 7.0 1.0 O A:HOH361 2.4 22.9 1.0 O A:HOH416 2.4 12.4 1.0 O A:HOH461 2.6 10.1 1.0 H A:ALA137 3.3 6.6 1.0 C A:ALA137 3.5 5.5 1.0 HG3 A:GLN136 3.7 9.6 1.0 O A:HOH559 3.7 26.2 1.0 HE21 A:GLN136 4.0 12.5 1.0 N A:ALA137 4.1 5.5 1.0 HA A:TRP138 4.1 7.1 1.0 HB3 A:ALA137 4.1 9.4 1.0 HG2 A:GLN136 4.3 9.6 1.0 CA A:ALA137 4.3 5.9 1.0 O A:HOH424 4.4 15.8 1.0 CG A:GLN136 4.4 8.0 1.0 O A:HOH481 4.5 17.7 1.0 N A:TRP138 4.5 5.3 1.0 NE2 A:GLN136 4.7 10.4 1.0 CB A:ALA137 4.7 7.8 1.0 CA A:TRP138 4.8 5.9 1.0 HA A:GLN136 4.9 7.4 1.0 O A:HOH479 4.9 24.6 1.0 O A:HOH432 4.9 15.7 0.6 O A:HOH558 5.0 17.6 0.7

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