Sodium in PDB 2ymw: Structure of the Epsilon-Lysine Oxidase From Marinomonas Mediterranea

All present enzymatic activity of Structure of the Epsilon-Lysine Oxidase From Marinomonas Mediterranea:
1.4.3.20;

The structure of Structure of the Epsilon-Lysine Oxidase From Marinomonas Mediterranea, PDB code: 2ymw was solved by F.J.Medrano, A.Romero, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.28 / 2.41
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.680, 127.883, 106.897, 90.00, 107.18, 90.00
R / Rfree (%)	19.19 / 27.92

The binding sites of Sodium atom in the Structure of the Epsilon-Lysine Oxidase From Marinomonas Mediterranea (pdb code 2ymw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of the Epsilon-Lysine Oxidase From Marinomonas Mediterranea, PDB code: 2ymw:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of the Epsilon-Lysine Oxidase From Marinomonas Mediterranea


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Epsilon-Lysine Oxidase From Marinomonas Mediterranea within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1687 b:26.9 occ:1.00 OD1 A:ASP250 2.7 41.5 1.0 O A:ILE255 2.9 28.4 1.0 O A:ALA252 3.1 32.0 1.0 O A:PRO583 3.2 34.4 1.0 OD2 A:ASP250 3.3 34.8 1.0 CG A:ASP250 3.4 38.0 1.0 C A:PRO583 3.6 34.2 1.0 NE2 A:GLN584 3.7 24.9 1.0 CB A:PRO583 3.7 29.5 1.0 C A:ALA252 4.0 31.7 1.0 C A:ILE255 4.1 29.2 1.0 CD A:GLN584 4.2 41.8 1.0 CA A:PRO583 4.2 28.2 1.0 N A:GLN584 4.2 29.0 1.0 CA A:PRO253 4.5 27.9 1.0 CG A:GLN584 4.5 35.3 1.0 CA A:GLN584 4.5 28.7 1.0 N A:PRO253 4.6 28.7 1.0 ND2 A:ASN257 4.7 47.8 1.0 O A:PRO253 4.7 30.2 1.0 C A:PRO253 4.7 31.9 1.0 OE1 A:GLN584 4.9 40.8 1.0 CB A:ASP250 4.9 29.2 1.0 CB A:ALA252 4.9 26.1 1.0 CA A:ALA252 4.9 25.9 1.0 CA A:ILE255 4.9 24.6 1.0 N A:ILE255 5.0 25.5 1.0

Sodium binding site 2 out of 4 in the Structure of the Epsilon-Lysine Oxidase From Marinomonas Mediterranea


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Epsilon-Lysine Oxidase From Marinomonas Mediterranea within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1688 b:27.7 occ:1.00 O A:THR517 2.8 18.1 1.0 O A:SER585 3.0 24.6 1.0 N A:PRO582 3.4 20.8 1.0 N A:TRQ581 3.5 17.7 1.0 C A:TRQ581 3.6 23.2 1.0 CA A:PRO582 3.7 19.9 1.0 C A:THR517 3.7 18.0 1.0 CD A:PRO582 3.7 21.6 1.0 O A:CYS516 3.8 26.2 1.0 N A:TRP580 3.9 19.9 1.0 CA A:THR517 3.9 16.2 1.0 O A:TRQ581 4.0 21.9 1.0 CG A:PRO582 4.1 25.6 1.0 CD1 A:TYR579 4.1 19.6 1.0 CA A:TRQ581 4.2 19.0 1.0 C A:SER585 4.2 24.8 1.0 C A:CYS516 4.2 25.8 1.0 C A:TRP580 4.3 19.9 1.0 N A:THR517 4.3 18.6 1.0 CA A:TRP580 4.3 19.0 1.0 CB A:PRO582 4.4 21.4 1.0 CB A:TRP580 4.4 17.7 1.0 CB A:TRP587 4.5 23.1 1.0 OG A:SER585 4.6 28.8 1.0 CB A:TYR579 4.6 18.2 1.0 CB A:SER585 4.6 23.4 1.0 C A:TYR579 4.8 22.8 1.0 C A:PRO582 4.8 25.9 1.0 CG A:TYR579 4.9 18.5 1.0 SG A:CYS516 4.9 27.4 1.0 CA A:SER585 4.9 23.1 1.0 N A:ILE518 4.9 16.8 1.0 CA A:TYR579 4.9 17.6 1.0

Sodium binding site 3 out of 4 in the Structure of the Epsilon-Lysine Oxidase From Marinomonas Mediterranea


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the Epsilon-Lysine Oxidase From Marinomonas Mediterranea within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1687 b:27.4 occ:1.00 O B:ALA252 2.5 44.4 1.0 OE1 B:GLN584 2.5 59.2 1.0 O B:ILE255 2.7 37.8 1.0 O B:PRO583 2.8 42.0 1.0 OD1 B:ASP250 2.8 56.1 1.0 C B:ALA252 3.4 45.1 1.0 OD2 B:ASP250 3.5 60.9 1.0 CG B:ASP250 3.5 54.1 1.0 CD B:GLN584 3.6 64.2 1.0 C B:PRO583 3.6 41.6 1.0 C B:ILE255 3.8 37.5 1.0 CB B:PRO583 4.0 37.9 1.0 CA B:PRO253 4.0 40.9 1.0 N B:PRO253 4.1 41.6 1.0 CA B:ALA252 4.3 39.9 1.0 C B:PRO253 4.3 42.2 1.0 CA B:PRO583 4.3 36.4 1.0 CB B:ALA252 4.4 40.4 1.0 N B:GLN584 4.4 36.1 1.0 NE2 B:GLN584 4.4 46.7 1.0 O B:PRO253 4.4 40.1 1.0 N B:ILE255 4.4 33.7 1.0 CG B:GLN584 4.4 54.2 1.0 CA B:GLN584 4.5 34.9 1.0 CA B:ILE255 4.5 33.6 1.0 N B:ALA252 4.6 40.5 1.0 CB B:ILE255 4.7 37.0 1.0 N B:VAL256 4.9 32.4 1.0 CG B:PRO583 5.0 42.1 1.0 CB B:ASP250 5.0 40.5 1.0

Sodium binding site 4 out of 4 in the Structure of the Epsilon-Lysine Oxidase From Marinomonas Mediterranea


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the Epsilon-Lysine Oxidase From Marinomonas Mediterranea within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1688 b:30.9 occ:1.00 O B:THR517 2.9 36.3 1.0 O B:SER585 3.1 30.3 1.0 N B:PRO582 3.4 21.4 1.0 N B:TRQ581 3.4 28.0 1.0 C B:TRQ581 3.5 24.9 1.0 O B:CYS516 3.6 33.8 1.0 CA B:PRO582 3.7 22.6 1.0 CD B:PRO582 3.7 22.7 1.0 C B:THR517 3.9 36.8 1.0 N B:TRP580 3.9 30.4 1.0 O B:TRQ581 3.9 22.1 1.0 CA B:TRQ581 4.1 25.1 1.0 CA B:THR517 4.1 30.7 1.0 CB B:TRP580 4.1 30.6 1.0 C B:CYS516 4.2 34.2 1.0 CB B:SER585 4.2 30.4 1.0 C B:SER585 4.2 29.8 1.0 C B:TRP580 4.2 34.1 1.0 CG B:PRO582 4.2 27.9 1.0 CA B:TRP580 4.3 31.2 1.0 N B:THR517 4.4 30.6 1.0 CB B:PRO582 4.5 24.4 1.0 CD2 B:TYR579 4.5 25.7 1.0 CB B:TYR579 4.6 25.8 1.0 SG B:CYS516 4.6 34.9 1.0 CB B:TRP587 4.7 25.8 1.0 OG B:SER585 4.7 43.9 1.0 CA B:SER585 4.8 28.2 1.0 C B:PRO582 4.8 34.3 1.0 CB B:TRQ581 4.8 24.2 1.0 C B:TYR579 4.9 30.8 1.0 O B:PRO582 5.0 35.7 1.0

F.J.Medrano, A.Sanchez-Amat, A.Romero. Structure of the Epsilon-Lysine Oxidase From Marinomonas Mediterranea To Be Published.