Magnesium in PDB 2zkj: Crystal Structure of Human PDK4-Adp Complex

All present enzymatic activity of Crystal Structure of Human PDK4-Adp Complex:
2.7.11.2;

The structure of Crystal Structure of Human PDK4-Adp Complex, PDB code: 2zkj was solved by M.Kato, R.M.Wynn, J.L.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)	49.22 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.616, 68.743, 81.554, 90.00, 100.10, 90.00
R / Rfree (%)	18.5 / 24

The binding sites of Magnesium atom in the Crystal Structure of Human PDK4-Adp Complex (pdb code 2zkj). 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 PDK4-Adp Complex, PDB code: 2zkj:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human PDK4-Adp Complex


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 PDK4-Adp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg500 b:34.8 occ:1.00 O3B A:ADP501 2.0 29.8 1.0 O1A A:ADP501 2.1 29.0 1.0 O1 A:PO4502 2.1 37.6 1.0 OD1 A:ASN258 2.1 36.5 1.0 O A:HOH597 2.1 30.9 1.0 O A:HOH521 2.2 38.1 1.0 CG A:ASN258 3.1 36.2 1.0 PA A:ADP501 3.1 31.1 1.0 PB A:ADP501 3.1 35.5 1.0 O3A A:ADP501 3.3 33.0 1.0 P A:PO4502 3.3 36.0 1.0 ND2 A:ASN258 3.4 32.9 1.0 O4 A:PO4502 3.7 41.3 1.0 O2B A:ADP501 3.8 33.3 1.0 O5' A:ADP501 3.9 29.8 1.0 O A:HOH524 3.9 31.1 1.0 O2 A:PO4502 4.0 33.0 1.0 O A:HOH566 4.2 31.8 1.0 OE1 A:GLU254 4.2 41.5 1.0 CA A:GLY333 4.2 37.1 1.0 O A:GLU254 4.3 41.1 1.0 N A:GLY333 4.4 36.6 1.0 O1B A:ADP501 4.4 37.1 1.0 CB A:ASN258 4.5 36.3 1.0 O2A A:ADP501 4.5 29.2 1.0 O3 A:PO4502 4.5 34.4 1.0 CA A:ASN258 4.8 37.0 1.0 O A:LEU327 4.8 42.9 1.0 N A:ASN258 4.8 37.6 1.0 CB A:ALA328 4.9 43.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human PDK4-Adp Complex


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 PDK4-Adp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg500 b:31.4 occ:1.00 O1A B:ADP501 2.0 29.1 1.0 O2 B:PO4502 2.0 31.2 1.0 O3B B:ADP501 2.1 33.5 1.0 O B:HOH517 2.1 30.9 1.0 OD1 B:ASN258 2.1 36.7 1.0 O B:HOH506 2.1 29.0 1.0 CG B:ASN258 3.1 38.0 1.0 PB B:ADP501 3.2 31.5 1.0 PA B:ADP501 3.2 29.1 1.0 O3A B:ADP501 3.3 29.9 1.0 P B:PO4502 3.4 34.9 1.0 ND2 B:ASN258 3.4 32.4 1.0 O1 B:PO4502 3.6 36.5 1.0 O2B B:ADP501 3.8 28.7 1.0 O B:HOH512 3.8 31.8 1.0 O5' B:ADP501 4.0 26.3 1.0 O4 B:PO4502 4.0 37.5 1.0 OE1 B:GLU254 4.0 40.9 1.0 CA B:GLY333 4.2 37.3 1.0 O B:HOH528 4.2 35.8 1.0 N B:GLY333 4.4 37.3 1.0 O1B B:ADP501 4.4 37.4 1.0 O2A B:ADP501 4.4 27.0 1.0 O B:GLU254 4.5 39.5 1.0 CB B:ASN258 4.5 38.1 1.0 O3 B:PO4502 4.6 33.3 1.0 O B:LEU327 4.7 43.0 1.0 N B:ASN258 4.8 37.1 1.0 CA B:ASN258 4.8 38.3 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