Magnesium in PDB 4kys: Clostridium Botulinum Thiaminase I in Complex with Thiamin

All present enzymatic activity of Clostridium Botulinum Thiaminase I in Complex with Thiamin:
2.5.1.2;

The structure of Clostridium Botulinum Thiaminase I in Complex with Thiamin, PDB code: 4kys was solved by M.D.Sikowitz, B.Shome, Y.Zhang, T.P.Begley, S.E.Ealick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.95 / 2.18
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.504, 36.306, 156.813, 90.00, 91.44, 90.00
R / Rfree (%)	15.6 / 21.1

The binding sites of Magnesium atom in the Clostridium Botulinum Thiaminase I in Complex with Thiamin (pdb code 4kys). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Clostridium Botulinum Thiaminase I in Complex with Thiamin, PDB code: 4kys:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Clostridium Botulinum Thiaminase I in Complex with Thiamin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Clostridium Botulinum Thiaminase I in Complex with Thiamin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:19.9 occ:1.00 O A:HOH796 2.3 26.6 1.0 O A:HOH711 2.4 23.4 1.0 OD1 A:ASN295 2.4 15.7 1.0 O A:ILE296 2.5 13.8 1.0 OD2 A:ASP205 2.6 21.4 1.0 OD1 A:ASP205 2.7 15.1 1.0 OD1 A:ASP201 2.8 22.4 1.0 CG A:ASP205 3.0 21.9 1.0 C A:ILE296 3.5 15.0 1.0 CG A:ASN295 3.6 16.1 1.0 CG A:ASP201 3.7 20.4 1.0 OD2 A:ASP201 3.9 25.9 1.0 N A:ILE296 4.0 11.5 1.0 O A:HOH671 4.0 21.7 1.0 CG1 A:ILE298 4.2 20.0 1.0 N A:ILE298 4.2 13.4 1.0 ND2 A:ASN295 4.2 17.3 1.0 CA A:ILE296 4.3 16.6 1.0 CA A:PRO297 4.4 16.0 1.0 N A:PRO297 4.4 13.2 1.0 CB A:ASP205 4.5 16.0 1.0 O A:ASP201 4.6 12.5 1.0 CB A:ILE298 4.6 15.8 1.0 C A:PRO297 4.8 17.9 1.0 C A:ASN295 4.8 18.5 1.0 CB A:ILE296 4.8 15.3 1.0 CB A:ASN295 4.8 20.1 1.0 O A:ILE288 4.8 13.7 1.0 CA A:ASN295 4.8 21.3 1.0 N A:LEU290 4.9 10.8 1.0

Magnesium binding site 2 out of 4 in the Clostridium Botulinum Thiaminase I in Complex with Thiamin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Clostridium Botulinum Thiaminase I in Complex with Thiamin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:20.9 occ:1.00 OG A:SER81 2.4 16.5 1.0 O A:HOH606 2.5 28.1 1.0 CB A:SER81 3.3 16.3 1.0 CA A:SER81 4.4 16.8 1.0 OD2 A:ASP78 4.4 18.3 1.0

Magnesium binding site 3 out of 4 in the Clostridium Botulinum Thiaminase I in Complex with Thiamin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Clostridium Botulinum Thiaminase I in Complex with Thiamin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:21.7 occ:1.00 O B:ILE296 2.3 17.2 1.0 O B:HOH700 2.5 24.9 1.0 OD1 B:ASN295 2.6 19.2 1.0 OD1 B:ASP201 2.7 28.3 1.0 OD2 B:ASP205 2.7 22.9 1.0 OD1 B:ASP205 2.7 21.0 1.0 O B:HOH770 2.7 22.9 1.0 CG B:ASP205 3.0 21.2 1.0 C B:ILE296 3.3 19.3 1.0 CG B:ASP201 3.6 27.3 1.0 OD2 B:ASP201 3.7 32.2 1.0 CG B:ASN295 3.8 21.4 1.0 N B:ILE296 3.9 15.4 1.0 CA B:ILE296 4.1 16.5 1.0 CG1 B:ILE298 4.1 22.2 1.0 N B:ILE298 4.2 17.1 1.0 N B:PRO297 4.2 20.4 1.0 CA B:PRO297 4.3 15.9 1.0 ND2 B:ASN295 4.4 16.9 1.0 O B:HOH671 4.4 22.6 1.0 CB B:ASP205 4.5 20.2 1.0 O B:ASP201 4.5 17.4 1.0 CB B:ILE296 4.6 17.6 1.0 C B:PRO297 4.7 17.0 1.0 C B:ASN295 4.7 19.7 1.0 CB B:ILE298 4.8 15.8 1.0 O B:ILE288 4.8 16.9 1.0 CA B:ASN295 4.9 23.6 1.0 CB B:ASN295 4.9 17.3 1.0 N B:LEU290 5.0 18.3 1.0

Magnesium binding site 4 out of 4 in the Clostridium Botulinum Thiaminase I in Complex with Thiamin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Clostridium Botulinum Thiaminase I in Complex with Thiamin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:30.5 occ:1.00 OG B:SER81 2.3 23.6 1.0 CB B:SER81 3.2 22.0 1.0 CA B:SER81 4.2 19.0 1.0 OD2 B:ASP78 4.4 31.8 1.0

M.D.Sikowitz, B.Shome, Y.Zhang, T.P.Begley, S.E.Ealick. Structure of A Clostridium Botulinum C143S Thiaminase I/Thiamin Complex Reveals Active Site Architecture. Biochemistry V. 52 7830 2013.
ISSN: ISSN 0006-2960
PubMed: 24079939
DOI: 10.1021/BI400841G