Magnesium in PDB 4nkb: Crystal Structure of the Cryptic Polo Box (Cpb)of Zyg-1

All present enzymatic activity of Crystal Structure of the Cryptic Polo Box (Cpb)of Zyg-1:
2.7.11.1;

The structure of Crystal Structure of the Cryptic Polo Box (Cpb)of Zyg-1, PDB code: 4nkb was solved by E.Shimanovskaya, G.Dong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.96 / 2.30
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	53.383, 60.093, 87.515, 90.00, 93.31, 90.00
R / Rfree (%)	24.3 / 27.6

The binding sites of Magnesium atom in the Crystal Structure of the Cryptic Polo Box (Cpb)of Zyg-1 (pdb code 4nkb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Cryptic Polo Box (Cpb)of Zyg-1, PDB code: 4nkb:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the Cryptic Polo Box (Cpb)of Zyg-1


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 the Cryptic Polo Box (Cpb)of Zyg-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:48.5 occ:0.50 NH2 A:ARG470 2.1 40.2 1.0 NH1 A:ARG471 2.2 44.4 1.0 CZ A:ARG470 3.2 47.9 1.0 CZ A:ARG471 3.2 35.1 1.0 NE A:ARG470 3.5 37.6 1.0 NH2 A:ARG471 3.5 42.0 1.0 O A:HOH787 4.0 28.6 1.0 O3 A:DTT603 4.3 65.5 1.0 NE A:ARG471 4.3 37.0 1.0 NH1 A:ARG470 4.4 34.1 1.0 CD A:ARG471 4.8 20.0 1.0 CD A:ARG470 5.0 19.7 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the Cryptic Polo Box (Cpb)of Zyg-1


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 the Cryptic Polo Box (Cpb)of Zyg-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:12.0 occ:1.00 O A:HOH783 2.1 31.4 1.0 O2 A:DTT603 2.5 46.8 1.0 C1 A:DTT603 2.7 58.3 1.0 C2 A:DTT603 3.0 41.8 1.0 C3 A:DTT603 3.5 53.3 1.0 O3 A:DTT603 3.5 65.5 1.0 O A:ALA478 3.7 24.8 1.0 C A:ALA478 3.7 19.8 1.0 CB A:GLN479 3.7 14.5 1.0 N A:GLN479 3.9 24.5 1.0 CG A:ARG470 4.2 18.6 1.0 S1 A:DTT603 4.2 78.1 1.0 NH1 A:ARG470 4.3 34.1 1.0 CA A:ALA478 4.3 42.3 1.0 CA A:GLN479 4.3 17.6 1.0 CG A:GLN479 4.3 17.6 1.0 OE1 A:GLN479 4.4 28.5 1.0 CZ A:ARG470 4.4 47.9 1.0 CB A:ARG470 4.5 23.8 1.0 NH1 A:ARG471 4.6 44.4 1.0 NE A:ARG470 4.7 37.6 1.0 CA A:ARG470 4.8 26.9 1.0 NH2 A:ARG470 4.8 40.2 1.0 CD A:GLN479 4.8 28.7 1.0 CZ A:ARG471 4.8 35.1 1.0 CG A:ARG471 4.8 24.6 1.0 N A:ARG471 4.8 23.9 1.0 N A:ALA478 4.9 47.0 1.0 CD A:ARG470 4.9 19.7 1.0 C4 A:DTT603 5.0 62.7 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the Cryptic Polo Box (Cpb)of Zyg-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Cryptic Polo Box (Cpb)of Zyg-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:34.4 occ:0.50 NH1 B:ARG471 2.3 28.9 1.0 O B:HOH771 2.5 34.3 1.0 O B:HOH774 2.9 41.3 1.0 CZ B:ARG471 3.4 25.3 1.0 O2 B:DTT603 3.7 53.7 1.0 NH2 B:ARG471 3.7 34.1 1.0 O B:HOH799 4.5 18.8 1.0 NE B:ARG471 4.6 19.0 1.0 C2 B:DTT603 4.7 56.0 1.0 NE B:ARG470 4.9 42.9 1.0 CD B:ARG470 5.0 34.7 1.0

E.Shimanovskaya, V.Viscardi, J.Lesigang, M.M.Lettman, R.Qiao, D.I.Svergun, A.Round, K.Oegema, G.Dong. Structure of the C. Elegans Zyg-1 Cryptic Polo Box Suggests A Conserved Mechanism For Centriolar Docking of PLK4 Kinases. Structure V. 22 1090 2014.
ISSN: ISSN 0969-2126
PubMed: 24980795
DOI: 10.1016/J.STR.2014.05.009