Magnesium in PDB 2jd5: SKY1P Bound to NPL3P-Derived Substrate Peptide

All present enzymatic activity of SKY1P Bound to NPL3P-Derived Substrate Peptide:
2.7.11.1;

The structure of SKY1P Bound to NPL3P-Derived Substrate Peptide, PDB code: 2jd5 was solved by B.Nolen, R.Lukasiewicz, J.A.Adams, D.Huang, G.Ghosh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.99 / 2.5
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.328, 88.558, 134.408, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 25.5

The binding sites of Magnesium atom in the SKY1P Bound to NPL3P-Derived Substrate Peptide (pdb code 2jd5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the SKY1P Bound to NPL3P-Derived Substrate Peptide, PDB code: 2jd5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the SKY1P Bound to NPL3P-Derived Substrate Peptide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of SKY1P Bound to NPL3P-Derived Substrate Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1739 b:43.6 occ:1.00 OD2 A:ASP550 2.1 35.4 1.0 OD1 A:ASN299 2.7 32.5 1.0 O A:HOH2013 2.8 38.4 1.0 CG A:ASP550 3.3 34.0 1.0 CG A:ASN299 3.6 31.6 1.0 ND2 A:ASN299 3.7 28.8 1.0 O A:HOH2014 3.7 48.5 1.0 CB A:ASP550 4.1 32.2 1.0 OD1 A:ASP550 4.2 33.7 1.0 CE A:LYS296 4.9 29.8 1.0 OD2 A:ASP294 4.9 29.0 1.0 CB A:ASN299 5.0 30.8 1.0

Magnesium binding site 2 out of 2 in the SKY1P Bound to NPL3P-Derived Substrate Peptide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of SKY1P Bound to NPL3P-Derived Substrate Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1739 b:66.3 occ:1.00 OD2 B:ASP550 2.3 34.9 1.0 CG B:ASP550 3.3 33.7 1.0 O B:HOH2030 3.9 40.7 1.0 CB B:ASP550 4.0 30.4 1.0 OD1 B:ASN299 4.0 23.2 1.0 OD1 B:ASP550 4.0 33.3 1.0 CG B:ASN299 5.0 23.3 1.0

R.Lukasiewicz, B.Nolen, J.A.Adams, G.Ghosh. The Rgg Domain of NPL3P Recruits SKY1P Through Docking Interactions J.Mol.Biol. V. 367 249 2007.
ISSN: ISSN 0022-2836
PubMed: 17239901
DOI: 10.1016/J.JMB.2006.12.031