Chlorine in PDB 6lin: Crystal Structure of Human PDK2 Complexed with GM10030

All present enzymatic activity of Crystal Structure of Human PDK2 Complexed with GM10030:
2.7.11.2;

The structure of Crystal Structure of Human PDK2 Complexed with GM10030, PDB code: 6lin was solved by J.Kang, J.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.08 / 2.67
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.420, 156.186, 102.012, 90.00, 103.97, 90.00
R / Rfree (%)	22.3 / 28

The structure of Crystal Structure of Human PDK2 Complexed with GM10030 also contains other interesting chemical elements:

Fluorine

(F)

8 atoms

The binding sites of Chlorine atom in the Crystal Structure of Human PDK2 Complexed with GM10030 (pdb code 6lin). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Human PDK2 Complexed with GM10030, PDB code: 6lin:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Human PDK2 Complexed with GM10030


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human PDK2 Complexed with GM10030 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl403 b:40.3 occ:1.00 CL9 A:EH0403 0.0 40.3 1.0 C04 A:EH0403 1.8 39.4 1.0 C05 A:EH0403 2.7 36.4 1.0 C03 A:EH0403 2.8 39.6 1.0 O08 A:EH0403 2.9 42.1 1.0 ND2 A:ASN255 3.2 38.3 1.0 CD2 A:LEU346 3.7 48.5 1.0 CD2 A:LEU330 3.7 44.8 1.0 CD1 A:LEU303 3.8 36.2 1.0 CG A:ASN255 4.0 39.7 1.0 C06 A:EH0403 4.0 39.2 1.0 C02 A:EH0403 4.1 32.8 1.0 CB A:ASN255 4.1 42.2 1.0 CD1 A:LEU330 4.2 43.0 1.0 CG A:LEU330 4.4 43.0 1.0 CB A:LEU303 4.4 36.3 1.0 CD1 A:LEU346 4.4 43.9 1.0 CG A:LEU303 4.5 35.4 1.0 C01 A:EH0403 4.5 36.3 1.0 CD2 A:LEU303 4.5 33.5 1.0 CB A:LEU330 4.6 41.0 1.0 CG A:LEU346 4.7 43.5 1.0 OD1 A:ASN255 5.0 39.8 1.0 C22 A:EH0403 5.0 60.0 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Human PDK2 Complexed with GM10030


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human PDK2 Complexed with GM10030 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl402 b:38.2 occ:1.00 CL9 B:EH0402 0.0 38.2 1.0 C04 B:EH0402 1.8 35.6 1.0 C05 B:EH0402 2.6 36.1 1.0 C03 B:EH0402 2.8 33.1 1.0 O08 B:EH0402 3.1 35.8 1.0 ND2 B:ASN255 3.3 38.5 1.0 CD2 B:LEU346 3.4 55.7 1.0 CD2 B:LEU330 3.6 46.9 1.0 CD1 B:LEU303 3.8 41.0 1.0 C06 B:EH0402 3.9 38.0 1.0 CG B:ASN255 4.0 41.3 1.0 C02 B:EH0402 4.1 31.8 1.0 CD1 B:LEU330 4.1 46.2 1.0 CB B:ASN255 4.2 40.2 1.0 CG B:LEU330 4.3 43.7 1.0 CB B:LEU303 4.4 42.9 1.0 C01 B:EH0402 4.4 36.2 1.0 CG B:LEU303 4.5 41.8 1.0 CB B:LEU330 4.6 41.3 1.0 CD2 B:LEU303 4.6 40.3 1.0 CG B:LEU346 4.8 50.5 1.0 C20 B:EH0402 4.9 51.9 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Human PDK2 Complexed with GM10030


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Human PDK2 Complexed with GM10030 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl402 b:42.8 occ:1.00 CL9 C:EH0402 0.0 42.8 1.0 C04 C:EH0402 1.7 38.2 1.0 C05 C:EH0402 2.6 36.3 1.0 C03 C:EH0402 2.7 39.7 1.0 O08 C:EH0402 3.0 37.8 1.0 ND2 C:ASN255 3.4 38.2 1.0 CD2 C:LEU346 3.7 40.0 1.0 CD2 C:LEU330 3.7 45.0 1.0 CD1 C:LEU303 3.8 36.1 1.0 C06 C:EH0402 3.9 39.7 1.0 C02 C:EH0402 4.0 35.6 1.0 CG C:ASN255 4.1 38.8 1.0 CB C:ASN255 4.2 39.4 1.0 CD1 C:LEU330 4.3 43.9 1.0 CB C:LEU303 4.3 41.6 1.0 CG C:LEU330 4.4 43.5 1.0 CG C:LEU303 4.4 38.2 1.0 C01 C:EH0402 4.4 35.9 1.0 CD1 C:LEU346 4.5 36.7 1.0 CD2 C:LEU303 4.5 40.0 1.0 CB C:LEU330 4.6 41.5 1.0 CG C:LEU346 4.7 36.7 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Human PDK2 Complexed with GM10030


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Human PDK2 Complexed with GM10030 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl401 b:40.5 occ:1.00 CL9 D:EH0401 0.0 40.5 1.0 C04 D:EH0401 1.8 33.7 1.0 C05 D:EH0401 2.7 32.5 1.0 C03 D:EH0401 2.7 28.5 1.0 O08 D:EH0401 3.0 24.4 1.0 ND2 D:ASN255 3.3 43.3 1.0 CD2 D:LEU346 3.6 46.3 1.0 CD2 D:LEU330 3.7 51.1 1.0 CD1 D:LEU303 3.8 42.7 1.0 C06 D:EH0401 3.9 34.9 1.0 CG D:ASN255 4.0 39.5 1.0 C02 D:EH0401 4.0 27.4 1.0 CB D:ASN255 4.1 37.5 1.0 CD1 D:LEU330 4.3 51.9 1.0 O40 D:EH0401 4.4 79.1 1.0 CB D:LEU303 4.4 41.3 1.0 CD1 D:LEU346 4.5 49.0 1.0 C01 D:EH0401 4.5 31.8 1.0 CG D:LEU330 4.5 51.3 1.0 CG D:LEU303 4.5 39.9 1.0 CD2 D:LEU303 4.5 39.9 1.0 CG D:LEU346 4.7 45.2 1.0 CB D:LEU330 4.8 49.5 1.0 C16 D:EH0401 4.9 43.9 1.0 C17 D:EH0401 5.0 46.9 1.0

J.Kang, H.S.Pagire, D.Kang, Y.H.Song, I.K.Lee, K.T.Lee, C.J.Park, J.H.Ahn, J.Kim. Structural Basis For the Inhibition of PDK2 By Novel Atp- and Lipoyl-Binding Site Targeting Compounds. Biochem.Biophys.Res.Commun. V. 527 778 2020.
ISSN: ESSN 1090-2104
PubMed: 32444142
DOI: 10.1016/J.BBRC.2020.04.102