Sodium in PDB 2uzz: X-Ray Structure of N-Methyl-L-Tryptophan Oxidase (Mtox)

The structure of X-Ray Structure of N-Methyl-L-Tryptophan Oxidase (Mtox), PDB code: 2uzz was solved by A.Ilari, A.Fiorillo, S.Franceschini, A.Bonamore, G.Colotti, A.Boffi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 3.2
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	88.188, 89.809, 91.915, 90.00, 104.75, 90.00
R / Rfree (%)	23.6 / 31.3

The binding sites of Sodium atom in the X-Ray Structure of N-Methyl-L-Tryptophan Oxidase (Mtox) (pdb code 2uzz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the X-Ray Structure of N-Methyl-L-Tryptophan Oxidase (Mtox), PDB code: 2uzz:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the X-Ray Structure of N-Methyl-L-Tryptophan Oxidase (Mtox)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of N-Methyl-L-Tryptophan Oxidase (Mtox) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1374 b:3.9 occ:1.00 O A:LEU335 2.9 41.2 1.0 N A:ASP311 3.1 40.7 1.0 N A:GLY337 3.5 41.0 1.0 O3' A:FAD1373 3.6 31.6 1.0 C3' A:FAD1373 3.6 31.5 1.0 CB A:ASP311 3.7 41.0 1.0 O A:THR309 3.7 40.5 1.0 CA A:TYR310 3.8 40.5 1.0 C A:TYR310 3.9 40.5 1.0 CA A:ASP311 4.0 40.9 1.0 CA A:GLY337 4.0 40.9 1.0 C1' A:FAD1373 4.0 31.8 1.0 C A:LEU335 4.0 41.2 1.0 CD1 A:LEU335 4.4 42.0 1.0 C2' A:FAD1373 4.4 31.6 1.0 OG A:SER42 4.4 40.1 1.0 C5' A:FAD1373 4.4 31.1 1.0 C A:SER336 4.5 41.0 1.0 C9 A:FAD1373 4.5 32.4 1.0 CB A:SER42 4.5 40.0 1.0 C A:THR309 4.6 40.5 1.0 CA A:SER336 4.6 41.1 1.0 CD2 A:TYR310 4.7 40.6 1.0 C4' A:FAD1373 4.7 31.5 1.0 N A:TYR310 4.7 40.5 1.0 C A:ASP311 4.8 40.9 1.0 CB A:TYR310 4.8 40.5 1.0 N A:SER336 4.8 41.1 1.0 O2' A:FAD1373 4.8 31.5 1.0 O A:ASP311 4.9 41.0 1.0 CB A:LEU335 4.9 41.3 1.0 C8M A:FAD1373 5.0 32.6 1.0

Sodium binding site 2 out of 4 in the X-Ray Structure of N-Methyl-L-Tryptophan Oxidase (Mtox)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of N-Methyl-L-Tryptophan Oxidase (Mtox) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1374 b:2.0 occ:1.00 O B:LEU335 2.7 41.5 1.0 O3' B:FAD1373 2.9 36.7 1.0 N B:GLY337 3.2 40.8 1.0 N B:ASP311 3.3 40.6 1.0 C3' B:FAD1373 3.6 36.0 1.0 C B:LEU335 3.7 41.4 1.0 CB B:ASP311 3.9 40.8 1.0 CA B:TYR310 3.9 40.5 1.0 CA B:GLY337 3.9 40.8 1.0 C B:TYR310 4.1 40.5 1.0 C1' B:FAD1373 4.1 37.0 1.0 C B:SER336 4.2 41.0 1.0 CA B:SER336 4.2 41.1 1.0 CA B:ASP311 4.2 40.8 1.0 CD1 B:LEU335 4.2 41.7 1.0 O B:THR309 4.2 40.5 1.0 N B:SER336 4.3 41.3 1.0 CD2 B:TYR310 4.5 40.6 1.0 C2' B:FAD1373 4.5 36.4 1.0 CB B:LEU335 4.6 41.4 1.0 C5' B:FAD1373 4.6 33.2 1.0 CB B:TYR310 4.6 40.5 1.0 C B:GLY337 4.7 40.8 1.0 CA B:LEU335 4.8 41.4 1.0 C4' B:FAD1373 4.8 35.0 1.0 C B:ASP311 4.8 40.9 1.0 CG B:TYR310 4.9 40.5 1.0 O B:ASP311 4.9 41.0 1.0 N B:TYR310 5.0 40.5 1.0 C9 B:FAD1373 5.0 39.0 1.0

Sodium binding site 3 out of 4 in the X-Ray Structure of N-Methyl-L-Tryptophan Oxidase (Mtox)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Ray Structure of N-Methyl-L-Tryptophan Oxidase (Mtox) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1372 b:9.3 occ:1.00 O C:LEU335 3.1 41.4 1.0 N C:ASP311 3.2 40.7 1.0 C3' C:FAD1371 3.4 35.9 1.0 O3' C:FAD1371 3.4 35.4 1.0 O C:THR309 3.6 40.6 1.0 CA C:TYR310 3.7 40.5 1.0 N C:GLY337 3.7 41.1 1.0 CB C:ASP311 3.8 40.9 1.0 C C:TYR310 3.9 40.6 1.0 C1' C:FAD1371 4.0 36.7 1.0 CG2 C:THR202 4.1 41.1 1.0 CA C:ASP311 4.1 40.9 1.0 OG C:SER42 4.2 40.5 1.0 C5' C:FAD1371 4.2 36.1 1.0 C C:LEU335 4.3 41.4 1.0 CB C:SER42 4.3 40.4 1.0 C2' C:FAD1371 4.3 36.2 1.0 CA C:GLY337 4.3 41.0 1.0 C4' C:FAD1371 4.4 36.2 1.0 C C:THR309 4.5 40.5 1.0 CD1 C:LEU335 4.6 42.1 1.0 N C:TYR310 4.6 40.5 1.0 C9 C:FAD1371 4.6 37.4 1.0 CD2 C:TYR310 4.7 40.7 1.0 CB C:TYR310 4.7 40.5 1.0 C C:SER336 4.8 41.1 1.0 CA C:SER336 4.9 41.2 1.0 O2' C:FAD1371 4.9 36.0 1.0 CG C:TYR310 5.0 40.5 1.0 N C:SER336 5.0 41.3 1.0

Sodium binding site 4 out of 4 in the X-Ray Structure of N-Methyl-L-Tryptophan Oxidase (Mtox)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of X-Ray Structure of N-Methyl-L-Tryptophan Oxidase (Mtox) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1373 b:2.0 occ:1.00 O D:LEU335 2.9 41.4 1.0 O3' D:FAD1372 3.0 33.9 1.0 N D:ASP311 3.1 40.6 1.0 N D:GLY337 3.3 41.0 1.0 C3' D:FAD1372 3.6 34.0 1.0 CA D:TYR310 3.7 40.5 1.0 C D:LEU335 3.9 41.3 1.0 CB D:ASP311 3.9 40.7 1.0 C D:TYR310 3.9 40.5 1.0 O D:THR309 3.9 40.7 1.0 CA D:GLY337 3.9 40.9 1.0 C1' D:FAD1372 4.0 36.7 1.0 CA D:ASP311 4.1 40.6 1.0 CD2 D:TYR310 4.2 40.3 1.0 C D:SER336 4.3 41.1 1.0 CA D:SER336 4.3 41.1 1.0 CB D:TYR310 4.4 40.5 1.0 C2' D:FAD1372 4.4 35.4 1.0 N D:SER336 4.4 41.2 1.0 CG D:TYR310 4.6 40.5 1.0 C D:GLY337 4.6 40.8 1.0 N D:TYR310 4.7 40.6 1.0 CD1 D:LEU335 4.7 41.8 1.0 C D:THR309 4.7 40.7 1.0 C5' D:FAD1372 4.7 31.2 1.0 C9 D:FAD1372 4.7 39.2 1.0 C D:ASP311 4.8 40.6 1.0 C4' D:FAD1372 4.8 32.4 1.0 CB D:LEU335 4.9 41.3 1.0 CB D:SER42 5.0 40.1 1.0 CA D:LEU335 5.0 41.3 1.0

A.Ilari, A.Bonamore, S.Franceschini, A.Fiorillo, A.Boffi, G.Colotti. The X-Ray Structure of N-Methyltryptophan Oxidase Reveals the Structural Determinants of Substrate Specificity. Proteins V. 71 2065 2008.
ISSN: ISSN 0887-3585
PubMed: 18186483
DOI: 10.1002/PROT.21898