Magnesium in PDB 6rjb: Human Transketolase Variant T382E

All present enzymatic activity of Human Transketolase Variant T382E:
2.2.1.1;

The structure of Human Transketolase Variant T382E, PDB code: 6rjb was solved by F.Rabe Von Pappenheim, K.Tittmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.81 / 1.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.000, 85.780, 92.790, 90.00, 94.15, 90.00
R / Rfree (%)	12.3 / 14.8

The structure of Human Transketolase Variant T382E also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Magnesium atom in the Human Transketolase Variant T382E (pdb code 6rjb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Transketolase Variant T382E, PDB code: 6rjb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Transketolase Variant T382E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Transketolase Variant T382E within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:11.0 occ:0.78 CA A:CA703 0.3 10.2 0.2 O12 A:TDP701 2.0 9.9 1.0 O A:LEU187 2.0 11.4 1.0 O21 A:TDP701 2.0 10.5 1.0 OD1 A:ASP155 2.1 10.2 1.0 OD1 A:ASN185 2.2 11.2 1.0 O A:HOH964 2.3 11.0 1.0 HD21 A:ASN185 3.1 13.5 1.0 CG A:ASN185 3.1 10.9 1.0 C A:LEU187 3.2 11.5 1.0 P2 A:TDP701 3.2 9.9 1.0 H A:ASP155 3.2 12.2 1.0 P1 A:TDP701 3.2 10.2 1.0 H A:GLY156 3.3 12.3 1.0 CG A:ASP155 3.3 10.7 1.0 HZ2 A:LYS244 3.4 13.3 1.0 O11 A:TDP701 3.4 10.1 1.0 H A:LEU187 3.5 12.9 1.0 ND2 A:ASN185 3.5 11.2 1.0 HA2 A:GLY188 3.5 12.2 1.0 O22 A:TDP701 3.7 11.2 1.0 HD2 A:LYS244 3.8 14.1 1.0 H A:ASN185 3.9 12.5 1.0 OD2 A:ASP155 3.9 12.2 1.0 N A:LEU187 4.0 10.8 1.0 N A:ASP155 4.0 10.1 1.0 O5G A:TDP701 4.0 11.1 1.0 N A:GLY188 4.1 10.5 1.0 N A:GLY156 4.1 10.2 1.0 CA A:LEU187 4.2 10.8 1.0 CA A:GLY188 4.2 10.2 1.0 NZ A:LYS244 4.2 11.1 1.0 HD22 A:ASN185 4.3 13.5 1.0 O13 A:TDP701 4.4 10.7 1.0 HB2 A:LEU187 4.4 14.3 1.0 O23 A:TDP701 4.4 10.5 1.0 CB A:ASP155 4.4 10.2 1.0 O A:ASP183 4.5 10.7 1.0 CB A:ASN185 4.5 11.2 1.0 HB2 A:ALA193 4.5 15.7 1.0 CA A:ASP155 4.6 10.2 1.0 HZ1 A:LYS244 4.6 13.3 1.0 N A:ASN185 4.7 10.4 1.0 HA3 A:GLY154 4.7 12.2 1.0 HZ3 A:LYS244 4.7 13.3 1.0 CD A:LYS244 4.7 11.7 1.0 C A:ASN185 4.7 11.0 1.0 H A:ARG186 4.7 13.3 1.0 N A:ARG186 4.8 11.1 1.0 HA3 A:GLY156 4.8 12.7 1.0 HA2 A:GLY154 4.8 12.2 1.0 CA A:ASN185 4.8 10.4 1.0 C A:ASP155 4.8 10.2 1.0 H A:GLY188 4.9 12.6 1.0 CB A:LEU187 4.9 11.9 1.0 HB3 A:ASP155 4.9 12.3 1.0 HA3 A:GLY188 4.9 12.2 1.0 CE A:LYS244 4.9 11.3 1.0 HE3 A:LYS244 4.9 13.5 1.0 HA A:LEU187 4.9 13.0 1.0 C A:ARG186 5.0 11.4 1.0 HB3 A:ASN185 5.0 13.4 1.0

Magnesium binding site 2 out of 2 in the Human Transketolase Variant T382E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Transketolase Variant T382E within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:10.7 occ:0.74 CA B:CA703 0.3 10.2 0.3 OD1 B:ASP155 2.0 10.7 1.0 O B:LEU187 2.0 10.7 1.0 OD1 B:ASN185 2.1 11.2 1.0 O13 B:TDP701 2.1 10.3 1.0 O23 B:TDP701 2.2 10.4 1.0 O B:HOH948 2.3 10.8 1.0 CG B:ASN185 3.1 10.9 1.0 HD21 B:ASN185 3.1 13.1 1.0 CG B:ASP155 3.2 10.6 1.0 C B:LEU187 3.2 10.2 1.0 H B:ASP155 3.2 12.3 1.0 H B:GLY156 3.3 12.1 1.0 P2 B:TDP701 3.3 10.2 1.0 P1 B:TDP701 3.3 10.0 1.0 H B:LEU187 3.3 12.3 1.0 HZ2 B:LYS244 3.5 12.4 1.0 ND2 B:ASN185 3.5 10.9 1.0 O11 B:TDP701 3.6 10.2 1.0 HA2 B:GLY188 3.6 12.1 1.0 H B:ASN185 3.8 12.3 1.0 OD2 B:ASP155 3.8 11.4 1.0 HD2 B:LYS244 3.8 13.3 1.0 O21 B:TDP701 3.8 11.7 1.0 N B:LEU187 3.9 10.3 1.0 N B:ASP155 4.0 10.2 1.0 CA B:LEU187 4.1 10.1 1.0 N B:GLY188 4.1 10.6 1.0 N B:GLY156 4.1 10.1 1.0 O5G B:TDP701 4.2 10.8 1.0 CA B:GLY188 4.3 10.1 1.0 HD22 B:ASN185 4.3 13.1 1.0 CB B:ASP155 4.3 10.2 1.0 NZ B:LYS244 4.4 10.4 1.0 O B:ASP183 4.4 11.0 1.0 HB2 B:LEU187 4.4 13.4 1.0 CB B:ASN185 4.4 10.9 1.0 O12 B:TDP701 4.5 10.8 1.0 CA B:ASP155 4.5 10.6 1.0 N B:ASN185 4.5 10.3 1.0 HB2 B:ALA193 4.5 14.4 1.0 H B:ARG186 4.5 12.7 1.0 C B:ASN185 4.6 10.0 1.0 O22 B:TDP701 4.6 10.6 1.0 N B:ARG186 4.6 10.6 1.0 HZ3 B:LYS244 4.7 12.4 1.0 CA B:ASN185 4.7 10.4 1.0 CD B:LYS244 4.7 11.1 1.0 HA3 B:GLY154 4.7 12.9 1.0 HB3 B:ASP155 4.8 12.3 1.0 HZ1 B:LYS244 4.8 12.4 1.0 C B:ARG186 4.8 10.8 1.0 C B:ASP155 4.8 10.1 1.0 CB B:LEU187 4.8 11.2 1.0 HA B:LEU187 4.8 12.2 1.0 HA2 B:GLY154 4.8 12.9 1.0 H B:GLY188 4.9 12.7 1.0 HA3 B:GLY156 4.9 11.8 1.0 HB3 B:ASN185 4.9 13.1 1.0 HA3 B:GLY188 4.9 12.1 1.0 HB2 B:ASN185 5.0 13.1 1.0 CE B:LYS244 5.0 11.3 1.0 O B:ASN185 5.0 10.9 1.0

S.Dai, L.M.Funk, F.R.Von Pappenheim, V.Sautner, M.Paulikat, B.Schroder, J.Uranga, R.A.Mata, K.Tittmann. Low-Barrier Hydrogen Bonds in Enzyme Cooperativity. Nature V. 573 609 2019.
ISSN: ESSN 1476-4687
PubMed: 31534226
DOI: 10.1038/S41586-019-1581-9