Magnesium in PDB 6y8d: 14-3-3 Sigma in Complex with Phosphorylated Caspase{PS164} Peptide

The structure of 14-3-3 Sigma in Complex with Phosphorylated Caspase{PS164} Peptide, PDB code: 6y8d was solved by A.Ballone, R.A.Lau, F.P.A.Zweipfenning, C.Ottmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.41 / 1.51
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.575, 112.713, 62.661, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 19.7

The structure of 14-3-3 Sigma in Complex with Phosphorylated Caspase{PS164} Peptide also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the 14-3-3 Sigma in Complex with Phosphorylated Caspase{PS164} Peptide (pdb code 6y8d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the 14-3-3 Sigma in Complex with Phosphorylated Caspase{PS164} Peptide, PDB code: 6y8d:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the 14-3-3 Sigma in Complex with Phosphorylated Caspase{PS164} Peptide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 14-3-3 Sigma in Complex with Phosphorylated Caspase{PS164} Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:34.1 occ:1.00 O A:HOH608 2.6 32.1 1.0 OG A:SER192 2.7 19.7 0.7 CG2 A:THR196 2.7 18.8 0.3 OG1 A:THR196 2.8 19.5 0.7 OG1 A:THR196 3.4 12.5 0.3 O A:SER192 3.6 15.9 1.0 CB A:THR196 3.6 15.3 0.7 CB A:THR196 3.6 15.3 0.3 CB A:SER192 3.9 15.5 0.3 CB A:SER192 3.9 15.5 0.7 C A:SER192 4.0 16.4 1.0 CG2 A:THR196 4.2 17.6 0.7 CA A:SER192 4.4 12.3 0.7 CA A:SER192 4.4 12.4 0.3 O A:HOH467 4.6 39.5 1.0 N A:LEU193 4.6 14.6 1.0 OG A:SER192 4.8 15.5 0.3 CA A:THR196 4.9 13.3 0.7 CA A:THR196 5.0 13.3 0.3 CA A:LEU193 5.0 13.5 1.0

Magnesium binding site 2 out of 4 in the 14-3-3 Sigma in Complex with Phosphorylated Caspase{PS164} Peptide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 14-3-3 Sigma in Complex with Phosphorylated Caspase{PS164} Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:27.4 occ:0.00 OE2 A:GLU188 2.0 21.5 1.0 O A:HOH454 2.4 36.9 1.0 CD A:GLU188 2.9 20.3 1.0 CG A:GLU188 3.3 16.6 1.0 OE1 A:GLU188 3.9 22.7 1.0 O A:HOH706 4.5 33.8 1.0 CB A:GLU188 4.6 15.9 1.0 O A:HOH625 4.7 23.5 1.0

Magnesium binding site 3 out of 4 in the 14-3-3 Sigma in Complex with Phosphorylated Caspase{PS164} Peptide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 14-3-3 Sigma in Complex with Phosphorylated Caspase{PS164} Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:23.5 occ:0.00 O A:HOH448 2.2 31.0 1.0 OE2 A:GLU89 2.3 20.8 1.0 O A:HOH638 2.3 33.1 1.0 CD A:GLU89 3.3 14.4 1.0 O A:HOH529 3.9 31.7 1.0 CG A:GLU89 4.1 13.6 1.0 O A:HOH681 4.2 36.1 1.0 OE1 A:GLU89 4.2 16.2 1.0 NH1 A:ARG85 4.3 22.0 1.0 OE1 A:GLN93 4.6 18.4 1.0 CG A:GLU86 4.7 20.1 1.0 CB A:GLU89 4.8 14.2 1.0 NE2 A:GLN93 4.8 17.0 1.0

Magnesium binding site 4 out of 4 in the 14-3-3 Sigma in Complex with Phosphorylated Caspase{PS164} Peptide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 14-3-3 Sigma in Complex with Phosphorylated Caspase{PS164} Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:22.0 occ:0.00 OE1 A:GLU2 2.2 16.4 1.0 O A:HOH456 2.2 18.4 1.0 O A:HOH503 2.2 35.3 1.0 O A:HOH644 2.6 34.0 1.0 CD A:GLU2 3.2 18.3 1.0 OE2 A:GLU2 3.5 16.6 1.0 O A:HOH588 4.3 17.3 1.0 O A:HOH718 4.4 19.0 1.0 CG A:GLU2 4.4 15.6 1.0 CA A:GLU2 4.8 13.4 1.0 O A:HOH453 4.8 26.3 1.0 CB A:GLU2 4.8 12.2 1.0 N A:ARG3 4.9 11.4 1.0

A.Ballone, R.A.Lau, F.P.A.Zweipfenning, C.Ottmann. A New Soaking Procedure For X-Ray Crystallographic Structural Determination of Protein-Peptide Complexes. Acta Crystallogr.,Sect.F V. 76 501 2020.
ISSN: ESSN 2053-230X
PubMed: 33006579
DOI: 10.1107/S2053230X2001122X