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Sodium in PDB 4kxx: Human Transketolase in Covalent Complex with Donor Ketose D- Sedoheptulose-7-Phosphate

Enzymatic activity of Human Transketolase in Covalent Complex with Donor Ketose D- Sedoheptulose-7-Phosphate

All present enzymatic activity of Human Transketolase in Covalent Complex with Donor Ketose D- Sedoheptulose-7-Phosphate:
2.2.1.1;

Protein crystallography data

The structure of Human Transketolase in Covalent Complex with Donor Ketose D- Sedoheptulose-7-Phosphate, PDB code: 4kxx was solved by P.Neumann, S.Luedtke, 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 / 1.03
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.675, 86.097, 73.017, 90.00, 125.43, 90.00
R / Rfree (%) 11.7 / 14.8

Other elements in 4kxx:

The structure of Human Transketolase in Covalent Complex with Donor Ketose D- Sedoheptulose-7-Phosphate also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Transketolase in Covalent Complex with Donor Ketose D- Sedoheptulose-7-Phosphate (pdb code 4kxx). 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 in Covalent Complex with Donor Ketose D- Sedoheptulose-7-Phosphate, PDB code: 4kxx:

Sodium binding site 1 out of 1 in 4kxx

Go back to Sodium Binding Sites List in 4kxx
Sodium binding site 1 out of 1 in the Human Transketolase in Covalent Complex with Donor Ketose D- Sedoheptulose-7-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 in Covalent Complex with Donor Ketose D- Sedoheptulose-7-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1015

b:8.1
occ:1.00
 O A:ALA461 2.2 7.5 1.0
O A:HOH8062 2.3 10.7 1.0
OD1 A:ASN411 2.4 7.3 1.0
O A:THR464 2.4 8.2 1.0
O A:HOH8091 2.4 8.9 1.0
SG A:CYS468 3.2 8.7 1.0
CG A:ASN411 3.3 6.5 1.0
C A:ALA461 3.3 7.7 1.0
C A:THR464 3.5 7.4 1.0
ND2 A:ASN411 3.5 8.1 1.0
N A:THR464 3.9 9.3 1.0
CB A:CYS468 4.0 7.2 1.0
CA A:THR464 4.1 8.4 1.0
CA A:ALA461 4.2 7.4 1.0
C A:ALA462 4.2 8.2 1.0
O A:ALA462 4.2 9.7 1.0
N A:ALA462 4.3 8.5 1.0
CA A:ALA462 4.3 8.9 1.0
CB A:THR464 4.3 8.1 1.0
O A:GLY466 4.5 9.5 1.0
O A:ILE410 4.5 6.8 1.0
CB A:ALA461 4.6 8.0 1.0
N A:LYS465 4.6 7.3 1.0
CB A:ASN411 4.7 6.1 1.0
O A:HOH8052 4.7 10.8 1.0
N A:ASN463 4.7 8.6 1.0
C A:ILE410 4.8 5.2 1.0
CA A:LYS465 4.9 8.6 1.0
C A:LYS465 4.9 7.8 1.0
C A:ASN463 5.0 10.7 1.0

Reference:

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
Page generated: Mon Oct 7 16:38:16 2024

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