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Sodium in PDB 5io2: Xanthomonas Campestris Peroxiredoxin Q - C48S Mutant

Protein crystallography data

The structure of Xanthomonas Campestris Peroxiredoxin Q - C48S Mutant, PDB code: 5io2 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) 29.48 / 1.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.630, 51.280, 39.680, 90.00, 103.80, 90.00
R / Rfree (%) 13.9 / 16.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Xanthomonas Campestris Peroxiredoxin Q - C48S Mutant (pdb code 5io2). 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 - C48S Mutant, PDB code: 5io2:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5io2

Go back to Sodium Binding Sites List in 5io2
Sodium binding site 1 out of 3 in the Xanthomonas Campestris Peroxiredoxin Q - C48S Mutant


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 - C48S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:11.4
occ:0.50
NA A:NA201 0.0 11.4 0.5
O A:HOH377 0.1 34.1 0.5
O A:HOH474 2.0 21.7 0.5
O A:HOH377 2.1 27.2 0.5
NA A:NA201 2.1 16.9 0.5
OG A:SER18 2.4 10.4 1.0
O A:HOH489 2.4 29.3 1.0
O A:HOH477 2.5 22.0 1.0
O A:HOH395 2.5 8.2 1.0
HB2 A:SER18 3.2 11.1 1.0
CB A:SER18 3.4 9.3 1.0
H A:SER18 3.4 8.7 1.0
O A:HOH500 3.8 18.0 1.0
O A:SER95 4.0 7.2 1.0
HB3 A:SER18 4.0 11.1 1.0
N A:SER18 4.1 7.3 1.0
O A:HOH578 4.2 36.4 1.0
O A:HOH337 4.3 7.4 1.0
O A:HOH313 4.3 22.5 1.0
CA A:SER18 4.3 7.0 1.0
O A:PRO16 4.4 7.9 1.0
O A:HOH348 4.4 20.4 1.0
O A:HOH594 4.6 35.6 1.0
H A:GLY97 4.7 8.8 1.0
HA A:LEU17 4.8 8.2 1.0
HA A:SER18 4.8 8.3 1.0

Sodium binding site 2 out of 3 in 5io2

Go back to Sodium Binding Sites List in 5io2
Sodium binding site 2 out of 3 in the Xanthomonas Campestris Peroxiredoxin Q - C48S Mutant


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 - C48S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:16.9
occ:0.50
NA A:NA201 0.0 16.9 0.5
O A:HOH377 0.0 27.2 0.5
NA A:NA201 2.1 11.4 0.5
O A:HOH377 2.2 34.1 0.5
O A:HOH500 2.7 18.0 1.0
O A:PRO16 2.8 7.9 1.0
HG2 A:PRO16 3.0 11.6 1.0
O A:HOH395 3.2 8.2 1.0
OG A:SER18 3.2 10.4 1.0
O A:HOH489 3.4 29.3 1.0
O A:HOH477 3.5 22.0 1.0
HB2 A:PRO16 3.5 11.0 1.0
H A:SER18 3.6 8.7 1.0
C A:PRO16 3.7 7.2 1.0
CG A:PRO16 3.9 9.7 1.0
O A:HOH418 4.0 8.5 1.0
CB A:PRO16 4.1 9.2 1.0
N A:SER18 4.1 7.3 1.0
O A:HOH474 4.1 21.7 0.5
HA A:LEU17 4.1 8.2 1.0
CB A:SER18 4.4 9.3 1.0
HG3 A:PRO16 4.4 11.6 1.0
O A:HOH337 4.5 7.4 1.0
HB2 A:SER18 4.5 11.1 1.0
CA A:PRO16 4.5 7.8 1.0
N A:LEU17 4.6 6.8 1.0
O A:HOH338 4.6 11.1 1.0
HG2 A:GLN24 4.6 18.4 1.0
O A:HOH313 4.6 22.5 1.0
CA A:LEU17 4.7 6.9 1.0
HG3 A:GLN24 4.7 18.4 1.0
C A:LEU17 4.8 7.6 1.0
CA A:SER18 4.8 7.0 1.0
HD2 A:PRO16 4.8 10.5 1.0
CD A:PRO16 4.9 8.7 1.0
HA A:SER18 4.9 8.3 1.0
HB3 A:PRO16 5.0 11.0 1.0

Sodium binding site 3 out of 3 in 5io2

Go back to Sodium Binding Sites List in 5io2
Sodium binding site 3 out of 3 in the Xanthomonas Campestris Peroxiredoxin Q - C48S Mutant


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 - C48S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:19.3
occ:1.00
O A:HOH464 2.8 13.0 1.0
HD23 A:LEU128 2.9 12.0 0.5
O A:SER129 2.9 8.4 1.0
O A:HIS33 2.9 8.2 1.0
O A:HIS30 3.1 9.9 1.0
HA A:PRO130 3.4 11.5 1.0
HB3 A:HIS30 3.4 11.0 1.0
HB2 A:LEU35 3.6 11.2 1.0
HG A:LEU128 3.6 12.9 0.5
HA A:ALA31 3.6 12.1 1.0
CD2 A:LEU128 3.7 10.0 0.5
C A:HIS30 3.7 9.1 1.0
HB3 A:LEU35 3.7 11.2 1.0
HB3 A:LEU128 3.8 11.4 0.5
H A:GLY132 3.8 14.3 1.0
HD21 A:LEU128 3.8 12.0 0.5
C A:SER129 3.9 8.7 1.0
HB2 A:HIS30 3.9 11.0 1.0
HA2 A:GLY132 3.9 14.2 1.0
HB3 A:LEU128 4.0 12.4 0.5
H A:HIS33 4.0 11.1 1.0
CB A:HIS30 4.0 9.2 1.0
CA A:PRO130 4.1 9.6 1.0
O A:LEU128 4.1 9.7 0.5
CG A:LEU128 4.1 10.7 0.5
CB A:LEU35 4.1 9.3 1.0
C A:HIS33 4.1 8.3 1.0
C A:PRO130 4.2 9.9 1.0
N A:ALA31 4.3 8.8 1.0
O A:PRO130 4.3 10.4 1.0
H A:LEU35 4.3 8.8 1.0
CA A:ALA31 4.3 10.1 1.0
N A:PRO130 4.4 9.3 1.0
HD22 A:LEU35 4.4 15.1 1.0
HA A:TRP34 4.4 9.8 1.0
N A:GLY132 4.4 11.9 1.0
H A:GLY32 4.4 11.7 1.0
HB2 A:LEU128 4.4 11.4 0.5
HD22 A:LEU128 4.4 12.0 0.5
O A:LEU128 4.5 8.7 0.5
N A:LEU35 4.5 7.3 1.0
CA A:HIS30 4.5 9.1 1.0
C A:LEU128 4.5 9.4 0.5
CB A:LEU128 4.5 10.3 0.5
CB A:LEU128 4.6 9.5 0.5
HD23 A:LEU35 4.6 15.1 1.0
CA A:GLY132 4.6 11.9 1.0
O A:LEU27 4.7 8.2 1.0
C A:LEU128 4.7 8.7 0.5
N A:HIS33 4.7 9.2 1.0
C A:TRP34 4.8 7.9 1.0
N A:GLY32 4.8 9.7 1.0
HD23 A:LEU128 4.9 11.5 0.5
H A:ALA31 4.9 10.5 1.0
CD2 A:LEU35 4.9 12.5 1.0
C A:ALA31 4.9 10.0 1.0
CA A:TRP34 4.9 8.2 1.0
N A:GLU131 4.9 11.3 1.0
N A:SER129 5.0 8.8 1.0
CA A:LEU35 5.0 7.8 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 11:06:26 2020

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