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Chlorine in PDB 7dkm: Phgdh Covalently Linked to Oridonin

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 7dkm:

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

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Phgdh Covalently Linked to Oridonin (pdb code 7dkm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Phgdh Covalently Linked to Oridonin, PDB code: 7dkm:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 7dkm

Go back to Chlorine Binding Sites List in 7dkm
Chlorine binding site 1 out of 2 in the Phgdh Covalently Linked to Oridonin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Phgdh Covalently Linked to Oridonin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:73.9
occ:1.00
O B:HOH705 4.1 42.5 1.0
O A:HOH702 4.5 37.2 1.0
O A:HOH687 4.6 43.3 1.0
O A:HOH589 4.6 34.7 1.0
O B:HOH538 4.7 33.7 1.0
O B:HOH734 4.8 38.0 1.0
O B:HOH726 4.9 60.7 1.0
O B:HOH569 4.9 42.4 1.0
O A:HOH720 4.9 52.5 1.0

Chlorine binding site 2 out of 2 in 7dkm

Go back to Chlorine Binding Sites List in 7dkm
Chlorine binding site 2 out of 2 in the Phgdh Covalently Linked to Oridonin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Phgdh Covalently Linked to Oridonin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:85.7
occ:1.00
O A:PRO176 3.9 35.8 1.0
O A:ILE178 4.1 36.9 1.0
O A:HOH537 4.3 54.0 1.0
CA A:SER179 4.3 37.9 1.0
C A:ILE178 4.5 36.2 1.0
CD A:PRO180 4.5 39.1 1.0
N A:SER179 4.6 37.0 1.0
C A:PRO176 4.6 35.8 1.0
C A:ILE177 4.7 37.9 1.0
O A:ILE177 4.8 43.2 1.0
CB A:SER179 5.0 40.0 1.0
O A:ASP175 5.0 35.3 1.0

Reference:

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
Page generated: Sun Jul 13 00:07:43 2025

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