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Sodium in PDB 4n9m: Joint Neutron/X-Ray Structure of Urate Oxidase in Complex with 8- Hydroxyxanthine

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

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

Protein crystallography data

The structure of Joint Neutron/X-Ray Structure of Urate Oxidase in Complex with 8- Hydroxyxanthine, PDB code: 4n9m 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 / 2.30
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 80.180, 96.260, 105.510, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 18.9

Other elements in 4n9m:

The structure of Joint Neutron/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 Joint Neutron/X-Ray Structure of Urate Oxidase in Complex with 8- Hydroxyxanthine (pdb code 4n9m). 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- Hydroxyxanthine, PDB code: 4n9m:

Sodium binding site 1 out of 1 in 4n9m

Go back to Sodium Binding Sites List in 4n9m
Sodium binding site 1 out of 1 in the Joint Neutron/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 Joint Neutron/X-Ray Structure of Urate Oxidase in Complex with 8- Hydroxyxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:43.7
occ:1.00
 OE2 A:GLU136 2.9 34.0 1.0
O A:TYR91 2.9 16.6 1.0
D2 A:DOD586 2.9 43.4 1.0
DD1 A:HIS95 3.0 25.6 1.0
O A:ILE94 3.0 31.5 1.0
D1 A:DOD586 3.0 45.1 1.0
O A:ILE88 3.0 22.3 1.0
HA A:ASN92 3.1 23.2 1.0
O A:ASN92 3.1 32.5 1.0
O A:DOD586 3.2 66.1 1.0
C A:ASN92 3.4 21.4 1.0
D A:ILE94 3.4 14.8 1.0
ND1 A:HIS95 3.5 25.3 1.0
CD A:GLU136 3.6 52.1 1.0
C A:ILE94 3.6 18.4 1.0
HA A:HIS95 3.6 18.7 1.0
CA A:ASN92 3.6 31.6 1.0
OE1 A:GLU136 3.7 59.2 1.0
HA A:ILE88 3.7 17.8 1.0
HE1 A:HIS95 3.8 27.1 1.0
N A:ILE94 3.8 16.4 1.0
C A:TYR91 3.9 26.9 1.0
CE1 A:HIS95 4.0 25.8 1.0
HB A:ILE88 4.0 23.8 1.0
C A:ILE88 4.0 13.6 1.0
N A:HIS93 4.1 19.2 1.0
N A:ASN92 4.2 20.2 1.0
CA A:ILE94 4.3 17.5 1.0
CA A:ILE88 4.3 16.8 1.0
N A:HIS95 4.4 11.3 1.0
HB A:ILE94 4.4 15.5 1.0
CA A:HIS95 4.4 12.1 1.0
C A:HIS93 4.5 18.6 1.0
HB2 A:GLU136 4.6 24.9 1.0
CG A:HIS95 4.6 23.7 1.0
D A:HIS93 4.6 17.1 1.0
CB A:ILE88 4.7 18.6 1.0
CA A:HIS93 4.7 15.7 1.0
HA A:HIS93 4.7 23.6 1.0
CB A:ILE94 4.9 10.2 1.0
CG A:GLU136 4.9 30.6 1.0
HG22 A:ILE88 4.9 17.4 1.0
CB A:ASN92 5.0 22.7 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 17:09:24 2024

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