Magnesium in PDB 8qmf: Transketolase From Vibrio Vulnificus in Complex with Thiamin Pyrophosphate

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

Resolution Low / High (Å)	34.95 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.23, 75.48, 130.39, 90, 99.87, 90
R / Rfree (%)	16.3 / 20.7

The structure of Transketolase From Vibrio Vulnificus in Complex with Thiamin Pyrophosphate also contains other interesting chemical elements:

Nickel

(Ni)

1 atom

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

Magnesium binding site 1 out of 2 in the Transketolase From Vibrio Vulnificus 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 Vibrio Vulnificus in Complex with Thiamin Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg708 b:22.2 occ:1.00 O A:ILE186 2.1 35.6 1.0 O2A A:TPP701 2.1 35.8 1.0 OD2 A:ASP154 2.3 32.8 1.0 O1B A:TPP701 2.3 36.3 1.0 O A:HOH870 2.3 33.9 1.0 OD1 A:ASN184 2.4 33.1 1.0 CG A:ASN184 3.3 33.6 1.0 CG A:ASP154 3.3 28.9 1.0 C A:ILE186 3.3 34.8 1.0 PA A:TPP701 3.4 38.0 1.0 PB A:TPP701 3.5 39.8 1.0 ND2 A:ASN184 3.5 34.6 1.0 O3A A:TPP701 3.7 42.8 1.0 CB A:ASP154 3.8 29.8 1.0 N A:ILE186 4.0 34.3 1.0 N A:ASP154 4.1 31.1 1.0 CA A:ILE186 4.2 33.5 1.0 O A:HOH853 4.3 36.0 1.0 O3B A:TPP701 4.3 44.7 1.0 O7 A:TPP701 4.3 41.9 1.0 O A:ASP182 4.3 35.4 1.0 N A:SER187 4.3 34.3 1.0 OD1 A:ASP154 4.4 29.4 1.0 O1A A:TPP701 4.5 43.1 1.0 CA A:SER187 4.6 33.0 1.0 CA A:ASP154 4.6 28.5 1.0 CB A:ILE186 4.6 36.1 1.0 O2B A:TPP701 4.7 41.6 1.0 CB A:ASN184 4.7 32.2 1.0 N A:ASN184 4.8 32.7 1.0 N A:GLY185 4.9 32.3 1.0 CB A:SER187 4.9 34.5 1.0

Magnesium binding site 2 out of 2 in the Transketolase From Vibrio Vulnificus 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 Vibrio Vulnificus in Complex with Thiamin Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg708 b:23.1 occ:1.00 O2A B:TPP702 2.0 44.1 1.0 OD2 B:ASP154 2.2 36.1 1.0 O B:ILE186 2.2 35.2 1.0 O2B B:TPP702 2.3 35.2 1.0 O B:HOH815 2.4 38.6 1.0 OD1 B:ASN184 2.5 36.4 1.0 CG B:ASP154 3.2 36.1 1.0 PA B:TPP702 3.3 41.8 1.0 CG B:ASN184 3.3 39.7 1.0 C B:ILE186 3.4 34.0 1.0 O3A B:TPP702 3.5 45.0 1.0 PB B:TPP702 3.5 38.9 1.0 ND2 B:ASN184 3.5 37.6 1.0 CB B:ASP154 3.7 35.6 1.0 N B:ILE186 4.0 33.8 1.0 N B:ASP154 4.0 37.1 1.0 O7 B:TPP702 4.2 43.0 1.0 O1B B:TPP702 4.2 43.8 1.0 OD1 B:ASP154 4.2 35.6 1.0 CA B:ILE186 4.2 38.6 1.0 O B:HOH903 4.3 41.6 1.0 O B:ASP182 4.3 42.6 1.0 O1A B:TPP702 4.4 42.9 1.0 N B:SER187 4.4 34.8 1.0 CA B:ASP154 4.5 34.0 1.0 CA B:SER187 4.6 38.9 1.0 O3B B:TPP702 4.6 43.6 1.0 CB B:ASN184 4.7 38.1 1.0 N B:GLY185 4.8 36.2 1.0 CB B:ILE186 4.8 42.9 1.0 N B:ASN184 4.9 38.0 1.0 CB B:SER187 4.9 33.1 1.0

R.N.Georges, L.Ballut, G.Octobre, A.Comte, L.Hecquet, F.Charmantray, B.Doumeche. Structural Determination and Kinetic Analysis of the Transketolase From Vibrio Vulnificus Reveal Unexpected Cooperative Behavior. Protein Sci. E4884 2023.
ISSN: ESSN 1469-896X
PubMed: 38145310
DOI: 10.1002/PRO.4884