Magnesium in PDB 4aw0: Human PDK1 Kinase Domain in Complex with Allosteric Compound PS182 Bound to the Pif-Pocket

All present enzymatic activity of Human PDK1 Kinase Domain in Complex with Allosteric Compound PS182 Bound to the Pif-Pocket:
2.7.11.1;

The structure of Human PDK1 Kinase Domain in Complex with Allosteric Compound PS182 Bound to the Pif-Pocket, PDB code: 4aw0 was solved by J.O.Schulze, K.Busschots, L.A.Lopez-Garcia, C.Lammi, A.Stroba, S.Zeuzem, A.Piiper, P.M.Alzari, S.Neimanis, J.M.Arencibia, M.Engel, R.M.Biondi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.427 / 1.43
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	148.270, 44.010, 47.390, 90.00, 101.57, 90.00
R / Rfree (%)	17.04 / 18.83

The structure of Human PDK1 Kinase Domain in Complex with Allosteric Compound PS182 Bound to the Pif-Pocket also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Human PDK1 Kinase Domain in Complex with Allosteric Compound PS182 Bound to the Pif-Pocket (pdb code 4aw0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human PDK1 Kinase Domain in Complex with Allosteric Compound PS182 Bound to the Pif-Pocket, PDB code: 4aw0:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human PDK1 Kinase Domain in Complex with Allosteric Compound PS182 Bound to the Pif-Pocket


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human PDK1 Kinase Domain in Complex with Allosteric Compound PS182 Bound to the Pif-Pocket within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg800 b:46.0 occ:1.00 O2B A:ATP500 2.1 29.5 1.0 OD2 A:ASP223 2.2 28.3 0.5 O2A A:ATP500 2.3 31.6 1.0 OD1 A:ASP223 2.7 28.5 0.5 CG A:ASP223 2.8 27.1 0.5 OD1 A:ASP223 3.0 28.4 0.5 O A:HOH2138 3.1 36.4 1.0 HZ3 A:LYS111 3.1 31.3 0.6 PB A:ATP500 3.2 28.8 1.0 O3A A:ATP500 3.2 26.6 1.0 HZ1 A:LYS111 3.2 30.7 0.4 PA A:ATP500 3.3 30.0 1.0 CG A:ASP223 3.3 26.0 0.5 HZ2 A:LYS111 3.4 31.3 0.6 HZ2 A:LYS111 3.5 30.7 0.4 O A:HOH2046 3.5 19.2 0.5 MG A:MG850 3.6 30.9 1.0 NZ A:LYS111 3.7 26.1 0.6 O A:HOH2136 3.7 32.9 1.0 NZ A:LYS111 3.8 25.6 0.4 OD2 A:ASP223 3.9 25.0 0.5 HA A:ASP223 3.9 23.9 1.0 O1G A:ATP500 3.9 34.6 1.0 HB2 A:ASP223 4.0 26.9 0.5 CB A:ASP223 4.1 23.2 0.5 O3B A:ATP500 4.1 36.8 1.0 CB A:ASP223 4.2 22.4 0.5 HB2 A:ASP223 4.2 27.9 0.5 HZ1 A:LYS111 4.3 31.3 0.6 HZ3 A:LYS111 4.3 30.7 0.4 O5' A:ATP500 4.4 24.1 1.0 O1A A:ATP500 4.4 31.0 1.0 O3G A:ATP500 4.4 35.6 1.0 PG A:ATP500 4.4 34.2 1.0 O1B A:ATP500 4.4 26.1 1.0 HE3 A:LYS111 4.5 29.9 0.6 CA A:ASP223 4.5 19.9 1.0 HE2 A:LYS111 4.6 28.1 0.4 CE A:LYS111 4.7 24.9 0.6 HG A:SER94 4.8 38.0 1.0 CE A:LYS111 4.8 23.4 0.4 HB3 A:ASP223 4.8 27.9 0.5 O A:HOH2021 4.9 33.2 1.0 OE1 A:GLU130 4.9 25.4 0.5

Magnesium binding site 2 out of 2 in the Human PDK1 Kinase Domain in Complex with Allosteric Compound PS182 Bound to the Pif-Pocket


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human PDK1 Kinase Domain in Complex with Allosteric Compound PS182 Bound to the Pif-Pocket within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg850 b:30.9 occ:1.00 OD2 A:ASP223 2.1 28.3 0.5 OD1 A:ASN210 2.3 16.1 1.0 O2B A:ATP500 2.4 29.5 1.0 O A:HOH2130 3.0 26.9 1.0 OD2 A:ASP223 3.1 25.0 0.5 CG A:ASP223 3.2 27.1 0.5 HB2 A:ASP223 3.3 26.9 0.5 CG A:ASN210 3.4 14.7 1.0 HB2 A:ASP223 3.4 27.9 0.5 PB A:ATP500 3.5 28.8 1.0 HD22 A:ASN210 3.5 17.4 1.0 CG A:ASP223 3.5 26.0 0.5 MG A:MG800 3.6 46.0 1.0 HG3 A:GLU209 3.6 21.3 0.2 O1B A:ATP500 3.6 26.1 1.0 O A:HOH2138 3.7 36.4 1.0 ND2 A:ASN210 3.8 14.5 1.0 OE2 A:GLU209 3.8 20.2 0.2 CB A:ASP223 3.9 23.2 0.5 CB A:ASP223 3.9 22.4 0.5 O A:HOH2136 4.0 32.9 1.0 OD1 A:ASP223 4.1 28.5 0.5 OD1 A:ASP223 4.1 28.4 0.5 O3G A:ATP500 4.2 35.6 1.0 HB3 A:ASP223 4.2 27.9 0.5 HE3 A:LYS207 4.3 17.7 1.0 HB3 A:ASP223 4.3 26.9 0.5 HA A:ASN210 4.3 16.3 1.0 HG21 A:THR222 4.4 19.6 1.0 CD A:GLU209 4.4 18.9 0.2 CG A:GLU209 4.4 17.8 0.2 O3B A:ATP500 4.6 36.8 1.0 O2A A:ATP500 4.7 31.6 1.0 HD21 A:ASN210 4.7 17.4 1.0 O3A A:ATP500 4.7 26.6 1.0 CB A:ASN210 4.7 13.8 1.0 HB3 A:GLU209 4.7 21.3 0.8 O A:GLU209 4.7 15.1 1.0 HZ2 A:LYS207 4.8 20.8 1.0 HG2 A:GLU209 4.9 21.3 0.2 CA A:ASN210 4.9 13.6 1.0 HE2 A:LYS207 4.9 17.7 1.0 HB2 A:GLU209 4.9 21.3 0.8 CE A:LYS207 5.0 14.8 1.0

K.Busschots, L.A.Lopez-Garcia, C.Lammi, A.Stroba, S.Zeuzem, A.Piiper, P.M.Alzari, S.Neimanis, J.M.Arencibia, M.Engel, J.O.Schulze, R.M.Biondi. Substrate-Selective Inhibition of Protein Kinase PDK1 By Small Compounds That Bind to the Pif-Pocket Allosteric Docking Site. Chem.Biol. V. 19 1152 2012.
ISSN: ISSN 1074-5521
PubMed: 22999883
DOI: 10.1016/J.CHEMBIOL.2012.07.017