Sodium in PDB 5ce9: Structure of Tyrosinase From Walnut (Juglans Regia)

The structure of Structure of Tyrosinase From Walnut (Juglans Regia), PDB code: 5ce9 was solved by A.Bijelic, M.Pretzler, F.Zekiri, A.Rompel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.10 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.430, 90.940, 86.580, 90.00, 130.18, 90.00
R / Rfree (%)	17 / 18.8

The structure of Structure of Tyrosinase From Walnut (Juglans Regia) also contains other interesting chemical elements:

Copper

(Cu)

4 atoms

The binding sites of Sodium atom in the Structure of Tyrosinase From Walnut (Juglans Regia) (pdb code 5ce9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Structure of Tyrosinase From Walnut (Juglans Regia), PDB code: 5ce9:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in the Structure of Tyrosinase From Walnut (Juglans Regia)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Tyrosinase From Walnut (Juglans Regia) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:63.8 occ:1.00 HG1 A:THR237 2.1 40.8 1.0 HD21 A:ASN241 2.4 39.8 1.0 O A:SER236 2.5 34.6 1.0 OD1 A:ASN241 2.5 31.6 1.0 OG1 A:THR237 2.8 34.0 1.0 ND2 A:ASN241 2.9 33.1 1.0 CG A:ASN241 2.9 31.1 1.0 HB2 A:ASN240 3.4 38.1 1.0 C A:SER236 3.6 33.6 1.0 HD22 A:ASN241 3.6 39.8 1.0 HA A:THR237 3.6 37.6 1.0 H A:ASN241 3.7 35.5 1.0 CB A:THR237 3.9 32.1 1.0 O A:HOH611 4.1 40.1 1.0 CA A:THR237 4.1 31.4 1.0 O A:HOH700 4.1 45.5 1.0 N A:ASN241 4.1 29.6 1.0 HG23 A:THR237 4.1 39.0 1.0 CB A:ASN240 4.2 31.7 1.0 N A:THR237 4.2 32.3 1.0 HB3 A:ASN240 4.3 38.1 1.0 CB A:ASN241 4.3 31.2 1.0 HB3 A:SER236 4.4 40.9 1.0 HA A:SER236 4.5 37.8 1.0 HA A:ASN241 4.5 38.2 1.0 HD22 A:ASN240 4.5 39.2 1.0 CG2 A:THR237 4.5 32.5 1.0 CA A:ASN241 4.6 31.9 1.0 CA A:SER236 4.6 31.5 1.0 HB A:THR237 4.7 38.5 1.0 HB2 A:ASN241 4.8 37.5 1.0 H A:ASN240 4.8 35.5 1.0 OD1 A:ASP181 4.8 55.0 1.0 HG21 A:THR237 4.8 39.0 1.0 HA A:PRO238 4.8 35.7 1.0 HB3 A:ASN241 4.8 37.5 1.0 C A:ASN240 4.8 28.6 1.0 CB A:SER236 5.0 34.1 1.0

Sodium binding site 2 out of 7 in the Structure of Tyrosinase From Walnut (Juglans Regia)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Tyrosinase From Walnut (Juglans Regia) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:56.9 occ:1.00 HE1 A:PHE100 3.0 33.9 1.0 HZ A:PHE100 3.3 33.5 1.0 CE1 A:PHE100 3.7 28.3 1.0 CZ A:PHE100 3.8 27.9 1.0 CD1 A:PHE100 4.9 28.4 1.0

Sodium binding site 3 out of 7 in the Structure of Tyrosinase From Walnut (Juglans Regia)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Tyrosinase From Walnut (Juglans Regia) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:63.8 occ:1.00 OD1 A:ASN259 1.9 44.6 1.0 HB2 A:PHE260 2.1 48.8 1.0 H A:PHE260 2.6 43.2 1.0 CG A:ASN259 2.8 43.1 1.0 HD21 A:ASN259 2.9 51.0 1.0 O A:HOH705 3.0 43.0 1.0 CB A:PHE260 3.1 40.7 1.0 H A:TYR261 3.1 34.6 1.0 OD1 A:ASP92 3.1 40.6 1.0 N A:PHE260 3.2 36.0 1.0 ND2 A:ASN259 3.2 42.5 1.0 HD2 A:PHE260 3.3 54.4 1.0 CA A:PHE260 3.6 37.2 1.0 HB3 A:PHE260 3.7 48.8 1.0 CG A:PHE260 3.7 43.7 1.0 HD3 A:PRO17 3.7 41.9 1.0 CD2 A:PHE260 3.8 45.3 1.0 N A:TYR261 3.8 28.9 1.0 HD1 A:TYR261 3.8 36.9 1.0 HG3 A:PRO17 3.9 44.5 1.0 HB3 A:TYR261 3.9 35.6 1.0 CG A:ASP92 4.0 37.7 1.0 HD22 A:ASN259 4.0 51.0 1.0 OD2 A:ASP92 4.1 40.9 1.0 C A:ASN259 4.1 35.5 1.0 CB A:ASN259 4.1 40.3 1.0 HA A:ASN259 4.2 43.6 1.0 C A:PHE260 4.2 34.3 1.0 CA A:ASN259 4.4 36.4 1.0 HB3 A:ASN259 4.5 48.3 1.0 HA A:PHE260 4.5 44.7 1.0 CD A:PRO17 4.5 35.0 1.0 CG A:PRO17 4.6 37.1 1.0 CD1 A:TYR261 4.7 30.7 1.0 HB3 A:PRO17 4.7 44.3 1.0 CB A:TYR261 4.8 29.6 1.0 O A:HOH669 4.8 37.2 1.0 HB2 A:ASN259 4.8 48.3 1.0 CD1 A:PHE260 4.8 42.7 1.0 CA A:TYR261 4.9 28.8 1.0 CE2 A:PHE260 4.9 45.7 1.0 HD2 A:PRO17 5.0 41.9 1.0

Sodium binding site 4 out of 7 in the Structure of Tyrosinase From Walnut (Juglans Regia)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Tyrosinase From Walnut (Juglans Regia) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:43.6 occ:1.00 O B:HOH734 2.5 41.1 1.0 O B:GLY209 2.5 34.0 1.0 O B:HOH659 2.8 49.6 1.0 HG22 B:THR233 3.0 33.6 1.0 HD22 B:LEU215 3.3 37.8 1.0 HA3 B:GLY209 3.3 43.5 1.0 HG21 B:THR233 3.3 33.6 1.0 C B:GLY209 3.4 34.0 1.0 CG2 B:THR233 3.5 28.0 1.0 HG23 B:THR233 3.5 33.6 1.0 HA2 B:GLY209 3.6 43.5 1.0 CA B:GLY209 3.7 36.2 1.0 HD13 B:LEU215 3.8 37.2 1.0 HB3 B:LEU215 4.0 33.3 1.0 CD2 B:LEU215 4.2 31.5 1.0 HH21 B:ARG204 4.3 71.3 1.0 O B:HOH640 4.3 27.6 1.0 NH2 B:ARG204 4.5 59.4 1.0 HD21 B:LEU215 4.6 37.8 1.0 CD1 B:LEU215 4.7 31.0 1.0 HH22 B:ARG204 4.7 71.3 1.0 N B:ALA210 4.7 33.3 1.0 HA B:ALA210 4.7 36.4 1.0 HD23 B:LEU215 4.8 37.8 1.0 CG B:LEU215 4.8 29.4 1.0 CB B:LEU215 4.8 27.8 1.0 CZ B:ARG204 4.9 57.9 1.0 HE B:ARG204 4.9 65.9 1.0 O B:HOH671 4.9 27.4 1.0 CB B:THR233 4.9 26.0 1.0 O B:HOH594 5.0 31.2 1.0

Sodium binding site 5 out of 7 in the Structure of Tyrosinase From Walnut (Juglans Regia)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Tyrosinase From Walnut (Juglans Regia) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:51.9 occ:1.00 OD2 B:ASP75 2.8 37.2 1.0 O B:HOH650 3.2 36.0 1.0 CG B:ASP75 3.8 35.2 1.0 OD1 B:ASP75 4.1 34.1 1.0 O B:HOH560 4.1 39.4 1.0

Sodium binding site 6 out of 7 in the Structure of Tyrosinase From Walnut (Juglans Regia)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Tyrosinase From Walnut (Juglans Regia) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:51.6 occ:1.00 OD1 B:ASP319 2.7 31.2 1.0 O B:HOH675 2.7 50.3 1.0 HA B:ASP319 2.8 30.8 1.0 HD11 B:LEU38 2.9 39.0 1.0 HD12 B:LEU38 3.4 39.0 1.0 CD1 B:LEU38 3.5 32.5 1.0 CG B:ASP319 3.8 29.3 1.0 CA B:ASP319 3.8 25.7 1.0 HD13 B:LEU38 3.8 39.0 1.0 O B:LYS318 3.9 25.9 1.0 HD2 B:LYS325 4.1 54.7 1.0 CB B:ASP319 4.2 24.8 1.0 HD3 B:LYS325 4.2 54.7 1.0 HB3 B:ASP319 4.3 29.7 1.0 O B:HOH743 4.3 48.5 1.0 HG3 B:LYS318 4.3 40.5 1.0 C B:LYS318 4.4 25.8 1.0 N B:ASP319 4.5 25.5 1.0 HE3 B:LYS325 4.5 59.2 1.0 CD B:LYS325 4.6 45.6 1.0 C B:ASP319 4.7 27.0 1.0 O B:ASP319 4.7 28.0 1.0 O B:HOH563 4.7 40.5 1.0 OD2 B:ASP319 4.8 32.5 1.0 HE3 B:LYS318 4.8 51.3 1.0 CG B:LEU38 4.9 29.3 1.0 HG B:LEU38 4.9 35.2 1.0

Sodium binding site 7 out of 7 in the Structure of Tyrosinase From Walnut (Juglans Regia)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of Tyrosinase From Walnut (Juglans Regia) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na407 b:60.7 occ:1.00 O B:HOH713 2.3 60.6 1.0 HG2 B:ARG204 2.7 54.9 1.0 O B:HOH738 2.9 52.1 1.0 OE1 B:GLN205 3.1 33.1 1.0 HG3 B:ARG204 3.3 54.9 1.0 CG B:ARG204 3.4 45.7 1.0 HB3 B:ARG204 3.6 48.7 1.0 HG2 B:GLN205 3.7 37.0 1.0 CD B:GLN205 3.8 29.8 1.0 HG23 B:ILE201 4.0 40.3 1.0 CB B:ARG204 4.1 40.6 1.0 HE B:ARG204 4.1 65.9 1.0 HA B:ILE201 4.2 44.9 1.0 HG12 B:ILE201 4.2 47.7 1.0 CG B:GLN205 4.2 30.8 1.0 HB2 B:ARG204 4.4 48.7 1.0 HG21 B:THR237 4.5 41.8 1.0 HG3 B:GLN205 4.5 37.0 1.0 CD B:ARG204 4.6 51.2 1.0 NE2 B:GLN205 4.6 30.2 1.0 O B:HOH659 4.7 49.6 1.0 NE B:ARG204 4.7 54.9 1.0 HE22 B:GLN205 4.8 36.3 1.0 HB B:THR237 4.8 40.0 1.0 CG2 B:ILE201 4.9 33.6 1.0 O B:ILE201 4.9 34.1 1.0 HD3 B:ARG204 5.0 61.4 1.0

A.Bijelic, M.Pretzler, C.Molitor, F.Zekiri, A.Rompel. The Structure of A Plant Tyrosinase From Walnut Leaves Reveals the Importance of """"Substrate-Guiding Residues"""" For Enzymatic Specificity. Angew.Chem.Int.Ed.Engl. V. 54 14677 2015.
ISSN: ESSN 1521-3773
PubMed: 26473311
DOI: 10.1002/ANIE.201506994