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Sodium in PDB 5imz: Xanthomonas Campestris Peroxiredoxin Q - Structure F7

Protein crystallography data

The structure of Xanthomonas Campestris Peroxiredoxin Q - Structure F7, PDB code: 5imz 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) 23.11 / 1.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.440, 51.190, 39.990, 90.00, 104.00, 90.00
R / Rfree (%) 13.3 / 15.5

Other elements in 5imz:

The structure of Xanthomonas Campestris Peroxiredoxin Q - Structure F7 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Xanthomonas Campestris Peroxiredoxin Q - Structure F7 (pdb code 5imz). 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 F7, PDB code: 5imz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5imz

Go back to Sodium Binding Sites List in 5imz
Sodium binding site 1 out of 2 in the Xanthomonas Campestris Peroxiredoxin Q - Structure F7


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 F7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:18.7
occ:1.00
O A:HOH434 2.8 14.6 1.0
HD23 A:LEU128 2.8 9.3 0.5
O A:HIS33 2.9 9.2 1.0
O A:SER129 2.9 8.0 1.0
O A:HIS30 3.4 9.9 1.0
HB3 A:HIS30 3.4 12.6 1.0
HG A:LEU128 3.4 9.8 0.5
HA A:PRO130 3.5 11.7 1.0
HB3 A:LEU35 3.5 10.4 1.0
HB3 A:LEU128 3.5 11.0 0.5
HB2 A:LEU35 3.6 10.4 1.0
CD2 A:LEU128 3.6 7.8 0.5
HB2 A:HIS30 3.7 12.6 1.0
HB3 A:LEU128 3.8 10.2 0.5
O A:LEU128 3.8 7.8 0.5
HD21 A:LEU128 3.8 9.3 0.5
C A:SER129 3.8 8.2 1.0
C A:HIS30 3.9 9.4 1.0
HA A:ALA31 3.9 11.9 1.0
CG A:LEU128 3.9 8.2 0.5
CB A:HIS30 4.0 10.5 1.0
H A:GLY132 4.0 12.7 1.0
CB A:LEU35 4.0 8.7 1.0
HA2 A:GLY132 4.0 12.9 1.0
C A:HIS33 4.1 8.5 1.0
H A:HIS33 4.1 11.8 1.0
O A:HOH450 4.1 9.3 0.3
CA A:PRO130 4.2 9.7 1.0
H A:LEU35 4.2 8.5 1.0
HA A:TRP34 4.2 9.2 1.0
HB2 A:LEU128 4.2 11.0 0.5
O A:LEU128 4.3 7.5 0.5
C A:LEU128 4.3 7.8 0.5
CB A:LEU128 4.3 9.2 0.5
N A:LEU35 4.3 7.1 1.0
CB A:LEU128 4.3 8.5 0.5
N A:PRO130 4.4 8.7 1.0
HD22 A:LEU35 4.4 13.4 1.0
HD22 A:LEU128 4.4 9.3 0.5
HD23 A:LEU35 4.4 13.4 1.0
C A:PRO130 4.4 10.5 1.0
N A:ALA31 4.4 9.4 1.0
C A:LEU128 4.5 7.8 0.5
O A:PRO130 4.5 11.3 1.0
C A:TRP34 4.6 7.6 1.0
CA A:HIS30 4.6 9.4 1.0
CA A:ALA31 4.6 9.9 1.0
N A:GLY132 4.6 10.5 1.0
HD23 A:LEU128 4.7 11.4 0.5
H A:GLY32 4.7 11.4 1.0
O A:LEU27 4.7 7.5 1.0
CA A:TRP34 4.7 7.7 1.0
CA A:GLY132 4.8 10.8 1.0
N A:SER129 4.8 7.9 1.0
CD2 A:LEU35 4.8 11.2 1.0
N A:HIS33 4.8 9.8 1.0
CA A:LEU35 4.9 6.7 1.0
N A:TRP34 4.9 7.8 1.0
CA A:SER129 4.9 7.7 1.0

Sodium binding site 2 out of 2 in 5imz

Go back to Sodium Binding Sites List in 5imz
Sodium binding site 2 out of 2 in the Xanthomonas Campestris Peroxiredoxin Q - Structure F7


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 F7 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 9.0 1.0
OG A:SER44 3.0 13.4 1.0
HA A:PHE83 3.1 8.5 1.0
HB3 A:LYS86 3.1 12.1 1.0
O A:HOH304 3.2 29.7 0.6
HB3 A:SER44 3.2 13.5 1.0
HG2 A:LYS86 3.2 17.3 1.0
OE1 A:GLN87 3.3 9.8 1.0
CD1 A:PHE83 3.5 7.5 1.0
CB A:SER44 3.6 11.3 1.0
HG2 A:GLN87 3.6 8.1 1.0
HA A:SER44 3.6 11.5 1.0
CG A:LYS86 3.9 14.4 1.0
CB A:LYS86 3.9 10.1 1.0
HG3 A:LYS86 4.0 17.3 1.0
CA A:PHE83 4.0 7.0 1.0
HE1 A:PHE83 4.1 9.1 1.0
HB2 A:LYS86 4.1 12.1 1.0
HD21 A:ASN82 4.1 16.6 0.4
CA A:SER44 4.1 9.6 1.0
CD A:GLN87 4.2 7.3 1.0
CE1 A:PHE83 4.3 7.6 1.0
CG A:GLN87 4.3 6.7 1.0
HD22 A:ASN82 4.3 16.6 0.4
HB2 A:SER44 4.4 13.5 1.0
ND2 A:ASN82 4.4 13.8 0.4
HG3 A:GLN87 4.5 8.1 1.0
CG A:PHE83 4.5 6.8 1.0
O A:PHE83 4.5 7.2 1.0
HB2 A:PHE83 4.6 8.4 1.0
CB A:PHE83 4.6 7.0 1.0
O A:HOH364 4.6 29.7 1.0
O A:ASN82 4.7 8.5 0.6
O A:ASN82 4.8 8.7 0.4
C A:PHE83 4.8 7.0 1.0
O A:HOH453 4.8 20.6 1.0
N A:PHE83 4.8 7.6 1.0
H A:SER44 5.0 9.9 1.0
N A:SER44 5.0 8.3 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 11:06:23 2020

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