Magnesium in PDB 4m9y: Crystal Structure of Ced-4 Bound Ced-3 Fragment

The structure of Crystal Structure of Ced-4 Bound Ced-3 Fragment, PDB code: 4m9y was solved by W.J.Huang, T.Y.Jinag, W.Y.Choi, J.W.Wang, Y.G.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.93 / 4.20
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	181.129, 181.129, 202.003, 90.00, 90.00, 90.00
R / Rfree (%)	24.7 / 30

The binding sites of Magnesium atom in the Crystal Structure of Ced-4 Bound Ced-3 Fragment (pdb code 4m9y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Ced-4 Bound Ced-3 Fragment, PDB code: 4m9y:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Ced-4 Bound Ced-3 Fragment


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 Ced-4 Bound Ced-3 Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:0.3 occ:1.00 OG A:SER166 2.2 0.1 1.0 OD1 A:ASP250 2.6 0.7 1.0 O2G A:ATP602 2.8 0.5 1.0 O1B A:ATP602 2.8 0.6 1.0 O1G A:ATP602 3.2 0.9 1.0 CG A:ASP250 3.3 0.0 1.0 OD2 A:ASP250 3.4 0.2 1.0 PG A:ATP602 3.5 0.2 1.0 CB A:SER166 3.5 0.0 1.0 CB A:ASP251 3.6 0.1 1.0 NZ A:LYS191 3.7 0.8 1.0 PB A:ATP602 4.1 0.9 1.0 CG A:ASP251 4.2 0.9 1.0 N A:ASP251 4.2 0.1 1.0 OG1 A:THR271 4.2 0.8 1.0 CE A:LYS191 4.3 0.7 1.0 CA A:ASP251 4.3 0.5 1.0 O3B A:ATP602 4.3 0.2 1.0 OD2 A:ASP251 4.6 0.3 1.0 C A:ASP250 4.6 0.5 1.0 CB A:ASP250 4.7 0.0 1.0 CA A:SER166 4.7 0.4 1.0 OD1 A:ASP251 4.7 0.4 1.0 CB A:THR271 4.8 0.3 1.0 N A:SER166 4.8 0.7 1.0 O3G A:ATP602 4.9 0.2 1.0 O2A A:ATP602 5.0 0.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Ced-4 Bound Ced-3 Fragment


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 Ced-4 Bound Ced-3 Fragment within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:0.4 occ:1.00 OG B:SER166 2.0 0.3 1.0 O1B B:ATP602 2.4 0.4 1.0 OD1 B:ASP250 2.6 0.4 1.0 O1G B:ATP602 2.8 0.7 1.0 O2G B:ATP602 2.9 0.2 1.0 CB B:SER166 3.3 0.4 1.0 PG B:ATP602 3.3 0.9 1.0 CG B:ASP250 3.5 0.3 1.0 OD2 B:ASP250 3.7 0.6 1.0 CB B:ASP251 3.7 0.3 1.0 PB B:ATP602 3.8 1.0 1.0 OG1 B:THR271 3.8 1.0 1.0 O3B B:ATP602 4.0 0.1 1.0 N B:ASP251 4.1 0.2 1.0 CG B:ASP251 4.1 0.0 1.0 CA B:ASP251 4.2 0.3 1.0 NZ B:LYS191 4.4 0.9 1.0 CA B:SER166 4.4 0.8 1.0 CB B:THR271 4.5 0.8 1.0 OD1 B:ASP251 4.5 0.5 1.0 N B:SER166 4.6 0.1 1.0 OD2 B:ASP251 4.6 0.5 1.0 C B:ASP250 4.6 0.5 1.0 O2B B:ATP602 4.7 0.9 1.0 O3G B:ATP602 4.7 0.9 1.0 CB B:ASP250 4.8 0.4 1.0 O2A B:ATP602 4.8 0.9 1.0 O3A B:ATP602 4.9 0.8 1.0 CE B:LYS191 4.9 0.7 1.0 CA B:ASP250 5.0 0.8 1.0

W.Huang, T.Jiang, W.Choi, S.Qi, Y.Pang, Q.Hu, Y.Xu, X.Gong, P.D.Jeffrey, J.Wang, Y.Shi. Mechanistic Insights Into Ced-4-Mediated Activation of Ced-3. Genes Dev. V. 27 2039 2013.
ISSN: ISSN 0890-9369
PubMed: 24065769
DOI: 10.1101/GAD.224428.113