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Sodium in PDB 4n9v: High Resolution X-Ray Structure of Urate Oxidase in Complex with 8- Azaxanthine

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

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

Protein crystallography data

The structure of High Resolution X-Ray Structure of Urate Oxidase in Complex with 8- Azaxanthine, PDB code: 4n9v 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) 35.16 / 1.10
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 79.800, 95.080, 104.490, 90.00, 90.00, 90.00
R / Rfree (%) 13.9 / 15.3

Other elements in 4n9v:

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

Zinc (Zn) 2 atoms
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- Azaxanthine (pdb code 4n9v). 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- Azaxanthine, PDB code: 4n9v:

Sodium binding site 1 out of 1 in 4n9v

Go back to Sodium Binding Sites List in 4n9v
Sodium binding site 1 out of 1 in the High Resolution X-Ray Structure of Urate Oxidase in Complex with 8- Azaxanthine


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- Azaxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:13.0
occ:1.00
 O A:ILE94 2.3 11.2 1.0
O A:ILE88 2.4 13.0 1.0
O A:DOD575 2.4 18.0 1.0
O A:TYR91 2.5 12.3 1.0
OE1 A:GLU136 2.5 17.9 0.9
O A:ASN92 3.0 16.5 1.0
HA A:ASN92 3.1 17.7 1.0
HA A:ILE88 3.2 13.3 1.0
C A:ILE88 3.4 11.2 1.0
C A:ASN92 3.4 14.1 1.0
CD A:GLU136 3.4 19.4 0.8
C A:ILE94 3.5 9.7 1.0
D A:ILE94 3.5 13.1 1.0
C A:TYR91 3.5 11.8 1.0
HB A:ILE88 3.6 14.9 1.0
CA A:ASN92 3.7 14.7 1.0
CA A:ILE88 3.8 11.1 1.0
OE2 A:GLU136 3.8 19.2 0.5
HA A:HIS95 3.8 13.2 1.0
N A:ILE94 3.9 10.9 1.0
O A:DOD977 4.0 33.7 1.0
ND1 A:HIS95 4.0 16.3 1.0
N A:ASN92 4.0 12.7 1.0
HB A:ILE94 4.1 12.5 1.0
O A:DOD811 4.1 27.7 1.0
CB A:ILE88 4.2 12.4 1.0
CA A:ILE94 4.2 10.1 1.0
N A:HIS93 4.3 12.8 1.0
O A:DOD728 4.3 24.0 1.0
HE1 A:HIS95 4.4 21.7 1.0
D A:TYR91 4.4 13.9 1.0
N A:HIS95 4.4 10.0 1.0
HB2 A:GLU136 4.5 26.5 1.0
CE1 A:HIS95 4.5 18.1 1.0
HA A:GLU89 4.5 15.3 1.0
N A:GLU89 4.6 11.7 1.0
CA A:HIS95 4.6 11.0 1.0
HG22 A:ILE88 4.6 18.4 1.0
CB A:ILE94 4.7 10.4 1.0
CG A:GLU136 4.7 22.8 1.0
C A:HIS93 4.7 11.6 1.0
CA A:TYR91 4.7 11.7 1.0
O A:PHE87 4.7 11.3 1.0
D A:HIS93 4.8 15.3 1.0
HG3 A:GLU136 4.8 27.4 1.0
N A:TYR91 4.8 11.6 1.0
HB2 A:TYR91 4.8 14.2 1.0
D A:ASN92 4.9 15.3 1.0
CA A:HIS93 4.9 12.2 1.0
CA A:GLU89 5.0 12.8 1.0
HG22 A:ILE94 5.0 13.8 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: Mon Oct 7 17:09:48 2024

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