Magnesium in PDB 4m9s: Crystal Structure of Ced-4 Bound Ced-3 Fragment

The structure of Crystal Structure of Ced-4 Bound Ced-3 Fragment, PDB code: 4m9s 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)	40.85 / 3.21
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	178.814, 178.814, 201.125, 90.00, 90.00, 90.00
R / Rfree (%)	28.3 / 33.4

The binding sites of Magnesium atom in the Crystal Structure of Ced-4 Bound Ced-3 Fragment (pdb code 4m9s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Ced-4 Bound Ced-3 Fragment, PDB code: 4m9s:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 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:41.9 occ:1.00 OG A:SER166 2.1 56.8 1.0 OD1 A:ASP250 2.5 55.1 1.0 O1B A:ATP602 2.8 58.3 1.0 O1G A:ATP602 3.2 53.4 1.0 CG A:ASP250 3.3 55.8 1.0 O2G A:ATP602 3.4 74.7 1.0 OD2 A:ASP250 3.4 57.0 1.0 CB A:SER166 3.5 59.2 1.0 OG1 A:THR271 3.7 52.3 1.0 PG A:ATP602 3.7 56.8 1.0 CB A:ASP251 4.0 51.6 1.0 PB A:ATP602 4.1 65.1 1.0 N A:ASP251 4.1 56.1 1.0 CA A:ASP251 4.3 50.4 1.0 O3B A:ATP602 4.4 62.2 1.0 CA A:SER166 4.5 58.3 1.0 CB A:THR271 4.5 52.2 1.0 N A:SER166 4.5 62.3 1.0 CG A:ASP251 4.6 59.6 1.0 C A:ASP250 4.6 51.0 1.0 CB A:ASP250 4.6 49.3 1.0 NZ A:LYS191 4.8 70.0 1.0 OD1 A:ASP251 4.9 59.0 1.0 CE A:LYS165 4.9 59.5 1.0 CA A:ASP250 4.9 47.6 1.0 O2B A:ATP602 5.0 60.1 1.0

Magnesium binding site 2 out of 4 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:51.3 occ:1.00 OG B:SER166 1.9 67.5 1.0 O1B B:ATP602 2.4 62.1 1.0 OD1 B:ASP250 3.0 62.3 1.0 CB B:SER166 3.0 68.0 1.0 OD2 B:ASP250 3.3 62.4 1.0 O1G B:ATP602 3.4 62.4 1.0 CG B:ASP250 3.5 62.3 1.0 O2G B:ATP602 3.6 59.9 1.0 PB B:ATP602 3.8 64.7 1.0 PG B:ATP602 3.9 72.0 1.0 O3B B:ATP602 4.3 68.9 1.0 CB B:ASP251 4.4 58.3 1.0 CA B:SER166 4.4 66.2 1.0 OG1 B:THR271 4.6 55.1 1.0 O2A B:ATP602 4.6 53.8 1.0 O3A B:ATP602 4.6 66.2 1.0 N B:SER166 4.7 67.1 1.0 N B:ASP251 4.7 59.2 1.0 CG B:ASP251 4.8 58.4 1.0 NZ B:LYS191 4.9 81.2 1.0 CA B:ASP251 4.9 55.9 1.0 CB B:ASP250 4.9 54.4 1.0 O2B B:ATP602 4.9 60.9 1.0

Magnesium binding site 3 out of 4 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 3 of Crystal Structure of Ced-4 Bound Ced-3 Fragment within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:62.3 occ:1.00 O2G C:ATP602 2.2 73.1 1.0 OG C:SER166 2.7 81.5 1.0 O1B C:ATP602 2.7 66.9 1.0 NZ C:LYS191 3.0 83.5 1.0 CB C:SER166 3.6 77.2 1.0 PG C:ATP602 3.6 75.2 1.0 PB C:ATP602 3.8 66.2 1.0 O2A C:ATP602 3.9 58.8 1.0 O3B C:ATP602 4.1 73.9 1.0 OD2 C:ASP250 4.1 66.5 1.0 O3A C:ATP602 4.2 72.2 1.0 OD1 C:ASP250 4.2 71.2 1.0 CE C:LYS191 4.3 81.4 1.0 O1G C:ATP602 4.5 70.2 1.0 PA C:ATP602 4.5 62.6 1.0 CE1 C:TYR369 4.5 70.5 1.0 CG C:ASP250 4.6 70.0 1.0 O3G C:ATP602 4.6 70.1 1.0 OG C:SER370 4.8 73.6 1.0 CA C:SER166 5.0 73.9 1.0 CD1 C:TYR369 5.0 74.3 1.0

Magnesium binding site 4 out of 4 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 4 of Crystal Structure of Ced-4 Bound Ced-3 Fragment within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:62.2 occ:1.00 OG D:SER166 2.0 77.9 1.0 O1B D:ATP602 2.6 65.1 1.0 O2G D:ATP602 2.6 72.7 1.0 OD1 D:ASP250 2.9 61.0 1.0 CB D:SER166 3.4 74.4 1.0 PG D:ATP602 3.6 78.4 1.0 PB D:ATP602 3.6 69.1 1.0 CG D:ASP250 3.7 60.7 1.0 OD2 D:ASP250 3.7 63.0 1.0 O1G D:ATP602 3.8 73.9 1.0 CB D:ASP251 3.9 64.4 1.0 O3B D:ATP602 4.0 76.8 1.0 O2B D:ATP602 4.2 63.2 1.0 N D:ASP251 4.3 71.2 1.0 OG1 D:THR271 4.3 55.6 1.0 CG D:ASP251 4.3 68.9 1.0 CA D:ASP251 4.4 63.0 1.0 CA D:SER166 4.5 66.4 1.0 N D:SER166 4.6 72.2 1.0 OD2 D:ASP251 4.7 70.1 1.0 CB D:THR271 4.7 60.5 1.0 OD1 D:ASP251 4.7 67.5 1.0 C D:ASP250 4.8 69.5 1.0 NZ D:LYS191 4.9 90.5 1.0 CE D:LYS165 5.0 70.0 1.0 CB D:ASP250 5.0 57.0 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