Sodium in PDB 7dkm: Phgdh Covalently Linked to Oridonin

All present enzymatic activity of Phgdh Covalently Linked to Oridonin:
1.1.1.37; 1.1.1.399; 1.1.1.95;

The structure of Phgdh Covalently Linked to Oridonin, PDB code: 7dkm was solved by Q.Sun, Y.Lei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.95 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.18, 126.47, 59.287, 90, 99.72, 90
R / Rfree (%)	13.6 / 17.1

The structure of Phgdh Covalently Linked to Oridonin also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Phgdh Covalently Linked to Oridonin (pdb code 7dkm). 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 Phgdh Covalently Linked to Oridonin, PDB code: 7dkm:

Sodium binding site 1 out of 1 in the Phgdh Covalently Linked to Oridonin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Phgdh Covalently Linked to Oridonin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:54.8 occ:1.00 OE1 B:GLN292 1.9 50.8 1.0 ND2 B:ASN102 2.6 43.0 1.0 CD B:GLN292 2.8 46.4 1.0 O B:HOH589 2.9 49.2 1.0 O B:ALA286 3.1 35.2 1.0 N B:GLN292 3.5 36.6 1.0 NE2 B:GLN292 3.5 50.1 1.0 C B:ALA291 3.5 35.4 1.0 CA B:GLN292 3.5 40.0 1.0 O B:HOH525 3.6 62.7 1.0 O B:ALA291 3.6 36.3 1.0 CG B:ASN102 3.6 40.5 1.0 CB B:ALA286 3.6 33.7 1.0 CG B:GLN292 3.7 43.3 1.0 SG B:CYS295 3.7 41.7 1.0 CB B:ALA291 3.8 33.2 1.0 OD1 B:ASN102 3.9 43.8 1.0 C B:ALA286 4.0 32.9 1.0 CB B:CYS295 4.2 42.9 1.0 CB B:GLN292 4.2 41.8 1.0 CA B:ALA291 4.3 33.2 1.0 CA B:ALA286 4.3 31.3 1.0 O B:ALA76 4.4 54.0 1.0 C B:GLN292 4.8 41.4 1.0 CB B:ASN102 4.9 37.7 1.0 NH2 B:ARG54 4.9 68.8 1.0

Y.Tan, X.Zhou, Y.Gong, K.Gou, Y.Luo, D.Jia, L.Dai, Y.Zhao, Q.Sun. Biophysical and Biochemical Properties of Phgdh Revealed By Studies on Phgdh Inhibitors. Cell.Mol.Life Sci. V. 79 27 2021.
ISSN: ESSN 1420-9071
PubMed: 34971423
DOI: 10.1007/S00018-021-04022-2