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Sodium in PDB 4kxw: Human Transketolase in Covalent Complex with Donor Ketose D-Xylulose- 5-Phosphate, Crystal 2

Enzymatic activity of Human Transketolase in Covalent Complex with Donor Ketose D-Xylulose- 5-Phosphate, Crystal 2

All present enzymatic activity of Human Transketolase in Covalent Complex with Donor Ketose D-Xylulose- 5-Phosphate, Crystal 2:
2.2.1.1;

Protein crystallography data

The structure of Human Transketolase in Covalent Complex with Donor Ketose D-Xylulose- 5-Phosphate, Crystal 2, PDB code: 4kxw 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 / 0.97
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.756, 86.017, 72.994, 90.00, 125.46, 90.00
R / Rfree (%) 9.5 / 12.1

Other elements in 4kxw:

The structure of Human Transketolase in Covalent Complex with Donor Ketose D-Xylulose- 5-Phosphate, Crystal 2 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-Xylulose- 5-Phosphate, Crystal 2 (pdb code 4kxw). 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-Xylulose- 5-Phosphate, Crystal 2, PDB code: 4kxw:

Sodium binding site 1 out of 1 in 4kxw

Go back to Sodium Binding Sites List in 4kxw
Sodium binding site 1 out of 1 in the Human Transketolase in Covalent Complex with Donor Ketose D-Xylulose- 5-Phosphate, Crystal 2


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-Xylulose- 5-Phosphate, Crystal 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1013

b:7.8
occ:1.00
 O A:ALA461 2.2 7.2 1.0
O A:HOH7081 2.2 11.6 1.0
O A:THR464 2.3 8.6 1.0
OD1 A:ASN411 2.4 7.2 1.0
O A:HOH7070 2.4 8.8 1.0
SG A:CYS468 3.2 9.2 1.0
CG A:ASN411 3.3 6.1 1.0
C A:ALA461 3.3 7.1 1.0
C A:THR464 3.5 7.6 1.0
ND2 A:ASN411 3.5 8.1 1.0
N A:THR464 3.9 8.4 1.0
CB A:CYS468 4.0 7.2 1.0
CA A:THR464 4.1 8.5 1.0
CA A:ALA461 4.2 7.1 1.0
C A:ALA462 4.2 8.0 1.0
O A:ALA462 4.2 9.2 1.0
N A:ALA462 4.3 7.3 1.0
CA A:ALA462 4.3 7.8 1.0
CB A:THR464 4.3 8.9 1.0
O A:GLY466 4.5 9.6 1.0
O A:ILE410 4.5 6.5 1.0
N A:LYS465 4.6 8.1 1.0
CB A:ALA461 4.6 7.7 1.0
CB A:ASN411 4.7 6.0 1.0
O A:HOH7052 4.7 10.5 1.0
N A:ASN463 4.8 8.2 1.0
O A:HOH7721 4.8 34.0 0.8
C A:ILE410 4.8 5.5 1.0
CA A:LYS465 4.9 8.5 1.0
C A:LYS465 4.9 7.6 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 16:37:39 2024

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