Sodium in PDB 7a0l: Joint Neutron/X-Ray Room Temperature Structure of Perdeuterated Aspergillus Flavus Urate Oxidase in Complex with the 8-Azaxanthine Inhibitor and Catalytic Water Bound in the Peroxo Hole

Enzymatic activity of Joint Neutron/X-Ray Room Temperature Structure of Perdeuterated Aspergillus Flavus Urate Oxidase in Complex with the 8-Azaxanthine Inhibitor and Catalytic Water Bound in the Peroxo Hole

All present enzymatic activity of Joint Neutron/X-Ray Room Temperature Structure of Perdeuterated Aspergillus Flavus Urate Oxidase in Complex with the 8-Azaxanthine Inhibitor and Catalytic Water Bound in the Peroxo Hole:
1.7.3.3;

Protein crystallography data

The structure of Joint Neutron/X-Ray Room Temperature Structure of Perdeuterated Aspergillus Flavus Urate Oxidase in Complex with the 8-Azaxanthine Inhibitor and Catalytic Water Bound in the Peroxo Hole, PDB code: 7a0l was solved by L.Mcgregor, S.Bui, M.P.Blakeley, R.A.Steiner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 1.33
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 80.628, 96.130, 105.397, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Sodium Binding Sites:

The binding sites of Sodium atom in the Joint Neutron/X-Ray Room Temperature Structure of Perdeuterated Aspergillus Flavus Urate Oxidase in Complex with the 8-Azaxanthine Inhibitor and Catalytic Water Bound in the Peroxo Hole (pdb code 7a0l). 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 Room Temperature Structure of Perdeuterated Aspergillus Flavus Urate Oxidase in Complex with the 8-Azaxanthine Inhibitor and Catalytic Water Bound in the Peroxo Hole, PDB code: 7a0l:

Sodium binding site 1 out of 1 in 7a0l

Go back to Sodium Binding Sites List in 7a0l
Sodium binding site 1 out of 1 in the Joint Neutron/X-Ray Room Temperature Structure of Perdeuterated Aspergillus Flavus Urate Oxidase in Complex with the 8-Azaxanthine Inhibitor and Catalytic Water Bound in the Peroxo Hole


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 Room Temperature Structure of Perdeuterated Aspergillus Flavus Urate Oxidase in Complex with the 8-Azaxanthine Inhibitor and Catalytic Water Bound in the Peroxo Hole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:25.5
occ:1.00
 O A:HOH680 2.3 42.6 0.8
O A:ILE94 2.4 20.7 1.0
O A:ILE88 2.4 23.6 1.0
D2 A:HOH680 2.4 50.0 0.8
D1 A:HOH680 2.5 50.0 0.8
O A:TYR91 2.5 21.7 1.0
OE2 A:GLU136 2.7 33.4 1.0
DA A:ASN92 3.1 29.3 0.5
DA A:ASN92 3.1 29.9 0.5
DA A:ILE88 3.2 24.0 1.0
O A:ASN92 3.3 30.4 1.0
C A:ILE88 3.4 21.5 1.0
CD A:GLU136 3.5 36.3 1.0
DD1 A:HIS95 3.5 29.1 1.0
C A:ILE94 3.5 19.2 1.0
DB A:ILE88 3.5 26.5 1.0
C A:ASN92 3.6 24.2 1.0
C A:TYR91 3.6 20.8 1.0
D A:ILE94 3.6 22.7 1.0
CA A:ASN92 3.7 24.8 0.5
CA A:ASN92 3.7 25.2 0.5
OE1 A:GLU136 3.7 42.3 1.0
CA A:ILE88 3.7 20.2 1.0
DA A:HIS95 3.8 22.1 1.0
O A:HOH654 4.0 56.2 1.0
ND1 A:HIS95 4.0 24.5 1.0
N A:ILE94 4.0 19.1 1.0
N A:ASN92 4.1 23.0 1.0
DB A:ILE94 4.1 22.0 1.0
O A:HOH748 4.2 56.2 1.0
CB A:ILE88 4.2 22.4 1.0
CA A:ILE94 4.3 18.0 1.0
DE1 A:HIS95 4.3 32.0 1.0
N A:HIS93 4.4 20.0 1.0
D A:TYR91 4.5 24.2 1.0
CE1 A:HIS95 4.5 26.9 1.0
N A:HIS95 4.5 18.4 1.0
DB2 A:GLU136 4.6 35.7 1.0
N A:GLU89 4.6 20.9 1.0
CA A:HIS95 4.6 18.6 1.0
DA A:GLU89 4.6 26.7 1.0
DG22 A:ILE88 4.7 29.0 1.0
O A:PHE87 4.7 20.5 1.0
CG A:GLU136 4.7 34.4 1.0
CB A:ILE94 4.8 18.5 1.0
CA A:TYR91 4.8 20.6 1.0
D A:HIS93 4.8 23.8 1.0
C A:HIS93 4.8 20.1 1.0
DG3 A:GLU136 4.8 40.5 1.0
N A:TYR91 4.9 20.4 1.0
DB2 A:TYR91 4.9 23.5 1.0
D A:ASN92 5.0 27.2 0.5
D A:ASN92 5.0 27.2 0.5
DG22 A:ILE94 5.0 23.1 1.0
CG A:HIS95 5.0 21.9 1.0

Reference:

L.Mc Gregor, T.Foldes, S.Bui, M.Moulin, N.Coquelle, M.P.Blakeley, E.Rosta, R.A.Steiner. Joint Neutron-X-Ray Crystal Structure of A Mechanistically Relevant Complex of Perdeuterated Urate Oxidase and Simulations Provide Insight Into the Hydration Step of Catalysis Iucrj V. 8 2021.
ISSN: ESSN 2052-2525
DOI: 10.1107/S2052252520013615
Page generated: Tue Dec 15 17:17:23 2020

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