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Sodium in PDB 4n3m: Joint Neutron/X-Ray Structure of Urate Oxidase in Complex with 8- Azaxanthine

Enzymatic activity of Joint Neutron/X-Ray Structure of Urate Oxidase in Complex with 8- Azaxanthine

All present enzymatic activity of Joint Neutron/X-Ray Structure of Urate Oxidase in Complex with 8- Azaxanthine:
1.7.3.3;

Protein crystallography data

The structure of Joint Neutron/X-Ray Structure of Urate Oxidase in Complex with 8- Azaxanthine, PDB code: 4n3m 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) N/A / 1.90
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 80.200, 96.200, 105.500, 90.00, 90.00, 90.00
R / Rfree (%) 14 / 17.2

Other elements in 4n3m:

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

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Joint Neutron/X-Ray Structure of Urate Oxidase in Complex with 8- Azaxanthine (pdb code 4n3m). 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 Joint Neutron/X-Ray Structure of Urate Oxidase in Complex with 8- Azaxanthine, PDB code: 4n3m:

Sodium binding site 1 out of 1 in 4n3m

Go back to Sodium Binding Sites List in 4n3m
Sodium binding site 1 out of 1 in the Joint Neutron/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 Joint Neutron/X-Ray Structure of Urate Oxidase in Complex with 8- Azaxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:25.8
occ:1.00
 O A:ILE88 2.3 26.8 1.0
O A:ILE94 2.3 21.8 1.0
O A:TYR91 2.4 22.6 1.0
O A:DOD659 2.4 33.6 1.0
OE1 A:GLU136 2.7 35.7 1.0
HA A:ILE88 3.2 23.5 1.0
HA A:ASN92 3.2 28.9 1.0
C A:ILE88 3.3 23.1 1.0
O A:ASN92 3.3 32.0 1.0
C A:ILE94 3.5 20.9 1.0
C A:TYR91 3.5 25.1 1.0
HB A:ILE88 3.5 27.3 1.0
DD1 A:HIS95 3.5 31.5 1.0
CD A:GLU136 3.5 43.9 1.0
C A:ASN92 3.6 26.9 1.0
CA A:ILE88 3.7 24.1 1.0
D A:ILE94 3.7 25.3 1.0
OE2 A:GLU136 3.8 53.8 1.0
HA A:HIS95 3.8 22.6 1.0
CA A:ASN92 3.8 27.8 1.0
HB A:ILE94 4.1 22.4 1.0
N A:ILE94 4.1 23.5 1.0
CB A:ILE88 4.1 26.7 1.0
N A:ASN92 4.1 24.9 1.0
ND1 A:HIS95 4.1 33.2 1.0
CA A:ILE94 4.3 21.8 1.0
D A:TYR91 4.4 24.8 0.8
N A:HIS93 4.4 23.1 1.0
O A:DOD658 4.4 44.1 1.0
N A:GLU89 4.5 23.0 1.0
N A:HIS95 4.5 17.9 1.0
HA A:GLU89 4.5 26.8 1.0
HE1 A:HIS95 4.5 32.2 1.0
CA A:HIS95 4.6 21.0 1.0
HB2 A:GLU136 4.6 27.1 1.0
CE1 A:HIS95 4.7 30.1 1.0
O A:PHE87 4.7 22.5 1.0
CB A:ILE94 4.7 20.3 1.0
CA A:TYR91 4.7 26.4 1.0
N A:TYR91 4.8 22.5 1.0
HG22 A:ILE88 4.8 21.2 1.0
D A:HIS93 4.8 23.7 1.0
C A:HIS93 4.9 23.3 1.0
HB2 A:TYR91 4.9 24.1 1.0
HG22 A:ILE94 4.9 21.4 1.0
CG A:GLU136 4.9 35.0 1.0
CA A:GLU89 4.9 25.1 1.0
D A:ASN92 5.0 27.5 0.9
N A:ILE88 5.0 19.4 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: Sun Aug 17 20:43:55 2025

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