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Sodium in PDB 3ld4: Urate Oxidase Complexed with 8-Nitro Xanthine

Enzymatic activity of Urate Oxidase Complexed with 8-Nitro Xanthine

All present enzymatic activity of Urate Oxidase Complexed with 8-Nitro Xanthine:
1.7.3.3;

Protein crystallography data

The structure of Urate Oxidase Complexed with 8-Nitro Xanthine, PDB code: 3ld4 was solved by T.Prange, N.Colloc'h, L.Gabison, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.35
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 78.582, 95.045, 104.371, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 22.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Urate Oxidase Complexed with 8-Nitro Xanthine (pdb code 3ld4). 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 Urate Oxidase Complexed with 8-Nitro Xanthine, PDB code: 3ld4:

Sodium binding site 1 out of 1 in 3ld4

Go back to Sodium Binding Sites List in 3ld4
Sodium binding site 1 out of 1 in the Urate Oxidase Complexed with 8-Nitro Xanthine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Urate Oxidase Complexed with 8-Nitro Xanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:11.8
occ:1.00
O A:ILE94 2.3 11.2 1.0
O A:ILE88 2.3 12.9 1.0
O A:HOH333 2.4 27.2 1.0
O A:TYR91 2.5 11.5 1.0
OE1 A:GLU136 2.6 24.6 1.0
O A:ASN92 3.0 21.1 1.0
C A:ILE88 3.4 10.2 1.0
C A:ILE94 3.4 9.9 1.0
C A:ASN92 3.5 18.6 1.0
CD A:GLU136 3.5 43.3 1.0
C A:TYR91 3.6 13.8 1.0
CA A:ASN92 3.7 14.0 1.0
CA A:ILE88 3.7 9.8 1.0
N A:ILE94 3.9 9.8 1.0
OE2 A:GLU136 3.9 48.8 1.0
ND1 A:HIS95 4.1 16.3 1.0
N A:ASN92 4.1 16.3 1.0
CA A:ILE94 4.2 10.2 1.0
CB A:ILE88 4.2 11.6 1.0
N A:HIS93 4.3 11.4 1.0
N A:HIS95 4.5 9.7 1.0
N A:GLU89 4.5 10.1 1.0
CE1 A:HIS95 4.5 17.1 1.0
CA A:HIS95 4.6 9.5 1.0
CG A:GLU136 4.6 30.4 1.0
O A:PHE87 4.7 10.2 1.0
CB A:ILE94 4.7 8.8 1.0
C A:HIS93 4.7 9.6 1.0
CA A:TYR91 4.8 11.1 1.0
N A:TYR91 4.9 8.4 1.0
CA A:GLU89 4.9 11.1 1.0
CA A:HIS93 5.0 12.6 1.0

Reference:

L.Gabison, M.Chiadmi, M.El Hajji, B.Castro, N.Colloc'h, T.Prange. Near-Atomic Resolution Structures of Urate Oxidase Complexed with Its Substrate and Analogues: the Protonation State of the Ligand. Acta Crystallogr.,Sect.D V. 66 714 2010.
ISSN: ISSN 0907-4449
PubMed: 20516624
DOI: 10.1107/S090744491001142X
Page generated: Tue Dec 15 06:16:44 2020

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