Magnesium in PDB 6ku1: The Structure of Eanb/Y353A Complex with Ergothioneine

The structure of The Structure of Eanb/Y353A Complex with Ergothioneine, PDB code: 6ku1 was solved by L.Wu, P.H.Liu, J.H.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.85 / 2.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.720, 88.000, 90.570, 90.00, 90.46, 90.00
R / Rfree (%)	17 / 21.4

The structure of The Structure of Eanb/Y353A Complex with Ergothioneine also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Magnesium atom in the The Structure of Eanb/Y353A Complex with Ergothioneine (pdb code 6ku1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Structure of Eanb/Y353A Complex with Ergothioneine, PDB code: 6ku1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the The Structure of Eanb/Y353A Complex with Ergothioneine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of Eanb/Y353A Complex with Ergothioneine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:29.5 occ:1.00 O A:THR414 2.2 23.9 1.0 O A:TRP216 2.3 32.7 1.0 O A:ASP437 2.4 27.8 1.0 OD1 A:ASN217 2.5 30.2 1.0 OD1 A:ASP437 2.5 32.8 1.0 O A:HOH685 2.7 31.6 1.0 C A:TRP216 3.1 33.5 1.0 C A:THR414 3.2 29.4 1.0 C A:ASP437 3.2 26.4 1.0 CG A:ASP437 3.5 31.3 1.0 CA A:ASN217 3.6 32.3 1.0 N A:ASN217 3.6 31.8 1.0 CG A:ASN217 3.6 32.4 1.0 CA A:THR414 3.8 30.0 1.0 NH1 A:ARG266 3.8 31.4 1.0 N A:GLY438 3.9 30.8 1.0 CA A:GLY438 4.0 26.2 1.0 O A:HOH666 4.0 28.7 1.0 CA A:ASP437 4.0 27.5 1.0 CB A:THR414 4.2 30.3 1.0 N A:GLY415 4.2 28.2 1.0 CB A:ASN217 4.2 32.7 1.0 CB A:ASP437 4.2 30.2 1.0 O A:THR215 4.3 35.1 1.0 OD2 A:ASP437 4.3 33.2 1.0 C A:GLY438 4.3 30.9 1.0 O A:GLY438 4.3 31.6 1.0 CA A:TRP216 4.3 28.4 1.0 CB A:TRP216 4.3 25.9 1.0 CA A:GLY415 4.5 28.1 1.0 CZ A:ARG266 4.5 29.2 1.0 NH2 A:ARG266 4.5 22.6 1.0 ND2 A:ASN217 4.7 39.2 1.0 C A:ASN217 4.8 33.6 1.0

Magnesium binding site 2 out of 4 in the The Structure of Eanb/Y353A Complex with Ergothioneine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of Eanb/Y353A Complex with Ergothioneine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:42.4 occ:1.00 O A:HOH780 2.2 37.3 1.0 O A:HOH671 2.3 37.9 1.0 O A:SER47 2.3 33.6 1.0 O A:VAL50 2.5 40.0 1.0 O A:HOH692 2.5 37.4 1.0 O A:HOH773 2.6 34.8 1.0 C A:SER47 3.5 36.3 1.0 C A:VAL50 3.6 32.4 1.0 O A:HOH787 3.7 44.0 1.0 O A:HOH652 4.1 32.7 1.0 CA A:GLU48 4.3 37.7 1.0 N A:VAL50 4.3 37.1 1.0 CA A:VAL50 4.3 30.5 1.0 O A:LEU45 4.3 33.0 1.0 CB A:VAL50 4.4 29.0 1.0 N A:GLU48 4.4 31.8 1.0 O A:HOH683 4.4 33.7 1.0 O A:HOH801 4.4 42.3 1.0 N A:SER47 4.5 34.3 1.0 CA A:SER47 4.6 35.9 1.0 C A:GLU48 4.6 39.5 1.0 N A:LYS51 4.6 32.9 1.0 CA A:LYS51 4.8 30.6 1.0 O A:GLU48 4.8 37.0 1.0 O A:LEU44 4.8 37.0 1.0 C A:GLY46 4.9 41.6 1.0 CG1 A:VAL50 5.0 30.9 1.0

Magnesium binding site 3 out of 4 in the The Structure of Eanb/Y353A Complex with Ergothioneine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structure of Eanb/Y353A Complex with Ergothioneine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:62.3 occ:1.00 O B:HOH734 2.2 52.0 1.0 O B:HOH740 2.2 57.8 1.0 O B:SER47 2.3 47.1 1.0 O B:HOH737 2.3 52.5 1.0 O B:VAL50 2.5 42.8 1.0 C B:SER47 3.4 47.1 1.0 C B:VAL50 3.7 37.5 1.0 O B:HOH745 4.2 43.8 1.0 CA B:GLU48 4.2 43.3 1.0 N B:GLU48 4.2 45.6 1.0 N B:VAL50 4.3 44.2 1.0 O B:HOH671 4.3 41.4 1.0 N B:SER47 4.3 43.8 1.0 CA B:VAL50 4.3 38.4 1.0 CB B:VAL50 4.4 41.5 1.0 CA B:SER47 4.4 52.9 1.0 C B:GLU48 4.5 46.8 1.0 O B:LEU45 4.5 53.1 1.0 O B:HOH618 4.6 44.0 1.0 C B:GLY46 4.7 50.4 1.0 N B:LYS51 4.7 41.2 1.0 O B:GLU48 4.7 44.0 1.0 O B:LEU44 4.9 43.0 1.0 CA B:LYS51 5.0 38.5 1.0

Magnesium binding site 4 out of 4 in the The Structure of Eanb/Y353A Complex with Ergothioneine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Structure of Eanb/Y353A Complex with Ergothioneine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:33.1 occ:1.00 O B:THR414 2.3 27.7 1.0 O B:TRP216 2.4 30.9 1.0 O B:ASP437 2.4 30.7 1.0 OD1 B:ASP437 2.4 30.6 1.0 OD1 B:ASN217 2.4 31.6 1.0 O B:HOH686 2.5 30.6 1.0 C B:ASP437 3.1 36.6 1.0 C B:TRP216 3.2 29.7 1.0 CG B:ASP437 3.3 37.0 1.0 C B:THR414 3.3 33.9 1.0 CA B:ASN217 3.5 33.2 1.0 CG B:ASN217 3.5 37.2 1.0 N B:ASN217 3.6 30.9 1.0 N B:GLY438 3.8 38.7 1.0 CA B:GLY438 3.8 31.9 1.0 CA B:ASP437 3.9 33.4 1.0 NH1 B:ARG266 3.9 29.1 1.0 CA B:THR414 4.0 29.3 1.0 CB B:ASP437 4.0 33.8 1.0 CB B:ASN217 4.1 32.4 1.0 OD2 B:ASP437 4.1 32.4 1.0 O B:GLY438 4.2 31.8 1.0 C B:GLY438 4.2 34.0 1.0 O B:HOH687 4.2 33.2 1.0 O B:THR215 4.3 35.3 1.0 N B:GLY415 4.3 33.6 1.0 CB B:THR414 4.4 35.6 1.0 CA B:TRP216 4.5 31.1 1.0 CA B:GLY415 4.5 32.9 1.0 CB B:TRP216 4.5 34.0 1.0 NH2 B:ARG266 4.6 29.3 1.0 CZ B:ARG266 4.6 31.6 1.0 ND2 B:ASN217 4.6 47.0 1.0 C B:ASN217 4.7 34.0 1.0

R.Cheng, L.Wu, R.Lai, C.Peng, N.Naowarojna, W.Hu, X.Li, S.A.Whelan, N.Lee, J.Lopez, C.Zhao, Y.Yong, J.Xue, X.Jiang, M.W.Grinstaff, Z.Deng, J.Chen, Q.Cui, J.H.Zhou, P.Liu. Single-Step Replacement of An Unreactive C-H Bond By A C-S Bond Using Polysulfide As the Direct Sulfur Source in the Anaerobic Ergothioneine Biosynthesis Acs Catalysis V. 10 8981 2020.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.0C01809