Atomistry » Sodium » PDB 4myq-4nij » 4n9v
Atomistry »
  Sodium »
    PDB 4myq-4nij »
      4n9v »

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: Tue Dec 15 06:55:06 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy