Sodium in PDB 5xao: Crystal Structure of Phaeospaeria Nodrum Fructosyl Peptide Oxidase Mutant ASN56ALA in Complexes with Sodium and Chloride Ions

The structure of Crystal Structure of Phaeospaeria Nodrum Fructosyl Peptide Oxidase Mutant ASN56ALA in Complexes with Sodium and Chloride Ions, PDB code: 5xao was solved by H.Yoshida, S.Kamitori, K.Sode, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.64 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.119, 109.065, 95.017, 90.00, 98.83, 90.00
R / Rfree (%)	20.9 / 26.6

The structure of Crystal Structure of Phaeospaeria Nodrum Fructosyl Peptide Oxidase Mutant ASN56ALA in Complexes with Sodium and Chloride Ions also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Sodium atom in the Crystal Structure of Phaeospaeria Nodrum Fructosyl Peptide Oxidase Mutant ASN56ALA in Complexes with Sodium and Chloride Ions (pdb code 5xao). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Phaeospaeria Nodrum Fructosyl Peptide Oxidase Mutant ASN56ALA in Complexes with Sodium and Chloride Ions, PDB code: 5xao:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Phaeospaeria Nodrum Fructosyl Peptide Oxidase Mutant ASN56ALA in Complexes with Sodium and Chloride Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Phaeospaeria Nodrum Fructosyl Peptide Oxidase Mutant ASN56ALA in Complexes with Sodium and Chloride Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Na506 b:33.1 occ:1.00 O A:ASN53 2.2 32.7 1.0 O A:HOH700 2.2 36.8 1.0 O A:HOH842 2.4 34.6 1.0 O A:HOH655 2.6 29.1 1.0 O A:HOH851 2.6 41.1 1.0 C A:ASN53 3.4 27.2 1.0 O A:SER48 3.9 32.7 1.0 O A:HOH728 4.0 34.3 1.0 CB A:ASP54 4.1 54.4 1.0 CA A:ASP54 4.1 42.5 1.0 N A:ASP54 4.2 36.1 1.0 ND2 A:ASN53 4.2 27.6 1.0 CG A:ASN53 4.2 27.8 1.0 CB A:ASN53 4.3 24.1 1.0 CA A:ASN53 4.5 24.8 1.0 OH A:TYR237 4.5 30.3 1.0 O A:HOH605 4.6 32.1 1.0 O A:HOH804 4.6 32.2 1.0 O A:HOH662 4.6 30.0 1.0 OD2 A:ASP54 4.6 59.5 1.0 OD1 A:ASN53 4.7 22.5 1.0 O A:SER50 4.8 24.8 1.0 O A:HOH734 4.8 38.9 1.0 CG A:ASP54 4.8 60.1 1.0 C A:SER48 5.0 28.9 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Phaeospaeria Nodrum Fructosyl Peptide Oxidase Mutant ASN56ALA in Complexes with Sodium and Chloride Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Phaeospaeria Nodrum Fructosyl Peptide Oxidase Mutant ASN56ALA in Complexes with Sodium and Chloride Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Na507 b:43.6 occ:1.00 O A:PRO137 2.3 37.2 1.0 O A:LEU139 2.4 34.5 1.0 C A:PRO137 3.5 42.6 1.0 C A:LEU139 3.6 32.9 1.0 C A:LEU138 4.0 37.0 1.0 CA A:LEU138 4.2 39.7 1.0 N A:LEU139 4.2 32.4 1.0 O A:LEU138 4.3 36.9 1.0 CD2 A:LEU133 4.3 41.9 1.0 N A:LEU138 4.3 41.1 1.0 CA A:SER140 4.4 37.2 1.0 N A:SER140 4.4 29.2 1.0 CA A:PRO137 4.6 49.5 1.0 CA A:LEU139 4.6 27.4 1.0 N A:ARG141 4.8 36.0 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Phaeospaeria Nodrum Fructosyl Peptide Oxidase Mutant ASN56ALA in Complexes with Sodium and Chloride Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Phaeospaeria Nodrum Fructosyl Peptide Oxidase Mutant ASN56ALA in Complexes with Sodium and Chloride Ions within 5.0Å range: probe atom residue distance (Å) B Occ C:Na505 b:50.3 occ:1.00 O C:HOH655 2.1 43.7 1.0 O C:LEU139 2.2 33.6 1.0 O C:PRO137 2.7 32.1 1.0 C C:LEU139 3.4 31.8 1.0 C C:PRO137 3.8 33.4 1.0 C C:LEU138 3.8 35.0 1.0 O C:LEU138 4.0 32.9 1.0 CA C:SER140 4.1 37.7 1.0 N C:LEU139 4.1 26.6 1.0 N C:SER140 4.1 30.8 1.0 CA C:LEU138 4.1 34.2 1.0 CD2 C:LEU133 4.3 32.5 1.0 CA C:LEU139 4.4 30.1 1.0 N C:LEU138 4.4 34.9 1.0 N C:ARG141 4.6 36.4 1.0 O C:HOH967 4.6 51.0 1.0 C C:SER140 4.9 35.7 1.0 CA C:PRO137 4.9 35.5 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Phaeospaeria Nodrum Fructosyl Peptide Oxidase Mutant ASN56ALA in Complexes with Sodium and Chloride Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Phaeospaeria Nodrum Fructosyl Peptide Oxidase Mutant ASN56ALA in Complexes with Sodium and Chloride Ions within 5.0Å range: probe atom residue distance (Å) B Occ C:Na506 b:36.3 occ:1.00 O C:HOH908 2.4 36.1 1.0 O C:ASN53 2.4 26.7 1.0 O C:HOH736 2.5 31.8 1.0 O C:HOH661 2.5 37.1 1.0 O C:HOH606 2.7 44.8 1.0 O C:HOH958 2.8 39.0 1.0 C C:ASN53 3.6 27.7 1.0 O C:SER48 3.9 27.4 1.0 O C:HOH718 4.2 35.9 1.0 CB C:ASN53 4.2 25.0 1.0 OH C:TYR237 4.3 27.5 1.0 O C:HOH697 4.3 49.1 1.0 CG C:ASN53 4.3 27.0 1.0 O C:HOH831 4.4 33.0 1.0 ND2 C:ASN53 4.5 25.9 1.0 CA C:ASN53 4.5 21.5 1.0 N C:ASP54 4.5 29.0 1.0 CA C:ASP54 4.6 37.1 1.0 OD2 C:ASP54 4.6 67.2 1.0 O C:SER50 4.6 22.8 1.0 CG C:ASP54 4.7 57.0 1.0 OD1 C:ASN53 4.8 31.3 1.0 O C:HOH933 4.8 23.0 1.0 OD1 C:ASP54 4.9 76.4 1.0

T.Shimasaki, H.Yoshida, S.Kamitori, K.Sode. X-Ray Structures of Fructosyl Peptide Oxidases Revealing Residues Responsible For Gating Oxygen Access in the Oxidative Half Reaction Sci Rep V. 7 2790 2017.
ISSN: ESSN 2045-2322
PubMed: 28584265
DOI: 10.1038/S41598-017-02657-5