Magnesium in PDB 4i3z: Structure of PCDK2/Cyclina Bound to Adp and 2 Magnesium Ions

All present enzymatic activity of Structure of PCDK2/Cyclina Bound to Adp and 2 Magnesium Ions:
2.7.11.22;

The structure of Structure of PCDK2/Cyclina Bound to Adp and 2 Magnesium Ions, PDB code: 4i3z was solved by D.M.Jacobsen, Z.-Q.Bao, P.J.O'brien, C.L.Brooks, M.A.Young, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.79 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	70.770, 164.130, 73.280, 90.00, 107.07, 90.00
R / Rfree (%)	19.7 / 22.8

The structure of Structure of PCDK2/Cyclina Bound to Adp and 2 Magnesium Ions also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Structure of PCDK2/Cyclina Bound to Adp and 2 Magnesium Ions (pdb code 4i3z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of PCDK2/Cyclina Bound to Adp and 2 Magnesium Ions, PDB code: 4i3z:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of PCDK2/Cyclina Bound to Adp and 2 Magnesium Ions


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 2 Magnesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:34.5 occ:1.00 O3B A:ADP301 2.0 35.3 1.0 O1A A:ADP301 2.0 32.2 1.0 O A:HOH402 2.1 50.8 1.0 OD1 A:ASN132 2.1 25.3 1.0 O A:HOH401 2.1 25.3 1.0 OD2 A:ASP145 2.1 36.5 1.0 CG A:ASP145 3.1 32.4 1.0 CG A:ASN132 3.1 28.4 1.0 PB A:ADP301 3.2 43.4 1.0 PA A:ADP301 3.3 34.9 1.0 ND2 A:ASN132 3.5 19.9 1.0 CB A:ASP145 3.6 23.0 1.0 O3A A:ADP301 3.7 43.3 1.0 O2B A:ADP301 3.8 52.3 1.0 MG A:MG303 4.0 52.8 1.0 OD1 A:ASP145 4.1 33.0 1.0 C5' A:ADP301 4.2 39.5 1.0 O5' A:ADP301 4.2 36.7 1.0 O A:HOH403 4.2 53.8 1.0 OE1 A:GLN131 4.4 60.4 1.0 O2A A:ADP301 4.4 35.0 1.0 O A:HOH466 4.5 57.0 1.0 O1B A:ADP301 4.5 40.5 1.0 CB A:ASN132 4.5 23.5 1.0 O3' A:ADP301 4.6 37.2 1.0 CG A:GLN131 4.6 41.0 1.0 O A:GLN131 4.8 30.0 1.0 C3' A:ADP301 4.8 37.3 1.0 CA A:ASN132 4.8 26.0 1.0 OD2 A:ASP127 5.0 35.0 1.0 CE A:LYS129 5.0 32.8 1.0

Magnesium binding site 2 out of 4 in the Structure of PCDK2/Cyclina Bound to Adp and 2 Magnesium Ions


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 2 Magnesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:52.8 occ:1.00 O2B A:ADP301 2.1 52.3 1.0 O A:HOH404 2.2 52.9 1.0 O A:HOH403 2.3 53.8 1.0 OD1 A:ASP145 2.5 33.0 1.0 OD2 A:ASP145 2.6 36.5 1.0 O A:HOH413 2.8 45.6 1.0 CG A:ASP145 2.9 32.4 1.0 O A:HOH467 3.2 49.6 1.0 PB A:ADP301 3.3 43.4 1.0 O A:HOH408 3.4 62.9 1.0 O3B A:ADP301 3.6 35.3 1.0 O A:HOH402 3.9 50.8 1.0 MG A:MG302 4.0 34.5 1.0 O A:HOH466 4.0 57.0 1.0 O3A A:ADP301 4.3 43.3 1.0 O1B A:ADP301 4.3 40.5 1.0 OD2 A:ASP127 4.4 35.0 1.0 CB A:ASP145 4.4 23.0 1.0 CA A:GLY147 4.5 22.6 1.0 NZ A:LYS33 4.5 34.6 1.0 O A:HOH407 4.5 65.8 1.0 O1A A:ADP301 4.7 32.2 1.0 N A:GLY147 4.7 21.5 1.0

Magnesium binding site 3 out of 4 in the Structure of PCDK2/Cyclina Bound to Adp and 2 Magnesium Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of PCDK2/Cyclina Bound to Adp and 2 Magnesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg302 b:33.8 occ:1.00 O3B C:ADP301 2.0 32.8 1.0 O1A C:ADP301 2.0 38.8 1.0 O C:HOH402 2.1 52.0 1.0 O C:HOH401 2.1 31.9 1.0 OD1 C:ASN132 2.1 29.5 1.0 OD2 C:ASP145 2.2 34.9 1.0 CG C:ASN132 3.2 31.0 1.0 CG C:ASP145 3.2 34.1 1.0 PB C:ADP301 3.3 41.8 1.0 PA C:ADP301 3.3 36.0 1.0 ND2 C:ASN132 3.6 25.2 1.0 O3A C:ADP301 3.7 35.2 1.0 CB C:ASP145 3.7 25.3 1.0 O2B C:ADP301 3.8 45.6 1.0 MG C:MG303 4.0 57.1 1.0 O C:HOH403 4.2 53.6 1.0 OD1 C:ASP145 4.2 34.0 1.0 OE1 C:GLN131 4.2 58.5 1.0 C5' C:ADP301 4.2 48.1 1.0 O5' C:ADP301 4.3 47.1 1.0 CG C:GLN131 4.4 41.4 1.0 O2A C:ADP301 4.5 35.8 1.0 O C:HOH502 4.5 61.7 1.0 O3' C:ADP301 4.5 47.6 1.0 CB C:ASN132 4.5 21.7 1.0 O1B C:ADP301 4.5 41.6 1.0 O C:GLN131 4.8 30.6 1.0 C3' C:ADP301 4.8 42.8 1.0 CD C:GLN131 4.8 58.9 1.0 CA C:ASN132 4.8 25.0 1.0 OD2 C:ASP127 4.9 37.2 1.0 CE C:LYS129 5.0 35.1 1.0

Magnesium binding site 4 out of 4 in the Structure of PCDK2/Cyclina Bound to Adp and 2 Magnesium Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of PCDK2/Cyclina Bound to Adp and 2 Magnesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg303 b:57.1 occ:1.00 O2B C:ADP301 2.2 45.6 1.0 O C:HOH403 2.3 53.6 1.0 O C:HOH404 2.3 57.5 1.0 OD2 C:ASP145 2.5 34.9 1.0 OD1 C:ASP145 2.6 34.0 1.0 O C:HOH410 2.8 81.6 1.0 CG C:ASP145 2.9 34.1 1.0 O C:HOH406 2.9 50.8 1.0 O C:HOH415 3.3 78.6 1.0 PB C:ADP301 3.3 41.8 1.0 O3B C:ADP301 3.5 32.8 1.0 O C:HOH502 3.7 61.7 1.0 O C:HOH402 3.8 52.0 1.0 MG C:MG302 4.0 33.8 1.0 OD2 C:ASP127 4.2 37.2 1.0 O1B C:ADP301 4.3 41.6 1.0 CB C:ASP145 4.4 25.3 1.0 O3A C:ADP301 4.5 35.2 1.0 O C:HOH407 4.7 53.2 1.0 CA C:GLY147 4.7 25.9 1.0 NZ C:LYS33 4.7 36.5 1.0 O1A C:ADP301 4.8 38.8 1.0 N C:GLY147 4.9 24.2 1.0

D.M.Jacobsen, Z.-Q.Bao, P.J.O'brien, C.L.Brooks, 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