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Sodium in PDB 5iow: Xanthomonas Campestris Peroxiredoxin Q - Structure Ffcumene (Hyperoxidized By Cumene Hydroperoxide)

Protein crystallography data

The structure of Xanthomonas Campestris Peroxiredoxin Q - Structure Ffcumene (Hyperoxidized By Cumene Hydroperoxide), PDB code: 5iow 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) 29.49 / 1.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.380, 51.370, 40.260, 90.00, 103.54, 90.00
R / Rfree (%) 17.9 / 22.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Xanthomonas Campestris Peroxiredoxin Q - Structure Ffcumene (Hyperoxidized By Cumene Hydroperoxide) (pdb code 5iow). 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 Ffcumene (Hyperoxidized By Cumene Hydroperoxide), PDB code: 5iow:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5iow

Go back to Sodium Binding Sites List in 5iow
Sodium binding site 1 out of 2 in the Xanthomonas Campestris Peroxiredoxin Q - Structure Ffcumene (Hyperoxidized By Cumene Hydroperoxide)


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 Ffcumene (Hyperoxidized By Cumene Hydroperoxide) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:23.1
occ:1.00
O A:HOH433 2.2 49.1 1.0
O A:HOH358 2.3 27.3 1.0
OG A:SER18 2.4 16.9 1.0
O A:HOH426 2.4 34.7 1.0
O A:HOH346 2.4 13.8 1.0
O A:HOH435 2.6 38.2 1.0
HB2 A:SER18 3.2 18.5 1.0
H A:SER18 3.3 16.9 1.0
CB A:SER18 3.3 15.4 1.0
HE21 A:GLN24 3.9 37.9 1.0
N A:SER18 4.0 14.1 1.0
O A:HOH421 4.0 41.1 1.0
HB3 A:SER18 4.0 18.5 1.0
O A:HOH461 4.1 43.2 1.0
O A:SER95 4.1 13.2 1.0
O A:HOH477 4.2 43.1 1.0
CA A:SER18 4.3 14.3 1.0
O A:PRO16 4.3 17.8 1.0
O A:HOH320 4.4 14.9 1.0
O A:HOH427 4.4 47.0 1.0
NE2 A:GLN24 4.6 31.5 1.0
HA A:LEU17 4.7 16.5 1.0
HA A:SER18 4.7 17.3 1.0
H A:GLY97 4.7 14.9 1.0
O A:HOH348 4.8 30.6 1.0
HE22 A:GLN24 4.8 37.9 1.0
HG2 A:PRO16 5.0 23.3 1.0

Sodium binding site 2 out of 2 in 5iow

Go back to Sodium Binding Sites List in 5iow
Sodium binding site 2 out of 2 in the Xanthomonas Campestris Peroxiredoxin Q - Structure Ffcumene (Hyperoxidized By Cumene Hydroperoxide)


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 Ffcumene (Hyperoxidized By Cumene Hydroperoxide) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:30.6
occ:1.00
O A:SER129 2.9 16.7 1.0
O A:HIS33 2.9 17.5 1.0
O A:HOH424 3.0 30.9 1.0
HD23 A:LEU128 3.2 16.6 0.6
O A:HIS30 3.2 20.9 1.0
HA A:PRO130 3.3 20.8 1.0
HB3 A:HIS30 3.4 25.3 1.0
HG A:LEU128 3.5 17.9 0.6
HB2 A:LEU35 3.5 18.1 1.0
HB3 A:LEU35 3.6 18.1 1.0
HA A:ALA31 3.7 25.3 1.0
C A:HIS30 3.8 21.1 1.0
H A:GLY132 3.8 24.6 1.0
HB3 A:LEU128 3.8 14.9 0.5
C A:SER129 3.8 15.4 1.0
HB2 A:HIS30 3.9 25.3 1.0
CD2 A:LEU128 3.9 13.8 0.6
HA2 A:GLY132 3.9 23.4 1.0
HB3 A:LEU128 3.9 17.6 0.6
O A:LEU128 3.9 12.9 0.6
CB A:HIS30 4.0 21.0 1.0
CB A:LEU35 4.0 15.1 1.0
CA A:PRO130 4.0 17.3 1.0
HD21 A:LEU128 4.0 16.6 0.6
CG A:LEU128 4.1 14.9 0.6
H A:HIS33 4.1 23.5 1.0
C A:HIS33 4.1 17.4 1.0
C A:PRO130 4.3 18.9 1.0
H A:LEU35 4.3 16.9 1.0
HA A:TRP34 4.3 18.1 1.0
N A:ALA31 4.3 21.1 1.0
O A:PRO130 4.3 19.3 1.0
N A:PRO130 4.3 16.6 1.0
HB2 A:LEU128 4.4 14.9 0.5
N A:GLY132 4.4 20.4 1.0
CA A:ALA31 4.4 21.1 1.0
HD22 A:LEU35 4.4 20.3 1.0
N A:LEU35 4.4 14.0 1.0
C A:LEU128 4.5 13.5 0.6
CB A:LEU128 4.5 14.6 0.6
O A:LEU128 4.5 13.3 0.5
CB A:LEU128 4.5 12.4 0.5
H A:GLY32 4.5 24.0 1.0
CA A:HIS30 4.6 21.0 1.0
CA A:GLY132 4.6 19.4 1.0
HD23 A:LEU35 4.7 20.3 1.0
C A:LEU128 4.7 13.3 0.5
C A:TRP34 4.7 14.4 1.0
HD22 A:LEU128 4.7 16.6 0.6
N A:HIS33 4.8 19.5 1.0
O A:LEU27 4.8 18.3 1.0
CA A:TRP34 4.9 15.0 1.0
HD23 A:LEU128 4.9 13.2 0.5
CA A:LEU35 4.9 13.6 1.0
CD2 A:LEU35 4.9 16.9 1.0
N A:SER129 4.9 14.2 1.0
N A:GLY32 4.9 20.0 1.0
H A:ALA31 4.9 25.4 1.0
C A:ALA31 5.0 21.2 1.0
N A:GLU131 5.0 21.3 1.0
N A:TRP34 5.0 15.8 1.0
CA A:SER129 5.0 14.1 1.0

Reference:

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
Page generated: Tue Dec 15 11:06:29 2020

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