Magnesium in PDB 7ebb: Crystal Structure of Human Pyruvate Dehydrogenase Kinase 4 in Complex with Compound 2

All present enzymatic activity of Crystal Structure of Human Pyruvate Dehydrogenase Kinase 4 in Complex with Compound 2:
2.7.11.2;

The structure of Crystal Structure of Human Pyruvate Dehydrogenase Kinase 4 in Complex with Compound 2, PDB code: 7ebb was solved by T.Orita, S.Doi, T.Iwanaga, T.Adachi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	80.02 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	70.624, 69.36, 81.283, 90, 100.12, 90
R / Rfree (%)	19.5 / 21.9

The binding sites of Magnesium atom in the Crystal Structure of Human Pyruvate Dehydrogenase Kinase 4 in Complex with Compound 2 (pdb code 7ebb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Human Pyruvate Dehydrogenase Kinase 4 in Complex with Compound 2, PDB code: 7ebb:

Magnesium binding site 1 out of 1 in the Crystal Structure of Human Pyruvate Dehydrogenase Kinase 4 in Complex with Compound 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Pyruvate Dehydrogenase Kinase 4 in Complex with Compound 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:26.4 occ:1.00 O2A B:ADP504 2.0 25.8 1.0 O2 B:SO4505 2.1 26.8 1.0 O3B B:ADP504 2.1 26.7 1.0 O B:HOH631 2.1 23.7 1.0 O B:HOH687 2.1 28.4 1.0 OD1 B:ASN258 2.2 26.9 1.0 CG B:ASN258 3.1 23.3 1.0 PA B:ADP504 3.1 27.6 1.0 PB B:ADP504 3.2 29.4 1.0 O3A B:ADP504 3.2 31.7 1.0 S B:SO4505 3.3 34.4 1.0 ND2 B:ASN258 3.4 22.9 1.0 O1 B:SO4505 3.7 33.9 1.0 O B:HOH616 3.8 26.7 1.0 O2B B:ADP504 3.8 29.6 1.0 O4 B:SO4505 3.9 30.1 1.0 O5' B:ADP504 3.9 26.4 1.0 OE1 B:GLU254 4.0 26.1 1.0 CA B:GLY333 4.1 23.0 1.0 O B:HOH736 4.2 29.0 1.0 O B:GLU254 4.3 23.3 1.0 O1A B:ADP504 4.4 23.9 1.0 N B:GLY333 4.4 28.4 1.0 O3 B:SO4505 4.5 29.9 1.0 O1B B:ADP504 4.5 33.0 1.0 CB B:ASN258 4.5 22.6 1.0 O B:LEU327 4.7 33.8 1.0 N B:ASN258 4.8 23.1 1.0 CA B:ASN258 4.9 23.4 1.0

T.Akaki, Y.Bessho, T.Ito, S.Fujioka, M.Ubukata, G.Mori, K.Yamanaka, T.Orita, S.Doi, T.Iwanaga, K.Ikegashira, Y.Hantani, I.Nakanishi, T.Adachi. Fragment-Based Lead Discovery to Identify Novel Inhibitors That Target the Atp Binding Site of Pyruvate Dehydrogenase Kinases. Bioorg.Med.Chem. V. 44 16283 2021.
ISSN: ESSN 1464-3391
PubMed: 34274549
DOI: 10.1016/J.BMC.2021.116283