Calcium in PDB 8waa: Human Transketolase Soaked with Donor Ketose D-Xylulose

The structure of Human Transketolase Soaked with Donor Ketose D-Xylulose, PDB code: 8waa was solved by Z.Liu, S.Dai, K.Tittmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.25 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.5, 86.55, 92.7, 90, 93.85, 90
R / Rfree (%)	15.7 / 18.1

The binding sites of Calcium atom in the Human Transketolase Soaked with Donor Ketose D-Xylulose (pdb code 8waa). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Human Transketolase Soaked with Donor Ketose D-Xylulose, PDB code: 8waa:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Human Transketolase Soaked with Donor Ketose D-Xylulose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Transketolase Soaked with Donor Ketose D-Xylulose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:22.2 occ:1.00 OD1 A:ASP155 2.1 15.2 1.0 O A:LEU187 2.1 16.7 1.0 O2A A:THD703 2.2 15.6 1.0 OD1 A:ASN185 2.2 16.1 1.0 O1B A:THD703 2.2 19.6 1.0 O A:HOH862 2.3 17.0 1.0 CG A:ASN185 3.1 17.4 1.0 CG A:ASP155 3.2 16.3 1.0 PB A:THD703 3.3 17.2 1.0 C A:LEU187 3.3 14.8 1.0 PA A:THD703 3.3 15.9 1.0 O3A A:THD703 3.5 15.6 1.0 ND2 A:ASN185 3.5 14.6 1.0 O3B A:THD703 3.7 20.9 1.0 OD2 A:ASP155 3.9 18.1 1.0 N A:ASP155 3.9 14.5 1.0 N A:LEU187 3.9 15.7 1.0 N A:GLY156 4.1 15.5 1.0 N A:GLY188 4.2 16.9 1.0 O7 A:THD703 4.2 16.7 1.0 CA A:LEU187 4.2 15.8 1.0 NZ A:LYS244 4.3 16.2 1.0 CA A:GLY188 4.3 17.3 1.0 O A:ASP183 4.4 14.8 1.0 CB A:ASP155 4.4 14.4 1.0 O1A A:THD703 4.5 17.0 1.0 CB A:ASN185 4.5 18.4 1.0 N A:ASN185 4.5 14.8 1.0 CA A:ASP155 4.5 16.1 1.0 O2B A:THD703 4.6 19.6 1.0 C A:ASN185 4.6 18.1 1.0 N A:ARG186 4.7 15.9 1.0 CD A:LYS244 4.7 16.9 1.0 CA A:ASN185 4.8 17.3 1.0 C A:ASP155 4.8 15.5 1.0 C A:ARG186 4.9 16.6 1.0 C A:GLY154 4.9 13.8 1.0 CB A:LEU187 4.9 16.7 1.0 CE A:LYS244 4.9 16.7 1.0

Calcium binding site 2 out of 2 in the Human Transketolase Soaked with Donor Ketose D-Xylulose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Transketolase Soaked with Donor Ketose D-Xylulose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca701 b:21.0 occ:1.00 OD1 B:ASP155 2.1 15.2 1.0 O B:LEU187 2.1 16.1 1.0 O3B B:THD703 2.1 14.9 1.0 O2A B:THD703 2.1 15.4 1.0 OD1 B:ASN185 2.1 15.9 1.0 O B:HOH973 2.3 14.9 1.0 CG B:ASN185 3.1 16.8 1.0 PB B:THD703 3.3 15.9 1.0 CG B:ASP155 3.3 15.2 1.0 C B:LEU187 3.3 16.3 1.0 PA B:THD703 3.3 15.1 1.0 O3A B:THD703 3.5 15.2 1.0 ND2 B:ASN185 3.5 16.0 1.0 O1B B:THD703 3.8 15.8 1.0 OD2 B:ASP155 3.9 17.1 1.0 N B:LEU187 4.0 15.7 1.0 N B:ASP155 4.0 13.3 1.0 O7 B:THD703 4.1 16.0 1.0 N B:GLY156 4.1 16.2 1.0 N B:GLY188 4.2 15.9 1.0 CA B:LEU187 4.2 16.9 1.0 NZ B:LYS244 4.3 14.9 1.0 O B:ASP183 4.4 15.8 1.0 CA B:GLY188 4.4 16.5 1.0 O1A B:THD703 4.4 15.9 1.0 CB B:ASP155 4.5 15.0 1.0 CB B:ASN185 4.5 16.6 1.0 N B:ASN185 4.5 14.1 1.0 O2B B:THD703 4.5 16.5 1.0 CA B:ASP155 4.6 14.7 1.0 C B:ASN185 4.6 15.6 1.0 N B:ARG186 4.7 16.5 1.0 CD B:LYS244 4.7 14.9 1.0 CA B:ASN185 4.8 14.9 1.0 C B:ASP155 4.9 13.7 1.0 C B:ARG186 4.9 17.2 1.0 CB B:LEU187 4.9 18.7 1.0 CE B:LYS244 4.9 14.6 1.0 C B:GLY154 5.0 16.3 1.0

Z.Liu, C.Xiao, S.Lin, K.Tittmann, S.Dai. Multifaceted Role of the Substrate Phosphate Group in Transketolase Catalysis Acs Catalysis V. 14 355 2024.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.3C04543