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Sodium in PDB 4n9s: High Resolution X-Ray Structure of Urate Oxidase in Complex with 8- Hydroxyxanthine

Enzymatic activity of High Resolution X-Ray Structure of Urate Oxidase in Complex with 8- Hydroxyxanthine

All present enzymatic activity of High Resolution X-Ray Structure of Urate Oxidase in Complex with 8- Hydroxyxanthine:
1.7.3.3;

Protein crystallography data

The structure of High Resolution X-Ray Structure of Urate Oxidase in Complex with 8- Hydroxyxanthine, PDB code: 4n9s was solved by E.Oksanen, M.P.Blakeley, M.Budayova-Spano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.27 / 1.06
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 79.930, 95.370, 104.810, 90.00, 90.00, 90.00
R / Rfree (%) 12.6 / 14.1

Other elements in 4n9s:

The structure of High Resolution X-Ray Structure of Urate Oxidase in Complex with 8- Hydroxyxanthine also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the High Resolution X-Ray Structure of Urate Oxidase in Complex with 8- Hydroxyxanthine (pdb code 4n9s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the High Resolution X-Ray Structure of Urate Oxidase in Complex with 8- Hydroxyxanthine, PDB code: 4n9s:

Sodium binding site 1 out of 1 in 4n9s

Go back to Sodium Binding Sites List in 4n9s
Sodium binding site 1 out of 1 in the High Resolution X-Ray Structure of Urate Oxidase in Complex with 8- Hydroxyxanthine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High Resolution X-Ray Structure of Urate Oxidase in Complex with 8- Hydroxyxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:13.4
occ:1.00
 O A:ILE94 2.3 11.9 1.0
O A:ILE88 2.4 14.3 1.0
O A:HOH594 2.5 18.7 1.0
O A:TYR91 2.5 13.4 1.0
OE1 A:GLU136 2.6 17.0 0.8
O A:ASN92 2.9 18.9 1.0
HA A:ASN92 3.2 18.2 1.0
HA A:ILE88 3.2 13.4 1.0
C A:ASN92 3.4 15.7 1.0
C A:ILE88 3.4 11.9 1.0
DD1 A:HIS95 3.4 22.5 1.0
CD A:GLU136 3.5 19.9 0.8
C A:ILE94 3.5 11.1 1.0
D A:ILE94 3.5 13.8 1.0
C A:TYR91 3.5 12.7 1.0
HB A:ILE88 3.6 14.8 1.0
CA A:ASN92 3.7 15.2 1.0
CA A:ILE88 3.8 11.2 1.0
OE2 A:GLU136 3.8 23.9 0.6
HA A:HIS95 3.8 13.6 1.0
N A:ILE94 3.9 11.5 1.0
ND1 A:HIS95 4.0 18.8 1.0
O A:HOH815 4.0 34.5 1.0
N A:ASN92 4.0 14.6 1.0
HB A:ILE94 4.0 12.8 1.0
O A:HOH695 4.1 30.2 1.0
CB A:ILE88 4.2 12.3 1.0
CA A:ILE94 4.2 10.5 1.0
N A:HIS93 4.3 12.7 1.0
HE1 A:HIS95 4.3 22.3 1.0
O A:HOH702 4.4 27.1 1.0
D A:TYR91 4.4 14.3 1.0
N A:HIS95 4.5 11.0 1.0
CE1 A:HIS95 4.5 18.6 1.0
HB2 A:GLU136 4.5 20.8 1.0
N A:GLU89 4.6 12.9 1.0
HA A:GLU89 4.6 16.0 1.0
CA A:HIS95 4.6 11.3 1.0
HG22 A:ILE88 4.6 16.3 1.0
CB A:ILE94 4.7 10.7 1.0
C A:HIS93 4.7 12.0 1.0
CG A:GLU136 4.7 18.4 1.0
O A:PHE87 4.7 12.5 1.0
CA A:TYR91 4.7 12.5 1.0
D A:HIS93 4.8 15.2 1.0
HB2 A:TYR91 4.8 15.2 1.0
N A:TYR91 4.8 11.9 1.0
D A:ASN92 4.9 17.5 1.0
HG3 A:GLU136 4.9 22.1 1.0
CA A:HIS93 4.9 12.4 1.0
HG22 A:ILE94 4.9 14.3 1.0
CA A:GLU89 5.0 13.3 1.0

Reference:

E.Oksanen, M.P.Blakeley, M.El-Hajji, U.Ryde, M.Budayova-Spano. The Neutron Structure of Urate Oxidase Resolves A Long-Standing Mechanistic Conundrum and Reveals Unexpected Changes in Protonation. Plos One V. 9 86651 2014.
ISSN: ESSN 1932-6203
PubMed: 24466188
DOI: 10.1371/JOURNAL.PONE.0086651
Page generated: Tue Dec 15 06:55:06 2020

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