Sodium in PDB 3kii: Agao 5-Phenoxy-2,3-Pentadienylamine Complex

All present enzymatic activity of Agao 5-Phenoxy-2,3-Pentadienylamine Complex:
1.4.3.21;

The structure of Agao 5-Phenoxy-2,3-Pentadienylamine Complex, PDB code: 3kii was solved by Y.H.Nguyen, K.E.Ernberg, J.M.Guss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	12.99 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	192.714, 62.984, 158.151, 90.00, 117.39, 90.00
R / Rfree (%)	17.4 / 21.8

The structure of Agao 5-Phenoxy-2,3-Pentadienylamine Complex also contains other interesting chemical elements:

Copper

(Cu)

2 atoms

The binding sites of Sodium atom in the Agao 5-Phenoxy-2,3-Pentadienylamine Complex (pdb code 3kii). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Agao 5-Phenoxy-2,3-Pentadienylamine Complex, PDB code: 3kii:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Agao 5-Phenoxy-2,3-Pentadienylamine Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Agao 5-Phenoxy-2,3-Pentadienylamine Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na702 b:35.9 occ:1.00 O A:MET441 2.3 32.0 1.0 OD1 A:ASP440 2.3 34.4 1.0 OD1 A:ASP581 2.4 37.4 1.0 O A:ILE582 2.4 29.2 1.0 O A:HOH687 2.7 17.8 1.0 N A:ILE582 3.3 32.8 1.0 N A:MET441 3.3 30.3 1.0 C A:MET441 3.4 30.6 1.0 C A:ILE582 3.5 28.8 1.0 CG A:ASP440 3.6 36.2 1.0 CG A:ASP581 3.6 42.5 1.0 C A:ASP440 3.8 26.1 1.0 CA A:MET441 3.9 29.6 1.0 C A:ASP581 3.9 35.6 1.0 CA A:ILE582 4.0 30.5 1.0 CD1 A:PHE446 4.0 39.2 1.0 NH2 A:ARG49 4.0 43.6 1.0 CA A:ASP581 4.2 36.1 1.0 CA A:ASP440 4.2 28.2 1.0 OD2 A:ASP440 4.4 31.7 1.0 CB A:MET441 4.5 28.8 1.0 OD2 A:ASP581 4.5 37.4 1.0 CE1 A:PHE446 4.5 39.3 1.0 CB A:ASP581 4.5 39.2 1.0 O A:ASP440 4.5 28.7 1.0 CB A:ASP440 4.5 30.0 1.0 N A:ALA442 4.6 30.5 1.0 N A:VAL583 4.6 27.4 1.0 O A:ASP581 4.7 34.7 1.0 CG2 A:VAL583 4.9 28.0 1.0 CB A:TYR546 4.9 35.6 1.0 O A:PHE446 4.9 35.1 1.0

Sodium binding site 2 out of 2 in the Agao 5-Phenoxy-2,3-Pentadienylamine Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Agao 5-Phenoxy-2,3-Pentadienylamine Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na702 b:31.5 occ:1.00 O B:MET441 2.3 24.6 1.0 OD1 B:ASP581 2.3 31.6 1.0 OD1 B:ASP440 2.4 25.7 1.0 O B:ILE582 2.5 25.7 1.0 O B:HOH839 2.7 19.0 1.0 N B:ILE582 3.3 29.8 1.0 N B:MET441 3.4 24.0 1.0 C B:MET441 3.4 24.2 1.0 C B:ILE582 3.5 22.8 1.0 CG B:ASP581 3.6 33.7 1.0 CG B:ASP440 3.6 30.7 1.0 C B:ASP440 3.8 21.6 1.0 C B:ASP581 3.9 31.3 1.0 CA B:MET441 3.9 27.5 1.0 CD1 B:PHE446 3.9 38.3 1.0 CA B:ILE582 4.0 27.2 1.0 NH2 B:ARG49 4.1 32.6 1.0 CA B:ASP581 4.1 31.8 1.0 CA B:ASP440 4.3 24.9 1.0 CE1 B:PHE446 4.4 35.3 1.0 OD2 B:ASP440 4.4 27.8 1.0 OD2 B:ASP581 4.4 36.3 1.0 CB B:MET441 4.4 23.8 1.0 CB B:ASP581 4.4 36.3 1.0 O B:ASP440 4.5 21.2 1.0 CB B:ASP440 4.6 25.4 1.0 N B:ALA442 4.6 27.5 1.0 N B:VAL583 4.7 26.9 1.0 O B:ASP581 4.7 29.6 1.0 CG2 B:VAL583 4.8 21.1 1.0 O B:PHE446 4.9 29.1 1.0 CB B:TYR546 4.9 28.0 1.0 OD1 B:ASN448 5.0 26.6 1.0 CG1 B:ILE582 5.0 28.5 1.0

Y.H.Nguyen, K.E.Ernberg, J.M.Guss. Agao 5-Phenoxy-2,3-Pentadienylamine Complex To Be Published.