Sodium 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:

Calcium

(Ca)

2 atoms

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

Sodium 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 Sodium with other atoms in the Na 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:Na708 b:7.5 occ:1.00 O A:HOH8041 2.2 10.7 1.0 O A:ALA461 2.3 7.8 1.0 OD1 A:ASN411 2.3 6.3 1.0 O A:HOH8042 2.3 7.6 1.0 O A:THR464 2.4 8.3 1.0 CG A:ASN411 3.2 6.3 1.0 SG A:CYS468 3.2 8.5 1.0 C A:ALA461 3.4 7.5 1.0 C A:THR464 3.5 7.0 1.0 ND2 A:ASN411 3.5 7.6 1.0 N A:THR464 4.0 8.1 1.0 CB A:CYS468 4.0 6.4 1.0 CA A:THR464 4.1 8.1 1.0 CA A:ALA461 4.2 7.4 1.0 C A:ALA462 4.2 8.5 1.0 O A:ALA462 4.2 9.6 1.0 N A:ALA462 4.3 7.0 1.0 CA A:ALA462 4.3 7.7 1.0 CB A:THR464 4.4 8.9 1.0 O A:GLY466 4.5 8.4 1.0 O A:ILE410 4.5 5.9 1.0 N A:LYS465 4.6 7.6 1.0 CB A:ALA461 4.6 6.9 1.0 CB A:ASN411 4.6 5.9 1.0 O A:HOH8020 4.6 10.2 1.0 C A:ILE410 4.8 5.7 1.0 N A:ASN463 4.8 7.8 1.0 CA A:LYS465 4.9 8.1 1.0 O A:HOH8634 4.9 53.6 1.0 C A:LYS465 4.9 7.9 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na1014 b:11.2 occ:1.00 O B:ALA461 2.2 11.2 1.0 O B:HOH1131 2.2 14.4 1.0 OD1 B:ASN411 2.4 9.9 1.0 O B:THR464 2.4 12.0 1.0 O B:HOH1166 2.4 12.9 1.0 SG B:CYS468 3.2 12.2 1.0 CG B:ASN411 3.3 7.9 1.0 C B:ALA461 3.3 10.6 1.0 C B:THR464 3.5 11.6 1.0 ND2 B:ASN411 3.5 10.1 1.0 N B:THR464 3.9 12.0 1.0 CB B:CYS468 4.0 9.2 1.0 CA B:THR464 4.1 12.2 1.0 CA B:ALA461 4.2 11.5 1.0 N B:ALA462 4.3 11.3 1.0 C B:ALA462 4.3 12.9 1.0 O B:ALA462 4.3 14.3 1.0 CB B:THR464 4.3 12.7 1.0 CA B:ALA462 4.3 12.6 1.0 O B:GLY466 4.4 11.5 1.0 O B:ILE410 4.5 9.5 1.0 CB B:ALA461 4.6 10.2 1.0 N B:LYS465 4.6 11.9 1.0 O B:HOH1151 4.6 13.3 1.0 CB B:ASN411 4.7 9.1 1.0 N B:ASN463 4.8 13.0 1.0 C B:ILE410 4.8 8.3 1.0 CA B:LYS465 4.9 11.5 1.0 C B:LYS465 5.0 10.6 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