Magnesium in PDB 4ii5: Structure of PCDK2/Cyclina Bound to Adp and 1 Magnesium Ion

All present enzymatic activity of Structure of PCDK2/Cyclina Bound to Adp and 1 Magnesium Ion:
2.7.11.22;

The structure of Structure of PCDK2/Cyclina Bound to Adp and 1 Magnesium Ion, PDB code: 4ii5 was solved by D.M.Jacobsen, Z.-Q.Bao, P.J.O'brien, C.L.Brooks Iii, M.A.Young, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.56 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.140, 164.140, 73.450, 90.00, 107.04, 90.00
R / Rfree (%)	20 / 22.6

The binding sites of Magnesium atom in the Structure of PCDK2/Cyclina Bound to Adp and 1 Magnesium Ion (pdb code 4ii5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of PCDK2/Cyclina Bound to Adp and 1 Magnesium Ion, PDB code: 4ii5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of PCDK2/Cyclina Bound to Adp and 1 Magnesium Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of PCDK2/Cyclina Bound to Adp and 1 Magnesium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:49.4 occ:1.00 O A:HOH513 2.1 46.5 1.0 O A:HOH512 2.1 35.7 1.0 OD2 A:ASP145 2.1 49.5 1.0 OD1 A:ASN132 2.1 36.7 1.0 O1A A:ADP301 2.2 51.5 1.0 O3B A:ADP301 2.3 57.1 1.0 CG A:ASN132 3.2 34.0 1.0 CG A:ASP145 3.2 42.8 1.0 PA A:ADP301 3.5 51.1 1.0 PB A:ADP301 3.6 58.1 1.0 ND2 A:ASN132 3.6 26.0 1.0 CB A:ASP145 3.7 35.5 1.0 O3A A:ADP301 3.7 0.2 1.0 OD1 A:ASP145 4.2 43.0 1.0 C5' A:ADP301 4.2 53.8 1.0 O A:HOH509 4.2 66.5 1.0 O A:HOH401 4.3 52.1 1.0 O5' A:ADP301 4.3 51.9 1.0 O2B A:ADP301 4.4 66.3 1.0 O3' A:ADP301 4.4 64.5 1.0 NE2 A:GLN131 4.4 64.5 1.0 CB A:ASN132 4.5 30.6 1.0 O A:HOH508 4.5 61.8 1.0 O A:HOH542 4.5 56.0 1.0 CG A:GLN131 4.5 45.4 1.0 O2A A:ADP301 4.6 56.8 1.0 C3' A:ADP301 4.7 63.2 1.0 O1B A:ADP301 4.7 65.1 1.0 CA A:ASN132 4.8 28.9 1.0 O A:HOH510 4.8 55.9 1.0 O A:GLN131 4.9 29.8 1.0 C4' A:ADP301 4.9 60.2 1.0 CE A:LYS129 5.0 37.5 1.0

Magnesium binding site 2 out of 2 in the Structure of PCDK2/Cyclina Bound to Adp and 1 Magnesium Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of PCDK2/Cyclina Bound to Adp and 1 Magnesium Ion within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg302 b:53.0 occ:1.00 O C:HOH500 2.1 52.6 1.0 O C:HOH501 2.1 67.1 1.0 O1A C:ADP301 2.1 57.3 1.0 OD1 C:ASN132 2.2 37.8 1.0 OD2 C:ASP145 2.2 49.1 1.0 O3B C:ADP301 2.3 48.5 1.0 CG C:ASN132 3.2 34.8 1.0 CG C:ASP145 3.3 42.4 1.0 ND2 C:ASN132 3.5 26.7 1.0 PA C:ADP301 3.5 45.2 1.0 PB C:ADP301 3.7 52.3 1.0 CB C:ASP145 3.8 35.6 1.0 O3A C:ADP301 3.9 0.6 1.0 O C:HOH401 4.0 60.2 1.0 O C:HOH533 4.2 41.2 1.0 NE2 C:GLN131 4.3 65.4 1.0 C5' C:ADP301 4.3 62.4 1.0 OD1 C:ASP145 4.3 43.6 1.0 O5' C:ADP301 4.4 57.7 1.0 CG C:GLN131 4.4 45.5 1.0 O2B C:ADP301 4.5 62.4 1.0 CB C:ASN132 4.5 30.2 1.0 O2A C:ADP301 4.6 45.9 1.0 O C:HOH493 4.7 61.2 1.0 O1B C:ADP301 4.7 64.8 1.0 O3' C:ADP301 4.7 68.7 1.0 CE C:LYS129 4.8 38.9 1.0 C3' C:ADP301 4.9 62.5 1.0 CA C:ASN132 4.9 29.1 1.0 CD C:GLN131 4.9 66.4 1.0 O C:GLN131 4.9 30.1 1.0

D.M.Jacobsen, Z.-Q.Bao, P.J.O'brien, C.L.Brooks Iii, M.A.Young. Price to Be Paid For Two-Metal Catalysis: Magnesium Ions That Accelerate Chemistry Unavoidably Limit Product Release From A Protein Kinase J.Am.Chem.Soc. V. 134 15357 2012.
ISSN: ISSN 0002-7863
PubMed: 22891849