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Sodium in PDB 5ipg: Xanthomonas Campestris Peroxiredoxin Q - Structure Fft-Butyl (Hyperoxodized By T-Butyl Hydroperoxide)

Protein crystallography data

The structure of Xanthomonas Campestris Peroxiredoxin Q - Structure Fft-Butyl (Hyperoxodized By T-Butyl Hydroperoxide), PDB code: 5ipg 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) 34.45 / 1.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.430, 51.450, 40.310, 90.00, 103.51, 90.00
R / Rfree (%) 16.3 / 19.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Xanthomonas Campestris Peroxiredoxin Q - Structure Fft-Butyl (Hyperoxodized By T-Butyl Hydroperoxide) (pdb code 5ipg). 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 Fft-Butyl (Hyperoxodized By T-Butyl Hydroperoxide), PDB code: 5ipg:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5ipg

Go back to Sodium Binding Sites List in 5ipg
Sodium binding site 1 out of 2 in the Xanthomonas Campestris Peroxiredoxin Q - Structure Fft-Butyl (Hyperoxodized By T-Butyl 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 Fft-Butyl (Hyperoxodized By T-Butyl Hydroperoxide) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:26.9
occ:1.00
O A:HOH407 2.0 40.5 1.0
O A:HOH335 2.2 28.4 1.0
OG A:SER18 2.4 19.1 1.0
O A:HOH422 2.4 32.1 1.0
O A:HOH431 2.4 32.9 1.0
O A:HOH341 2.5 17.2 1.0
HB2 A:SER18 3.3 20.9 1.0
H A:SER18 3.3 17.2 1.0
CB A:SER18 3.4 17.4 1.0
O A:HOH428 3.8 35.3 1.0
O A:HOH447 3.9 45.0 1.0
O A:HOH460 3.9 45.8 1.0
N A:SER18 4.0 14.4 1.0
HB3 A:SER18 4.1 20.9 1.0
O A:SER95 4.2 15.1 1.0
O A:PRO16 4.3 19.1 1.0
CA A:SER18 4.3 14.7 1.0
O A:HOH320 4.4 17.4 1.0
O A:HOH455 4.4 36.6 1.0
HA A:LEU17 4.7 17.4 1.0
HA A:SER18 4.7 17.6 1.0
H A:GLY97 4.7 17.1 1.0
O A:HOH347 4.9 29.8 1.0

Sodium binding site 2 out of 2 in 5ipg

Go back to Sodium Binding Sites List in 5ipg
Sodium binding site 2 out of 2 in the Xanthomonas Campestris Peroxiredoxin Q - Structure Fft-Butyl (Hyperoxodized By T-Butyl 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 Fft-Butyl (Hyperoxodized By T-Butyl Hydroperoxide) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:35.1
occ:1.00
O A:HOH401 2.8 33.9 1.0
O A:SER129 2.9 16.8 1.0
O A:HIS33 3.0 17.9 1.0
O A:HIS30 3.1 22.5 1.0
HD23 A:LEU128 3.3 24.6 0.5
HB3 A:HIS30 3.3 27.6 1.0
HA A:PRO130 3.3 21.3 1.0
HG A:LEU128 3.5 24.1 0.5
HB2 A:LEU35 3.6 20.1 1.0
HA A:ALA31 3.6 27.0 1.0
C A:HIS30 3.7 23.2 1.0
HB3 A:LEU35 3.7 20.1 1.0
H A:GLY132 3.8 24.1 1.0
HA2 A:GLY132 3.8 22.4 1.0
C A:SER129 3.9 16.2 1.0
HB2 A:HIS30 3.9 27.6 1.0
CD2 A:LEU128 3.9 20.5 0.5
HB3 A:LEU128 4.0 14.3 0.5
HB3 A:LEU128 4.0 21.9 0.5
CB A:HIS30 4.0 23.0 1.0
CA A:PRO130 4.0 17.8 1.0
O A:LEU128 4.0 17.2 0.5
H A:HIS33 4.0 25.7 1.0
HD21 A:LEU128 4.1 24.6 0.5
CG A:LEU128 4.1 20.1 0.5
CB A:LEU35 4.1 16.8 1.0
C A:HIS33 4.2 18.1 1.0
N A:ALA31 4.2 23.1 1.0
C A:PRO130 4.2 19.2 1.0
O A:PRO130 4.3 19.4 1.0
CA A:ALA31 4.3 22.5 1.0
N A:GLY132 4.3 20.0 1.0
N A:PRO130 4.3 18.2 1.0
H A:GLY32 4.4 27.3 1.0
HA A:TRP34 4.4 18.7 1.0
H A:LEU35 4.4 16.8 1.0
HD22 A:LEU35 4.5 21.5 1.0
CA A:HIS30 4.5 23.3 1.0
HB2 A:LEU128 4.5 14.3 0.5
CA A:GLY132 4.5 18.7 1.0
C A:LEU128 4.6 16.5 0.5
N A:LEU35 4.6 14.0 1.0
CB A:LEU128 4.6 18.3 0.5
O A:LEU128 4.6 12.8 0.5
CB A:LEU128 4.7 12.0 0.5
HD23 A:LEU35 4.7 21.5 1.0
O A:LEU27 4.7 21.2 1.0
N A:HIS33 4.8 21.4 1.0
C A:LEU128 4.8 13.8 0.5
HD22 A:LEU128 4.8 24.6 0.5
H A:ALA31 4.8 27.8 1.0
N A:GLY32 4.8 22.7 1.0
C A:TRP34 4.8 15.3 1.0
N A:GLU131 4.9 21.5 0.6
C A:ALA31 4.9 23.4 1.0
N A:GLU131 4.9 21.9 0.4
HA3 A:GLY132 4.9 22.4 1.0
CD2 A:LEU35 4.9 17.9 1.0
CA A:TRP34 5.0 15.6 1.0
N A:SER129 5.0 14.6 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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