Magnesium in PDB 2zdy: Inhibitor-Bound Structures of Human Pyruvate Dehydrogenase Kinase 4

All present enzymatic activity of Inhibitor-Bound Structures of Human Pyruvate Dehydrogenase Kinase 4:
2.7.11.2;

The structure of Inhibitor-Bound Structures of Human Pyruvate Dehydrogenase Kinase 4, PDB code: 2zdy was solved by M.Kawamoto, I.Shiromizu, M.Kukimoto-Niino, A.Tokmakov, T.Terada, M.Shirouzu, T.Matsusue, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.78 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	70.713, 69.090, 81.492, 90.00, 99.66, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Magnesium atom in the Inhibitor-Bound Structures of Human Pyruvate Dehydrogenase Kinase 4 (pdb code 2zdy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Inhibitor-Bound Structures of Human Pyruvate Dehydrogenase Kinase 4, PDB code: 2zdy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Inhibitor-Bound Structures of Human Pyruvate Dehydrogenase Kinase 4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Inhibitor-Bound Structures of Human Pyruvate Dehydrogenase Kinase 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg500 b:47.1 occ:1.00 OD1 A:ASN258 2.4 21.8 1.0 O2B A:ADP501 2.5 42.5 1.0 O1A A:ADP501 2.6 39.0 1.0 O A:HOH676 2.8 32.7 1.0 CG A:ASN258 3.3 22.6 1.0 OE1 A:GLU254 3.5 23.3 1.0 ND2 A:ASN258 3.7 20.7 1.0 PB A:ADP501 3.7 41.7 1.0 PA A:ADP501 3.8 39.2 1.0 O A:GLU254 4.0 22.4 1.0 O3A A:ADP501 4.0 41.8 1.0 O A:LEU327 4.1 61.6 1.0 CE A:LYS257 4.3 32.4 1.0 CA A:GLY333 4.3 26.8 1.0 O5' A:ADP501 4.4 35.7 1.0 O3B A:ADP501 4.5 40.0 1.0 CB A:LYS257 4.6 24.4 1.0 NZ A:LYS257 4.6 35.2 1.0 N A:ASN258 4.6 25.7 1.0 CB A:ASN258 4.7 23.3 1.0 O A:HOH639 4.7 36.9 1.0 CD A:GLU254 4.8 19.9 1.0 O1B A:ADP501 4.8 41.6 1.0 C A:GLU254 4.8 20.5 1.0 N A:GLY333 4.8 29.6 1.0 CA A:ASN258 4.9 25.4 1.0 CA A:GLU254 5.0 20.2 1.0

Magnesium binding site 2 out of 2 in the Inhibitor-Bound Structures of Human Pyruvate Dehydrogenase Kinase 4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Inhibitor-Bound Structures of Human Pyruvate Dehydrogenase Kinase 4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1500 b:60.4 occ:1.00 O3B B:ADP1501 2.5 51.7 1.0 OD1 B:ASN258 2.6 27.8 1.0 O1A B:ADP1501 2.7 50.7 1.0 OE1 B:GLU254 3.2 40.7 1.0 CG B:ASN258 3.4 25.8 1.0 O B:GLU254 3.7 25.1 1.0 ND2 B:ASN258 3.7 25.7 1.0 PA B:ADP1501 3.9 49.7 1.0 CE B:LYS257 3.9 41.0 1.0 PB B:ADP1501 4.0 52.7 1.0 CB B:LYS257 4.2 29.7 1.0 O3A B:ADP1501 4.2 52.2 1.0 CA B:GLY333 4.4 38.2 1.0 CD B:GLU254 4.4 37.0 1.0 O5' B:ADP1501 4.5 48.2 1.0 NZ B:LYS257 4.5 39.5 1.0 N B:ASN258 4.5 29.2 1.0 C B:GLU254 4.5 24.9 1.0 CA B:GLU254 4.6 25.6 1.0 O1B B:ADP1501 4.6 52.9 1.0 CB B:ASN258 4.7 27.1 1.0 CD B:LYS257 4.7 38.2 1.0 CB B:GLU254 4.7 27.4 1.0 CA B:ASN258 4.9 27.0 1.0 N B:GLY333 5.0 42.2 1.0

M.Kukimoto-Niino, A.Tokmakov, T.Terada, N.Ohbayashi, T.Fujimoto, S.Gomi, I.Shiromizu, M.Kawamoto, T.Matsusue, M.Shirouzu, S.Yokoyama. Inhibitor-Bound Structures of Human Pyruvate Dehydrogenase Kinase 4. Acta Crystallogr.,Sect.D V. 67 763 2011.
ISSN: ISSN 0907-4449
PubMed: 21904029
DOI: 10.1107/S090744491102405X