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Sodium in PDB 5frc: Structure of Urate Oxidase Prepared By the 'Soak-and-Freeze' Method Under 42 Bar of Oxygen Pressure

Enzymatic activity of Structure of Urate Oxidase Prepared By the 'Soak-and-Freeze' Method Under 42 Bar of Oxygen Pressure

All present enzymatic activity of Structure of Urate Oxidase Prepared By the 'Soak-and-Freeze' Method Under 42 Bar of Oxygen Pressure:
1.7.3.3;

Protein crystallography data

The structure of Structure of Urate Oxidase Prepared By the 'Soak-and-Freeze' Method Under 42 Bar of Oxygen Pressure, PDB code: 5frc was solved by B.Lafumat, C.Mueller-Dieckmann, N.Colloc'h, T.Prange, A.Royant, P.Van Derlinden, P.Carpentier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.68 / 1.44
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 80.898, 95.351, 104.672, 90.00, 90.00, 90.00
R / Rfree (%) 14.2 / 16.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Urate Oxidase Prepared By the 'Soak-and-Freeze' Method Under 42 Bar of Oxygen Pressure (pdb code 5frc). 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 Structure of Urate Oxidase Prepared By the 'Soak-and-Freeze' Method Under 42 Bar of Oxygen Pressure, PDB code: 5frc:

Sodium binding site 1 out of 1 in 5frc

Go back to Sodium Binding Sites List in 5frc
Sodium binding site 1 out of 1 in the Structure of Urate Oxidase Prepared By the 'Soak-and-Freeze' Method Under 42 Bar of Oxygen Pressure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Urate Oxidase Prepared By the 'Soak-and-Freeze' Method Under 42 Bar of Oxygen Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:25.6
occ:1.00
 O A:HOH2143 2.3 52.3 1.0
O A:ILE88 2.3 24.4 1.0
O A:ILE94 2.3 22.3 1.0
O A:TYR91 2.4 25.0 1.0
O A:HOH2129 2.4 38.2 1.0
OE1 A:GLU136 2.8 59.2 1.0
C A:ILE88 3.3 22.5 1.0
O A:ASN92 3.4 31.6 1.0
C A:ILE94 3.4 21.7 1.0
C A:TYR91 3.5 24.7 1.0
C A:ASN92 3.6 29.5 1.0
O A:HOH2144 3.7 49.9 1.0
CA A:ILE88 3.7 21.1 1.0
CA A:ASN92 3.8 31.4 1.0
CD A:GLU136 3.9 60.1 1.0
N A:ILE94 3.9 22.8 1.0
N A:ASN92 4.1 27.1 1.0
CA A:ILE94 4.2 21.4 1.0
CB A:ILE88 4.2 22.5 1.0
ND1 A:HIS95 4.2 34.8 1.0
O A:HOH2130 4.3 50.0 1.0
OE2 A:GLU136 4.3 70.2 1.0
N A:HIS93 4.4 26.1 1.0
N A:HIS95 4.4 21.5 1.0
N A:GLU89 4.5 22.0 1.0
CA A:HIS95 4.6 22.2 1.0
CB A:ILE94 4.6 21.0 1.0
CA A:TYR91 4.6 23.1 1.0
O A:PHE87 4.7 22.7 1.0
N A:TYR91 4.7 24.3 1.0
C A:HIS93 4.8 23.3 1.0
CE1 A:HIS95 4.8 34.5 1.0
CA A:GLU89 4.9 23.5 1.0

Reference:

B.Lafumat, C.Mueller-Dieckmann, N.Colloc'h, T.Prange, A.Royant, P.Van Der Linden, P.Carpentier. Gas-Sensitive Biological Crystals Processed in Pressurized Oxygen and Krypton Atmospheres: Deciphering Gas Channels in Proteins Using A Novel `Soak-and-Freeze' Methodology. J.Appl.Crystallogr. V. 49 1478 2016.
ISSN: ISSN 0021-8898
DOI: 10.1107/S1600576716010992
Page generated: Mon Oct 7 21:05:10 2024

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