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Sodium in PDB 6ha3: Human Transketolase Variant E160Q in Covalent Complex with Donor Ketose D-Fructose-6-Phosphate

Enzymatic activity of Human Transketolase Variant E160Q in Covalent Complex with Donor Ketose D-Fructose-6-Phosphate

All present enzymatic activity of Human Transketolase Variant E160Q in Covalent Complex with Donor Ketose D-Fructose-6-Phosphate:
2.2.1.1;

Protein crystallography data

The structure of Human Transketolase Variant E160Q in Covalent Complex with Donor Ketose D-Fructose-6-Phosphate, PDB code: 6ha3 was solved by S.Dai, V.Sautner, K.Tittmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.56 / 1.08
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 114.070, 86.090, 73.210, 90.00, 125.22, 90.00
R / Rfree (%) 11.1 / 13

Other elements in 6ha3:

The structure of Human Transketolase Variant E160Q in Covalent Complex with Donor Ketose D-Fructose-6-Phosphate also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Transketolase Variant E160Q in Covalent Complex with Donor Ketose D-Fructose-6-Phosphate (pdb code 6ha3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Human Transketolase Variant E160Q in Covalent Complex with Donor Ketose D-Fructose-6-Phosphate, PDB code: 6ha3:

Sodium binding site 1 out of 1 in 6ha3

Go back to Sodium Binding Sites List in 6ha3
Sodium binding site 1 out of 1 in the Human Transketolase Variant E160Q in Covalent Complex with Donor Ketose D-Fructose-6-Phosphate


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 E160Q in Covalent Complex with Donor Ketose D-Fructose-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na708

b:11.3
occ:1.00
 O A:HOH897 2.3 15.3 1.0
O A:ALA461 2.3 11.2 1.0
O A:THR464 2.3 11.5 1.0
OD1 A:ASN411 2.4 10.6 1.0
O A:HOH1165 2.4 11.8 1.0
HG A:CYS468 2.6 14.0 1.0
HD21 A:ASN411 3.1 13.5 1.0
SG A:CYS468 3.2 11.7 1.0
CG A:ASN411 3.3 10.0 1.0
H A:THR464 3.3 13.8 1.0
C A:ALA461 3.4 10.7 1.0
C A:THR464 3.5 11.3 1.0
ND2 A:ASN411 3.5 11.2 1.0
HB2 A:CYS468 3.5 12.4 1.0
HB A:THR464 3.6 14.6 1.0
HA A:ALA462 3.9 13.9 1.0
N A:THR464 3.9 11.5 1.0
CB A:CYS468 4.0 10.4 1.0
HA A:ALA461 4.0 13.2 1.0
HB1 A:ALA461 4.0 13.7 1.0
CA A:THR464 4.1 12.1 1.0
O A:ALA462 4.2 12.6 1.0
C A:ALA462 4.2 11.9 1.0
CA A:ALA461 4.2 11.0 1.0
N A:ALA462 4.3 11.5 1.0
CA A:ALA462 4.3 11.6 1.0
HD22 A:ASN411 4.3 13.5 1.0
CB A:THR464 4.4 12.2 1.0
HB3 A:ASN409 4.4 13.0 1.0
HA A:LYS465 4.4 14.2 1.0
HB3 A:CYS468 4.5 12.4 1.0
O A:GLY466 4.5 11.8 1.0
O A:ILE410 4.5 10.3 1.0
H A:CYS468 4.6 11.2 1.0
N A:LYS465 4.6 11.8 1.0
CB A:ALA461 4.7 11.4 1.0
CB A:ASN411 4.7 9.9 1.0
O A:HOH1096 4.7 13.0 1.0
N A:ASN463 4.8 12.2 1.0
C A:ILE410 4.8 9.4 1.0
HA A:ASN411 4.8 11.4 1.0
HG22 A:THR464 4.8 15.8 1.0
CA A:LYS465 4.9 11.8 1.0
C A:LYS465 4.9 11.3 1.0
HB3 A:ASN411 4.9 11.9 1.0
HG13 A:VAL383 5.0 13.7 1.0

Reference:

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
Page generated: Tue Oct 8 09:16:06 2024

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