Magnesium in PDB 3d2r: Crystal Structure of Pyruvate Dehydrogenase Kinase Isoform 4 in Complex with Adp

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

The structure of Crystal Structure of Pyruvate Dehydrogenase Kinase Isoform 4 in Complex with Adp, PDB code: 3d2r was solved by M.Kato, R.M.Wynn, L.C.Chuang, S.-C.Tso, J.Li, D.T.Chuang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.03
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	70.595, 69.374, 82.328, 90.00, 99.26, 90.00
R / Rfree (%)	18.3 / 23

The binding sites of Magnesium atom in the Crystal Structure of Pyruvate Dehydrogenase Kinase Isoform 4 in Complex with Adp (pdb code 3d2r). 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 Pyruvate Dehydrogenase Kinase Isoform 4 in Complex with Adp, PDB code: 3d2r:
Jump to Magnesium binding site number: 1; 2;

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


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 Pyruvate Dehydrogenase Kinase Isoform 4 in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg500 b:31.9 occ:1.00 O1A A:ADP501 2.0 28.2 1.0 O A:HOH508 2.1 24.6 1.0 OD1 A:ASN258 2.1 33.2 1.0 O3B A:ADP501 2.2 27.8 1.0 O A:HOH516 2.2 27.8 1.0 O A:HOH534 2.3 32.9 1.0 CG A:ASN258 3.1 33.0 1.0 PA A:ADP501 3.2 27.5 1.0 PB A:ADP501 3.2 32.2 1.0 ND2 A:ASN258 3.3 28.9 1.0 O3A A:ADP501 3.4 30.8 1.0 O2B A:ADP501 3.8 28.8 1.0 O A:HOH528 3.9 31.1 1.0 O5' A:ADP501 4.0 24.2 1.0 OE1 A:GLU254 4.1 35.2 1.0 O A:GLU254 4.2 36.0 1.0 O A:HOH553 4.2 37.9 1.0 CA A:GLY333 4.2 34.1 1.0 O A:HOH515 4.3 27.2 1.0 CB A:ASN258 4.4 34.0 1.0 O2A A:ADP501 4.5 24.7 1.0 O1B A:ADP501 4.6 31.8 1.0 N A:GLY333 4.6 33.4 1.0 N A:ASN258 4.8 34.7 1.0 CA A:ASN258 4.8 34.4 1.0 O A:LEU327 4.8 42.4 1.0 CB A:ALA328 4.9 40.6 1.0

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


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 Pyruvate Dehydrogenase Kinase Isoform 4 in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg500 b:30.4 occ:1.00 O B:HOH525 2.0 29.1 1.0 O1A B:ADP501 2.0 29.1 1.0 O B:HOH527 2.1 29.4 1.0 O3B B:ADP501 2.1 31.7 1.0 OD1 B:ASN258 2.1 33.3 1.0 O B:HOH513 2.2 25.1 1.0 CG B:ASN258 3.1 33.8 1.0 PB B:ADP501 3.2 29.2 1.0 PA B:ADP501 3.3 27.2 1.0 O3A B:ADP501 3.4 28.9 1.0 ND2 B:ASN258 3.5 33.3 1.0 O2B B:ADP501 3.7 30.8 1.0 O B:HOH523 3.9 28.6 1.0 O5' B:ADP501 3.9 25.2 1.0 OE1 B:GLU254 4.1 35.9 1.0 O B:HOH528 4.2 30.2 1.0 CA B:GLY333 4.3 33.5 1.0 O B:GLU254 4.3 36.9 1.0 O B:LEU327 4.5 46.5 1.0 CB B:ASN258 4.5 33.1 1.0 O1B B:ADP501 4.5 32.9 1.0 O2A B:ADP501 4.5 25.5 1.0 O B:HOH649 4.6 54.9 1.0 N B:GLY333 4.7 34.0 1.0 N B:ASN258 4.7 32.1 1.0 CA B:ASN258 4.8 33.1 1.0 CB B:ALA328 4.8 41.0 1.0

R.M.Wynn, M.Kato, J.L.Chuang, S.C.Tso, J.Li, D.T.Chuang. Pyruvate Dehydrogenase Kinase-4 Structures Reveal A Metastable Open Conformation Fostering Robust Core-Free Basal Activity. J.Biol.Chem. V. 283 25305 2008.
ISSN: ISSN 0021-9258
PubMed: 18658136
DOI: 10.1074/JBC.M802249200