Sodium in PDB 6wn2: Tyrosyl T-Rna Synthetase Mutant From E.Coli Complexed with Sulfotyrosine

All present enzymatic activity of Tyrosyl T-Rna Synthetase Mutant From E.Coli Complexed with Sulfotyrosine:
6.1.1.1;

The structure of Tyrosyl T-Rna Synthetase Mutant From E.Coli Complexed with Sulfotyrosine, PDB code: 6wn2 was solved by D.G.Beltran, L.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.14 / 1.78
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.093, 93.904, 99.900, 90.00, 92.63, 90.00
R / Rfree (%)	18.2 / 22.3

The binding sites of Sodium atom in the Tyrosyl T-Rna Synthetase Mutant From E.Coli Complexed with Sulfotyrosine (pdb code 6wn2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Tyrosyl T-Rna Synthetase Mutant From E.Coli Complexed with Sulfotyrosine, PDB code: 6wn2:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Tyrosyl T-Rna Synthetase Mutant From E.Coli Complexed with Sulfotyrosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Tyrosyl T-Rna Synthetase Mutant From E.Coli Complexed with Sulfotyrosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:45.6 occ:1.00 O A:HOH582 2.2 34.3 1.0 O4 A:SO4408 2.6 47.1 1.0 O A:HOH593 2.9 29.7 1.0 S A:SO4408 3.5 56.1 1.0 O A:HOH658 3.6 53.7 1.0 O3 A:SO4408 3.7 70.0 1.0 CD A:LYS154 3.7 38.4 1.0 O2 A:SO4408 3.8 53.9 1.0 CA A:GLY203 3.8 27.4 1.0 CD1 A:TRP202 3.9 33.7 1.0 N A:GLU155 3.9 29.0 1.0 N A:GLY203 4.3 27.3 1.0 O A:HOH588 4.3 30.4 1.0 CA A:LYS154 4.3 28.7 1.0 CB A:GLU155 4.4 36.2 1.0 NE1 A:TRP202 4.5 33.8 1.0 CB A:LYS154 4.5 31.7 1.0 C A:LYS154 4.6 31.7 1.0 NZ A:LYS154 4.6 37.8 1.0 CG A:LYS154 4.7 34.1 1.0 O A:HOH631 4.7 30.6 1.0 CE A:LYS154 4.8 39.5 1.0 CA A:GLU155 4.8 32.9 1.0 O1 A:SO4408 4.8 56.0 1.0

Sodium binding site 2 out of 4 in the Tyrosyl T-Rna Synthetase Mutant From E.Coli Complexed with Sulfotyrosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Tyrosyl T-Rna Synthetase Mutant From E.Coli Complexed with Sulfotyrosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:52.2 occ:1.00 OE1 A:GLU172 2.6 36.5 1.0 O A:ILE79 2.7 30.6 1.0 O A:HOH522 2.9 41.2 1.0 O A:HOH575 3.0 40.0 1.0 CG A:GLU172 3.4 27.8 1.0 CD A:GLU172 3.4 32.0 1.0 O A:ARG89 3.5 38.7 1.0 CD2 A:LEU91 3.7 38.5 1.0 C A:ILE79 3.8 33.9 1.0 CB A:ARG89 3.9 41.3 1.0 CA A:GLY80 3.9 27.4 1.0 C A:ARG89 4.2 43.0 1.0 N A:GLY80 4.3 29.4 1.0 OE2 A:GLU88 4.3 35.9 1.0 N A:ARG89 4.4 32.8 1.0 CA A:ARG89 4.4 40.0 1.0 O A:GLY80 4.5 28.1 1.0 O A:HOH630 4.5 46.1 1.0 O A:LYS90 4.5 43.2 1.0 C A:GLY80 4.6 26.0 1.0 CG A:ARG89 4.6 46.6 1.0 OE2 A:GLU172 4.7 28.6 1.0 CD A:ARG89 4.7 40.3 1.0 CG A:LEU91 4.7 38.4 1.0 C A:LYS90 4.8 40.2 1.0 CB A:GLU172 4.9 26.7 1.0 CA A:ILE79 5.0 30.6 1.0

Sodium binding site 3 out of 4 in the Tyrosyl T-Rna Synthetase Mutant From E.Coli Complexed with Sulfotyrosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Tyrosyl T-Rna Synthetase Mutant From E.Coli Complexed with Sulfotyrosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:48.1 occ:1.00 OE1 B:GLU172 2.6 36.5 1.0 O B:HOH535 2.7 41.2 1.0 O B:ILE79 2.7 31.6 1.0 O B:HOH541 2.9 50.4 1.0 O B:ARG89 3.1 52.1 1.0 CD2 B:LEU91 3.4 42.7 1.0 CD B:GLU172 3.4 36.6 1.0 CG B:GLU172 3.5 27.9 1.0 C B:ILE79 3.8 29.5 1.0 C B:ARG89 3.9 49.6 1.0 CB B:ARG89 4.0 49.5 1.0 CA B:GLY80 4.1 28.1 1.0 N B:ARG89 4.2 51.0 1.0 CG B:LEU91 4.2 42.4 1.0 CA B:ARG89 4.3 44.9 1.0 OE1 B:GLU88 4.3 33.3 1.0 N B:GLY80 4.4 25.6 1.0 O B:LYS90 4.6 40.3 1.0 OE2 B:GLU172 4.6 34.0 1.0 N B:LEU91 4.6 37.2 1.0 C B:LYS90 4.7 35.1 1.0 CG2 B:THR171 4.7 30.4 1.0 O B:GLY80 4.9 26.2 1.0 CA B:LEU91 4.9 35.8 1.0 CA B:ILE79 4.9 31.2 1.0 C B:GLY80 4.9 24.0 1.0 CB B:GLU172 5.0 28.2 1.0 N B:LYS90 5.0 55.0 1.0 CG B:ARG89 5.0 54.9 1.0

Sodium binding site 4 out of 4 in the Tyrosyl T-Rna Synthetase Mutant From E.Coli Complexed with Sulfotyrosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Tyrosyl T-Rna Synthetase Mutant From E.Coli Complexed with Sulfotyrosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:50.4 occ:1.00 O B:ALA26 2.5 26.1 1.0 O B:HOH642 2.7 35.5 1.0 OD1 B:ASN5 3.4 69.6 1.0 C B:ALA26 3.4 27.9 1.0 N B:ALA30 3.6 33.5 1.0 CA B:ALA26 3.6 27.4 1.0 CB B:LEU29 3.7 29.6 1.0 CB B:ALA30 3.8 35.9 1.0 CB B:ALA26 3.9 30.1 1.0 CA B:ALA30 4.0 36.4 1.0 CG B:ASN5 4.1 65.8 1.0 C B:LEU29 4.1 33.5 1.0 CA B:ASN5 4.3 46.9 1.0 CA B:LEU29 4.4 28.4 1.0 N B:LEU6 4.4 31.3 1.0 O B:HOH676 4.6 58.2 1.0 CB B:ASN5 4.6 50.1 1.0 N B:GLU27 4.6 29.6 1.0 CD1 B:LEU29 4.7 30.2 1.0 CG B:LEU29 4.7 29.7 1.0 N B:LEU29 4.7 26.5 1.0 C B:ASN5 4.8 39.5 1.0 ND2 B:ASN5 4.8 67.9 1.0 O B:HOH599 4.9 31.9 1.0 N B:ALA26 4.9 25.1 1.0 O B:LEU29 4.9 35.8 1.0 O B:LEU25 5.0 25.1 1.0

D.G.Beltran, L.Zhang. Tyrosyl T-Rna Synthetase Mutant From E.Coli Complexed with Sulfotyrosine To Be Published.