Magnesium in PDB 8r3r: Transketolase From Streptococcus Pneumoniae in Complex with Thiamin Pyrophosphate

All present enzymatic activity of Transketolase From Streptococcus Pneumoniae in Complex with Thiamin Pyrophosphate:
2.2.1.1;

The structure of Transketolase From Streptococcus Pneumoniae in Complex with Thiamin Pyrophosphate, PDB code: 8r3r was solved by L.Ballut, R.N.Georges, N.Aghajari, L.Hecquet, F.Charmantray, B.Doumeche, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.05 / 2.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	93.76, 119.13, 136.68, 90, 106.46, 90
R / Rfree (%)	15.4 / 21.6

The binding sites of Magnesium atom in the Transketolase From Streptococcus Pneumoniae in Complex with Thiamin Pyrophosphate (pdb code 8r3r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Transketolase From Streptococcus Pneumoniae in Complex with Thiamin Pyrophosphate, PDB code: 8r3r:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Transketolase From Streptococcus Pneumoniae in Complex with Thiamin Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Transketolase From Streptococcus Pneumoniae in Complex with Thiamin Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:11.6 occ:1.00 O2B A:TPP701 2.0 8.8 1.0 O A:ILE186 2.2 14.1 1.0 O2A A:TPP701 2.2 15.2 1.0 OD2 A:ASP154 2.2 10.5 1.0 OD1 A:ASN184 2.3 12.0 1.0 O A:HOH1013 2.4 13.2 1.0 CG A:ASN184 3.2 14.6 1.0 CG A:ASP154 3.3 15.9 1.0 C A:ILE186 3.4 13.8 1.0 PB A:TPP701 3.4 15.6 1.0 ND2 A:ASN184 3.4 10.1 1.0 PA A:TPP701 3.4 14.1 1.0 O3A A:TPP701 3.6 13.5 1.0 CB A:ASP154 3.7 14.2 1.0 N A:ILE186 4.0 11.7 1.0 N A:ASP154 4.1 12.6 1.0 CA A:ILE186 4.3 12.2 1.0 O1B A:TPP701 4.3 19.9 1.0 O A:HOH897 4.3 17.3 1.0 N A:ASN187 4.4 11.5 1.0 OD1 A:ASP154 4.4 12.0 1.0 O1A A:TPP701 4.4 13.3 1.0 O3B A:TPP701 4.4 16.4 1.0 O7 A:TPP701 4.5 19.2 1.0 CA A:ASP154 4.6 16.5 1.0 CA A:ASN187 4.6 8.8 1.0 CB A:ASN184 4.6 13.8 1.0 N A:ASN184 4.7 10.4 1.0 O A:ASP182 4.7 14.1 1.0 CB A:ILE186 4.8 12.8 1.0 N A:ASP185 4.9 11.8 1.0

Magnesium binding site 2 out of 4 in the Transketolase From Streptococcus Pneumoniae in Complex with Thiamin Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Transketolase From Streptococcus Pneumoniae in Complex with Thiamin Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg703 b:12.3 occ:1.00 O2A B:TPP702 2.1 11.9 1.0 O B:HOH903 2.2 14.5 1.0 O2B B:TPP702 2.2 17.6 1.0 O B:ILE186 2.3 12.8 1.0 OD1 B:ASN184 2.3 16.4 1.0 OD2 B:ASP154 2.3 9.0 1.0 CG B:ASN184 3.1 18.0 1.0 ND2 B:ASN184 3.3 11.2 1.0 PA B:TPP702 3.3 16.7 1.0 PB B:TPP702 3.3 17.6 1.0 CG B:ASP154 3.4 10.8 1.0 O3A B:TPP702 3.4 17.3 1.0 C B:ILE186 3.5 15.4 1.0 CB B:ASP154 3.7 16.0 1.0 O1B B:TPP702 4.0 25.0 1.0 N B:ILE186 4.1 18.9 1.0 N B:ASP154 4.1 9.2 1.0 O B:HOH910 4.2 18.9 1.0 CA B:ILE186 4.3 14.4 1.0 O7 B:TPP702 4.4 23.1 1.0 O1A B:TPP702 4.4 20.9 1.0 N B:ASN187 4.4 13.8 1.0 OD1 B:ASP154 4.5 11.1 1.0 O3B B:TPP702 4.5 18.9 1.0 CA B:ASN187 4.6 17.5 1.0 CB B:ASN184 4.6 14.0 1.0 CA B:ASP154 4.6 15.2 1.0 N B:ASN184 4.8 16.8 1.0 O B:ASP182 4.8 15.4 1.0 CB B:ILE186 4.8 15.6 1.0 N B:ASP185 4.9 16.3 1.0

Magnesium binding site 3 out of 4 in the Transketolase From Streptococcus Pneumoniae in Complex with Thiamin Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Transketolase From Streptococcus Pneumoniae in Complex with Thiamin Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:11.1 occ:1.00 OD2 C:ASP154 2.1 15.9 1.0 O C:ILE186 2.2 13.6 1.0 O2B C:TPP701 2.2 14.1 1.0 O2A C:TPP701 2.2 13.4 1.0 O C:HOH845 2.2 10.9 1.0 OD1 C:ASN184 2.3 12.8 1.0 CG C:ASP154 3.2 13.3 1.0 CG C:ASN184 3.2 17.7 1.0 PB C:TPP701 3.4 18.1 1.0 C C:ILE186 3.4 14.5 1.0 PA C:TPP701 3.4 19.6 1.0 O3A C:TPP701 3.5 15.9 1.0 ND2 C:ASN184 3.5 11.8 1.0 CB C:ASP154 3.8 9.4 1.0 N C:ILE186 4.0 14.6 1.0 O1B C:TPP701 4.0 21.0 1.0 N C:ASP154 4.2 8.9 1.0 CA C:ILE186 4.2 13.9 1.0 O C:HOH1139 4.2 15.8 1.0 OD1 C:ASP154 4.3 10.5 1.0 N C:ASN187 4.4 15.9 1.0 O7 C:TPP701 4.4 15.3 1.0 O1A C:TPP701 4.5 20.1 1.0 O3B C:TPP701 4.6 16.0 1.0 CA C:ASN187 4.6 15.5 1.0 CA C:ASP154 4.6 14.1 1.0 CB C:ASN184 4.7 13.1 1.0 CB C:ILE186 4.7 15.2 1.0 N C:ASN184 4.7 13.3 1.0 O C:ASP182 4.8 12.4 1.0 N C:ASP185 4.9 15.4 1.0 C C:ASN184 4.9 18.3 1.0

Magnesium binding site 4 out of 4 in the Transketolase From Streptococcus Pneumoniae in Complex with Thiamin Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Transketolase From Streptococcus Pneumoniae in Complex with Thiamin Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg702 b:8.8 occ:1.00 O D:HOH989 2.1 14.9 1.0 OD1 D:ASN184 2.2 8.0 1.0 O2A D:TPP701 2.2 13.4 1.0 O D:ILE186 2.2 12.9 1.0 O1B D:TPP701 2.2 14.7 1.0 OD2 D:ASP154 2.3 8.9 1.0 CG D:ASN184 3.2 13.5 1.0 CG D:ASP154 3.3 8.7 1.0 C D:ILE186 3.4 12.2 1.0 PB D:TPP701 3.5 18.7 1.0 ND2 D:ASN184 3.5 8.4 1.0 PA D:TPP701 3.5 16.6 1.0 O3A D:TPP701 3.7 17.8 1.0 CB D:ASP154 3.8 9.4 1.0 N D:ILE186 4.0 11.8 1.0 N D:ASP154 4.1 7.1 1.0 CA D:ILE186 4.2 9.9 1.0 O D:HOH1093 4.2 19.3 1.0 O3B D:TPP701 4.4 24.8 1.0 OD1 D:ASP154 4.4 9.6 1.0 N D:ASN187 4.4 8.7 1.0 O1A D:TPP701 4.5 21.2 1.0 O7 D:TPP701 4.5 26.9 1.0 CB D:ASN184 4.6 11.6 1.0 O2B D:TPP701 4.6 16.3 1.0 N D:ASN184 4.6 12.7 1.0 CA D:ASP154 4.6 10.5 1.0 CA D:ASN187 4.6 12.1 1.0 CB D:ILE186 4.7 15.8 1.0 N D:ASP185 4.8 9.9 1.0 O D:ASP182 4.8 14.1 1.0 C D:ASN184 4.9 15.9 1.0 CA D:ASN184 4.9 14.9 1.0

R.N.Georges, L.Ballut, N.Aghajari, L.Hecquet, F.Charmantray, B.Doumeche. Are Transketolases Relevant Targets Fighting Human Pathogens? A Comparative Biochemical, Bioinformatic and Structural Study To Be Published.