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Sodium in PDB 5im9: Xanthomonas Campestris Peroxiredoxin Q - Structure F1

Protein crystallography data

The structure of Xanthomonas Campestris Peroxiredoxin Q - Structure F1, PDB code: 5im9 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) 38.80 / 1.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.560, 51.485, 39.900, 90.00, 103.51, 90.00
R / Rfree (%) 11.6 / 13.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Xanthomonas Campestris Peroxiredoxin Q - Structure F1 (pdb code 5im9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Xanthomonas Campestris Peroxiredoxin Q - Structure F1, PDB code: 5im9:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5im9

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Sodium binding site 1 out of 5 in the Xanthomonas Campestris Peroxiredoxin Q - Structure F1


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 F1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:29.4
occ:0.70
 O A:HOH432 2.3 41.1 1.0
OE1 A:GLN24 2.4 18.9 1.0
O A:GLY22 2.5 17.3 1.0
O A:HOH473 2.9 39.6 1.0
HE22 A:GLN24 3.1 22.0 1.0
CD A:GLN24 3.3 17.2 1.0
C A:GLY22 3.6 11.9 1.0
NE2 A:GLN24 3.6 18.4 1.0
HA A:THR23 3.8 12.9 1.0
O A:HOH503 3.8 44.4 1.0
NA A:NA204 3.9 31.9 1.0
O A:HOH394 4.0 11.5 1.0
HA2 A:GLY22 4.2 14.4 1.0
CA A:THR23 4.4 10.8 1.0
N A:THR23 4.4 10.5 1.0
O A:HOH494 4.4 42.6 1.0
CA A:GLY22 4.4 12.0 1.0
HE21 A:GLN24 4.4 22.0 1.0
C A:THR23 4.5 9.1 1.0
O A:HOH476 4.5 40.0 1.0
O A:THR23 4.6 8.6 1.0
HA3 A:GLY22 4.7 14.4 1.0
CG A:GLN24 4.7 15.5 1.0
HG3 A:GLN24 4.8 18.6 1.0
N A:GLN24 5.0 10.1 1.0

Sodium binding site 2 out of 5 in 5im9

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Sodium binding site 2 out of 5 in the Xanthomonas Campestris Peroxiredoxin Q - Structure F1


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 F1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:12.0
occ:1.00
 O A:HOH347 2.4 13.3 1.0
O A:HOH466 2.4 18.9 1.0
OG A:SER18 2.4 10.4 1.0
O A:HOH459 2.5 24.8 1.0
O A:HOH415 2.5 49.5 1.0
O A:HOH356 2.5 8.0 1.0
HB2 A:SER18 3.3 9.6 1.0
H A:SER18 3.4 7.5 1.0
CB A:SER18 3.4 8.0 1.0
O A:HOH475 3.9 20.1 1.0
O A:SER95 4.1 6.4 1.0
N A:SER18 4.1 6.3 1.0
HB3 A:SER18 4.1 9.6 1.0
O A:HOH324 4.3 8.1 1.0
NA A:NA204 4.3 31.9 1.0
CA A:SER18 4.4 6.3 1.0
O A:PRO16 4.4 8.3 1.0
O A:HOH547 4.4 36.8 1.0
H A:GLY97 4.6 7.5 1.0
O A:HOH333 4.7 21.4 1.0
HA A:LEU17 4.8 7.0 1.0
HA A:SER18 4.8 7.6 1.0

Sodium binding site 3 out of 5 in 5im9

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Sodium binding site 3 out of 5 in the Xanthomonas Campestris Peroxiredoxin Q - Structure F1


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 F1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:17.8
occ:1.00
 HD23 A:LEU128 2.8 11.7 0.5
O A:HOH411 2.8 14.3 1.0
O A:SER129 2.9 6.9 1.0
O A:HIS33 2.9 7.6 1.0
O A:HIS30 3.2 9.3 1.0
HA A:PRO130 3.4 10.0 1.0
HB3 A:HIS30 3.4 10.4 1.0
HG A:LEU128 3.5 11.4 0.5
HB2 A:LEU35 3.5 8.7 1.0
CD2 A:LEU128 3.6 9.7 0.5
HB3 A:LEU35 3.6 8.7 1.0
HB3 A:LEU128 3.7 9.7 0.5
HA A:ALA31 3.7 10.6 1.0
C A:HIS30 3.7 8.4 1.0
HD21 A:LEU128 3.8 11.7 0.5
HB2 A:HIS30 3.8 10.4 1.0
H A:GLY132 3.8 11.8 1.0
HB3 A:LEU128 3.8 12.2 0.5
C A:SER129 3.9 6.5 1.0
HA2 A:GLY132 3.9 13.6 1.0
CG A:LEU128 4.0 9.5 0.5
CB A:HIS30 4.0 8.7 1.0
H A:HIS33 4.0 9.9 1.0
CB A:LEU35 4.0 7.3 1.0
O A:LEU128 4.0 6.5 0.5
CA A:PRO130 4.1 8.3 1.0
C A:HIS33 4.1 7.0 1.0
N A:ALA31 4.3 8.3 1.0
HB2 A:LEU128 4.3 9.7 0.5
H A:LEU35 4.3 7.3 1.0
C A:PRO130 4.3 8.4 1.0
HA A:TRP34 4.3 7.4 1.0
HD22 A:LEU35 4.3 13.4 1.0
HD22 A:LEU128 4.4 11.7 0.5
N A:PRO130 4.4 7.5 1.0
CA A:ALA31 4.4 8.8 1.0
CB A:LEU128 4.4 10.2 0.5
N A:GLY132 4.4 9.8 1.0
CB A:LEU128 4.4 8.1 0.5
O A:PRO130 4.5 9.9 1.0
N A:LEU35 4.5 6.0 1.0
C A:LEU128 4.5 7.4 0.5
O A:LEU128 4.5 7.0 0.5
H A:GLY32 4.5 10.8 1.0
CA A:HIS30 4.5 8.7 1.0
HD23 A:LEU35 4.5 13.4 1.0
CA A:GLY132 4.7 11.4 1.0
C A:LEU128 4.7 6.3 0.5
HD23 A:LEU128 4.7 8.2 0.5
C A:TRP34 4.7 6.2 1.0
O A:LEU27 4.8 7.4 1.0
N A:HIS33 4.8 8.3 1.0
CD2 A:LEU35 4.8 11.1 1.0
CA A:TRP34 4.9 6.2 1.0
N A:SER129 4.9 6.9 1.0
H A:ALA31 4.9 10.0 1.0
N A:GLY32 4.9 9.0 1.0
CA A:LEU35 4.9 6.1 1.0
HD2 A:HIS33 4.9 12.4 1.0
N A:TRP34 5.0 6.7 1.0
C A:ALA31 5.0 8.9 1.0
CA A:SER129 5.0 7.0 1.0

Sodium binding site 4 out of 5 in 5im9

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Sodium binding site 4 out of 5 in the Xanthomonas Campestris Peroxiredoxin Q - Structure F1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Xanthomonas Campestris Peroxiredoxin Q - Structure F1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:31.9
occ:1.00
 O A:HOH503 2.2 44.4 1.0
OG A:SER18 2.6 10.4 1.0
OE1 A:GLN24 2.8 18.9 1.0
O A:HOH475 2.9 20.1 1.0
O A:HOH473 3.1 39.6 1.0
HG3 A:GLN24 3.2 18.6 1.0
HB3 A:SER18 3.3 9.6 1.0
CB A:SER18 3.4 8.0 1.0
CD A:GLN24 3.4 17.2 1.0
HA A:SER18 3.5 7.6 1.0
CG A:GLN24 3.7 15.5 1.0
HG2 A:GLN24 3.7 18.6 1.0
O A:HOH466 3.8 18.9 1.0
NA A:NA201 3.9 29.4 0.7
O A:HOH394 3.9 11.5 1.0
CA A:SER18 4.0 6.3 1.0
HB2 A:SER18 4.2 9.6 1.0
NA A:NA202 4.3 12.0 1.0
NE2 A:GLN24 4.5 18.4 1.0
O A:HOH347 4.5 13.3 1.0
N A:SER18 4.7 6.3 1.0
HE22 A:GLN24 4.7 22.0 1.0
H A:SER18 4.8 7.5 1.0
O A:HOH538 4.9 33.3 1.0
HG21 A:VAL77 5.0 10.7 1.0
O A:THR23 5.0 8.6 1.0

Sodium binding site 5 out of 5 in 5im9

Go back to Sodium Binding Sites List in 5im9
Sodium binding site 5 out of 5 in the Xanthomonas Campestris Peroxiredoxin Q - Structure F1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Xanthomonas Campestris Peroxiredoxin Q - Structure F1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:16.0
occ:0.40
 O A:HOH478 2.1 31.1 1.0
O A:ALA137 2.3 7.6 1.0
O A:HOH416 2.3 12.9 1.0
O A:HOH379 2.4 29.5 1.0
O A:HOH443 2.7 11.2 1.0
H A:ALA137 3.4 7.0 1.0
C A:ALA137 3.5 5.8 1.0
HG3 A:GLN136 3.6 9.5 1.0
O A:HOH535 3.8 28.1 1.0
HE21 A:GLN136 3.9 12.4 1.0
HA A:TRP138 4.0 6.6 1.0
N A:ALA137 4.1 5.8 1.0
HB3 A:ALA137 4.1 8.8 1.0
HG2 A:GLN136 4.2 9.5 1.0
O A:HOH418 4.3 20.5 1.0
CA A:ALA137 4.3 5.8 1.0
CG A:GLN136 4.4 8.0 1.0
O A:HOH474 4.4 35.1 1.0
N A:TRP138 4.5 5.0 1.0
NE2 A:GLN136 4.6 10.3 1.0
CA A:TRP138 4.7 5.5 1.0
CB A:ALA137 4.8 7.3 1.0
O A:HOH533 4.9 31.3 1.0
O A:HOH465 4.9 30.2 1.0
HA A:GLN136 4.9 7.4 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: Mon Oct 7 21:38:30 2024

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