Sodium 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:

Magnesium	(Mg)	2 atoms
Calcium	(Ca)	2 atoms

The binding sites of Sodium atom in the Human Transketolase Variant T382E (pdb code 6rjb). 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 Variant T382E, PDB code: 6rjb:
Jump to Sodium binding site number: 1; 2;

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Transketolase Variant T382E within 5.0Å range: probe atom residue distance (Å) B Occ A:Na725 b:11.2 occ:1.00 O A:ALA461 2.2 11.4 1.0 O A:HOH844 2.3 14.5 1.0 OD1 A:ASN411 2.3 11.0 1.0 O A:THR464 2.4 11.7 1.0 O A:HOH1143 2.4 11.9 1.0 HG A:CYS468 2.5 14.2 1.0 HD21 A:ASN411 3.1 13.8 1.0 SG A:CYS468 3.2 11.8 1.0 CG A:ASN411 3.3 10.5 1.0 H A:THR464 3.3 13.9 1.0 C A:ALA461 3.4 10.9 1.0 C A:THR464 3.5 10.9 1.0 ND2 A:ASN411 3.5 11.5 1.0 HB2 A:CYS468 3.6 13.5 1.0 HB A:THR464 3.6 14.9 1.0 H12 A:EDO723 3.8 62.3 1.0 HA A:ALA462 3.9 13.9 1.0 N A:THR464 3.9 11.6 1.0 HA A:ALA461 4.0 13.1 1.0 HB1 A:ALA461 4.0 14.8 1.0 CB A:CYS468 4.0 11.3 1.0 CA A:THR464 4.1 11.7 1.0 CA A:ALA461 4.2 10.9 1.0 O A:ALA462 4.2 12.8 1.0 C A:ALA462 4.2 11.5 1.0 N A:ALA462 4.3 10.8 1.0 HB3 A:ASN409 4.3 12.8 1.0 CA A:ALA462 4.3 11.6 1.0 CB A:THR464 4.3 12.4 1.0 HD22 A:ASN411 4.4 13.8 1.0 H21 A:EDO723 4.4 62.5 1.0 HA A:LYS465 4.5 15.5 0.5 O A:GLY466 4.5 12.6 1.0 O A:ILE410 4.5 10.0 1.0 HA A:LYS465 4.5 13.5 0.5 HB3 A:CYS468 4.5 13.5 1.0 H A:CYS468 4.5 12.2 1.0 N A:LYS465 4.6 10.6 0.5 N A:LYS465 4.6 11.6 0.5 CB A:ALA461 4.6 12.3 1.0 CB A:ASN411 4.6 10.4 1.0 O A:HOH1043 4.7 14.1 1.0 C1 A:EDO723 4.7 51.9 1.0 N A:ASN463 4.8 12.0 1.0 C A:ILE410 4.8 9.2 1.0 HG22 A:THR464 4.8 14.8 1.0 HA A:ASN411 4.8 11.3 1.0 H11 A:EDO723 4.9 62.3 1.0 C A:LYS465 4.9 11.4 0.5 CA A:LYS465 4.9 11.2 0.5 CA A:LYS465 4.9 12.9 0.5 HB3 A:ASN411 4.9 12.4 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Transketolase Variant T382E within 5.0Å range: probe atom residue distance (Å) B Occ A:Na726 b:16.7 occ:1.00 H A:GLN127 2.2 11.3 1.0 H A:GLY128 2.5 11.4 1.0 HG A:SER74 2.9 12.1 1.0 O A:SER124 2.9 11.9 1.0 O A:SER74 3.0 9.9 1.0 N A:GLN127 3.0 9.4 1.0 H A:GLY126 3.0 11.2 1.0 HA A:LEU125 3.0 12.1 1.0 HB2 A:GLN127 3.0 12.0 1.0 HB A:THR122 3.1 13.1 0.6 OG A:SER74 3.1 10.1 1.0 N A:GLY128 3.1 9.5 1.0 HG22 A:THR122 3.2 13.9 0.6 HB A:THR122 3.3 16.7 0.4 N A:GLY126 3.3 9.3 1.0 O A:THR122 3.3 14.8 0.4 HA A:SER74 3.4 11.6 1.0 OE2 A:GLU157 3.5 11.1 1.0 O A:HOH1087 3.5 12.9 0.6 CA A:GLN127 3.6 9.2 1.0 C A:LEU125 3.7 9.6 1.0 CA A:LEU125 3.7 10.1 1.0 CB A:GLN127 3.7 10.0 1.0 C A:GLN127 3.8 9.6 1.0 CG2 A:THR122 3.8 11.6 0.6 CB A:THR122 3.8 10.9 0.6 C A:SER74 3.8 9.5 1.0 HG21 A:THR122 3.9 13.9 0.6 C A:SER124 3.9 11.0 1.0 HA3 A:GLY128 3.9 11.9 1.0 O A:HOH995 3.9 16.0 1.0 H A:GLY123 3.9 14.9 0.6 HA A:THR122 3.9 17.1 0.4 CA A:SER74 3.9 9.6 1.0 HG22 A:THR122 4.0 17.2 0.4 C A:GLY126 4.0 9.1 1.0 HG3 A:GLN127 4.0 12.9 1.0 CB A:THR122 4.0 13.9 0.4 CA A:GLY128 4.0 10.0 1.0 CB A:SER74 4.1 10.2 1.0 C A:THR122 4.1 13.8 0.4 CA A:GLY126 4.2 9.7 1.0 HA A:THR122 4.2 15.0 0.6 N A:LEU125 4.3 10.6 1.0 CA A:THR122 4.3 14.2 0.4 HD23 A:LEU125 4.3 17.6 1.0 HA2 A:GLY128 4.3 11.9 1.0 CG2 A:THR122 4.4 14.3 0.4 CG A:GLN127 4.5 10.8 1.0 O A:HOH901 4.5 11.8 0.3 HA2 A:GLY126 4.5 11.6 1.0 HG21 A:THR122 4.5 17.2 0.4 HB3 A:GLN127 4.5 12.0 1.0 O A:LEU125 4.5 10.4 1.0 HA A:GLN127 4.6 11.1 1.0 CA A:THR122 4.6 12.5 0.6 HG23 A:THR122 4.7 13.9 0.6 N A:GLY123 4.7 12.4 0.6 CD A:GLU157 4.7 10.4 1.0 HB2 A:SER74 4.7 12.3 1.0 HB3 A:SER74 4.7 12.3 1.0 O A:HOH823 4.8 22.5 1.0 HG1 A:THR122 4.8 12.2 0.6 H A:GLY76 4.9 11.9 1.0 OG1 A:THR122 4.9 10.1 0.6 O A:GLN127 4.9 10.2 1.0 H A:SER124 4.9 13.6 0.6 HA3 A:GLY126 5.0 11.6 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