Calcium in PDB 4kxy: Human Transketolase in Complex with Thdp Analogue (R)-2-(1,2- Dihydroxyethyl)-3-Deaza-Thdp

All present enzymatic activity of Human Transketolase in Complex with Thdp Analogue (R)-2-(1,2- Dihydroxyethyl)-3-Deaza-Thdp:
2.2.1.1;

The structure of Human Transketolase in Complex with Thdp Analogue (R)-2-(1,2- Dihydroxyethyl)-3-Deaza-Thdp, PDB code: 4kxy was solved by P.Neumann, S.Luedtke, K.M.Erixon, F.Leeper, R.Kluger, R.Ficner, K.Tittmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.26
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.150, 86.050, 92.730, 90.00, 94.12, 90.00
R / Rfree (%)	16.4 / 20.4

The structure of Human Transketolase in Complex with Thdp Analogue (R)-2-(1,2- Dihydroxyethyl)-3-Deaza-Thdp also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Calcium atom in the Human Transketolase in Complex with Thdp Analogue (R)-2-(1,2- Dihydroxyethyl)-3-Deaza-Thdp (pdb code 4kxy). 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 in Complex with Thdp Analogue (R)-2-(1,2- Dihydroxyethyl)-3-Deaza-Thdp, PDB code: 4kxy:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Human Transketolase in Complex with Thdp Analogue (R)-2-(1,2- Dihydroxyethyl)-3-Deaza-Thdp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Transketolase in Complex with Thdp Analogue (R)-2-(1,2- Dihydroxyethyl)-3-Deaza-Thdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca707 b:6.0 occ:1.00 OD1 A:ASP155 2.2 6.1 1.0 O1A A:1U0709 2.2 5.9 1.0 O A:LEU187 2.3 6.3 1.0 OD1 A:ASN185 2.3 6.5 1.0 O1B A:1U0709 2.3 5.5 1.0 O A:HOH8484 2.5 6.4 1.0 CG A:ASN185 3.2 6.1 1.0 C A:LEU187 3.4 6.2 1.0 PB A:1U0709 3.4 6.5 1.0 CG A:ASP155 3.4 5.6 1.0 ND2 A:ASN185 3.4 7.7 1.0 PA A:1U0709 3.5 6.2 1.0 O3A A:1U0709 3.5 6.9 1.0 O2B A:1U0709 3.8 6.5 1.0 N A:LEU187 4.0 7.2 1.0 OD2 A:ASP155 4.0 6.5 1.0 N A:ASP155 4.1 5.7 1.0 NZ A:LYS244 4.1 8.5 1.0 N A:GLY156 4.2 5.6 1.0 O7 A:1U0709 4.2 6.0 1.0 N A:GLY188 4.3 6.8 1.0 CA A:LEU187 4.3 6.2 1.0 CA A:GLY188 4.4 7.5 1.0 O A:ASP183 4.5 6.2 1.0 CB A:ASN185 4.5 6.6 1.0 CB A:ASP155 4.6 5.5 1.0 N A:ARG186 4.6 6.1 1.0 C A:ASN185 4.6 7.1 1.0 O2A A:1U0709 4.6 6.0 1.0 N A:ASN185 4.6 6.5 1.0 O3B A:1U0709 4.7 6.6 1.0 CA A:ASP155 4.7 5.0 1.0 CD A:LYS244 4.7 6.2 1.0 CA A:ASN185 4.8 6.8 1.0 C A:ARG186 4.9 6.2 1.0 C A:ASP155 4.9 4.3 1.0 CE A:LYS244 4.9 6.5 1.0

Calcium binding site 2 out of 2 in the Human Transketolase in Complex with Thdp Analogue (R)-2-(1,2- Dihydroxyethyl)-3-Deaza-Thdp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Transketolase in Complex with Thdp Analogue (R)-2-(1,2- Dihydroxyethyl)-3-Deaza-Thdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1007 b:6.0 occ:1.00 O2A B:1U01006 2.2 6.7 1.0 O B:LEU187 2.2 7.1 1.0 OD1 B:ASP155 2.3 7.1 1.0 OD1 B:ASN185 2.3 6.3 1.0 O3B B:1U01006 2.3 6.5 1.0 O B:HOH1101 2.5 6.3 1.0 CG B:ASN185 3.2 5.6 1.0 C B:LEU187 3.4 5.2 1.0 PB B:1U01006 3.4 7.1 1.0 CG B:ASP155 3.4 5.3 1.0 PA B:1U01006 3.5 6.6 1.0 ND2 B:ASN185 3.5 6.5 1.0 O3A B:1U01006 3.6 6.7 1.0 O1B B:1U01006 3.8 7.5 1.0 N B:LEU187 4.0 5.6 1.0 OD2 B:ASP155 4.1 6.7 1.0 N B:ASP155 4.1 5.3 1.0 NZ B:LYS244 4.1 9.2 1.0 N B:GLY156 4.2 5.9 1.0 O7 B:1U01006 4.2 6.8 1.0 N B:GLY188 4.3 6.4 1.0 CA B:LEU187 4.3 5.8 1.0 CA B:GLY188 4.4 5.7 1.0 O B:ASP183 4.5 6.2 1.0 CB B:ASN185 4.5 5.7 1.0 CB B:ASP155 4.5 5.4 1.0 O1A B:1U01006 4.6 7.0 1.0 N B:ARG186 4.6 5.2 1.0 N B:ASN185 4.6 5.8 1.0 C B:ASN185 4.6 6.6 1.0 O2B B:1U01006 4.7 7.9 1.0 CA B:ASP155 4.7 5.7 1.0 CD B:LYS244 4.7 6.0 1.0 CA B:ASN185 4.8 6.0 1.0 C B:ARG186 4.9 5.2 1.0 C B:ASP155 4.9 5.2 1.0 CE B:LYS244 5.0 6.6 1.0

S.Ludtke, P.Neumann, K.M.Erixon, F.Leeper, R.Kluger, R.Ficner, K.Tittmann. Sub-Angstrom-Resolution Crystallography Reveals Physical Distortions That Enhance Reactivity of A Covalent Enzymatic Intermediate. Nat Chem V. 5 762 2013.
PubMed: 23965678
DOI: 10.1038/NCHEM.1728