Magnesium in PDB 2e0a: Crystal Structure of Human Pyruvate Dehydrogenase Kinase 4 in Complex with Amppnp

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

The structure of Crystal Structure of Human Pyruvate Dehydrogenase Kinase 4 in Complex with Amppnp, PDB code: 2e0a was solved by M.Kukimoto-Niino, A.Tokmakov, T.Terada, I.Shiromizu, M.Kawamoto, T.Matsusue, M.Shirouzu, S.Yokoyama, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.67 / 1.86
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.121, 68.456, 79.755, 90.00, 101.05, 90.00
R / Rfree (%)	19.6 / 23.1

The binding sites of Magnesium atom in the Crystal Structure of Human Pyruvate Dehydrogenase Kinase 4 in Complex with Amppnp (pdb code 2e0a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human Pyruvate Dehydrogenase Kinase 4 in Complex with Amppnp, PDB code: 2e0a:
Jump to Magnesium binding site number: 1; 2;

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


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 Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg500 b:41.9 occ:1.00 O A:HOH627 1.9 27.0 1.0 O2B A:ANP501 2.3 37.4 1.0 O A:HOH546 2.3 24.1 1.0 O1G A:ANP501 2.3 40.8 1.0 OD1 A:ASN258 2.3 22.2 1.0 O2A A:ANP501 2.4 18.8 1.0 CG A:ASN258 3.1 17.1 1.0 ND2 A:ASN258 3.4 14.9 1.0 PB A:ANP501 3.5 24.9 1.0 OE1 A:GLU254 3.6 19.7 1.0 PG A:ANP501 3.6 26.9 1.0 PA A:ANP501 3.6 19.7 1.0 O A:GLU254 3.7 14.6 1.0 O3A A:ANP501 3.8 22.4 1.0 O A:HOH527 4.1 18.3 1.0 O A:HOH606 4.2 36.7 1.0 N3B A:ANP501 4.2 33.6 1.0 CA A:GLY333 4.3 20.4 1.0 O5' A:ANP501 4.3 21.9 1.0 CB A:ASN258 4.4 18.9 1.0 CE A:LYS257 4.5 26.8 1.0 N A:ASN258 4.5 16.5 1.0 O3G A:ANP501 4.5 29.6 1.0 CB A:LYS257 4.6 17.6 1.0 C A:GLU254 4.6 18.2 1.0 O2G A:ANP501 4.6 31.1 1.0 CA A:ASN258 4.7 18.1 1.0 O A:LEU327 4.7 33.9 1.0 CD A:GLU254 4.7 23.6 1.0 O1B A:ANP501 4.7 41.1 1.0 N A:GLY333 4.8 20.5 1.0 CA A:GLU254 4.8 16.0 1.0 O1A A:ANP501 4.8 18.4 1.0 CB A:GLU254 4.9 18.0 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Pyruvate Dehydrogenase Kinase 4 in Complex with Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1500 b:26.9 occ:1.00 O2B B:ANP1501 2.1 25.7 1.0 O B:HOH1624 2.1 25.3 1.0 OD1 B:ASN258 2.2 21.8 1.0 O1G B:ANP1501 2.2 25.9 1.0 O2A B:ANP1501 2.2 21.1 1.0 O B:HOH1516 2.4 22.3 1.0 CG B:ASN258 3.1 22.6 1.0 PB B:ANP1501 3.2 26.5 1.0 ND2 B:ASN258 3.3 21.8 1.0 PA B:ANP1501 3.3 22.6 1.0 PG B:ANP1501 3.4 27.5 1.0 O3A B:ANP1501 3.5 26.8 1.0 N3B B:ANP1501 3.9 27.2 1.0 CA B:GLY333 4.0 21.5 1.0 O3G B:ANP1501 4.0 27.9 1.0 OE1 B:GLU254 4.0 22.3 1.0 O5' B:ANP1501 4.1 22.8 1.0 O B:GLU254 4.2 21.9 1.0 O B:HOH1520 4.2 25.5 1.0 O B:HOH1599 4.2 43.0 1.0 N B:GLY333 4.4 22.8 1.0 O B:HOH1574 4.4 32.5 1.0 CB B:ASN258 4.4 22.2 1.0 O1B B:ANP1501 4.5 28.9 1.0 O1A B:ANP1501 4.5 23.6 1.0 O2G B:ANP1501 4.7 29.6 1.0 N B:ASN258 4.8 21.7 1.0 CA B:ASN258 4.8 23.1 1.0 C B:GLY333 4.9 23.0 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