Magnesium in PDB 4m9z: Crystal Structure of Ced-4 Bound Ced-3 Fragment

The structure of Crystal Structure of Ced-4 Bound Ced-3 Fragment, PDB code: 4m9z 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)	43.21 / 3.40
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	178.167, 178.167, 200.738, 90.00, 90.00, 90.00
R / Rfree (%)	27 / 32.7

The binding sites of Magnesium atom in the Crystal Structure of Ced-4 Bound Ced-3 Fragment (pdb code 4m9z). 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: 4m9z:
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:60.8 occ:1.00 OG A:SER166 2.3 81.1 1.0 OD1 A:ASP250 2.7 72.4 1.0 O1B A:ATP602 2.9 73.0 1.0 O1G A:ATP602 2.9 82.2 1.0 O2G A:ATP602 3.0 85.7 1.0 PG A:ATP602 3.5 96.9 1.0 CG A:ASP250 3.6 78.5 1.0 CB A:SER166 3.7 90.2 1.0 OG1 A:THR271 3.7 50.9 1.0 CB A:ASP251 3.7 64.5 1.0 N A:ASP251 3.9 84.4 1.0 OD2 A:ASP250 3.9 83.8 1.0 CA A:ASP251 4.0 57.2 1.0 PB A:ATP602 4.1 70.7 1.0 CG A:ASP251 4.2 83.3 1.0 CB A:THR271 4.2 67.1 1.0 O3B A:ATP602 4.2 83.6 1.0 OD1 A:ASP251 4.4 73.3 1.0 C A:ASP250 4.5 73.2 1.0 CE A:LYS165 4.7 81.5 1.0 CA A:SER166 4.7 89.7 1.0 N A:SER166 4.7 95.7 1.0 O3G A:ATP602 4.8 69.7 1.0 CB A:ASP250 4.8 66.6 1.0 OD2 A:ASP251 4.8 77.0 1.0 CA A:ASP250 4.9 61.6 1.0 O2B A:ATP602 4.9 69.6 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:58.2 occ:1.00 OG B:SER166 2.4 80.7 1.0 O1B B:ATP602 2.4 83.7 1.0 O2G B:ATP602 2.9 88.5 1.0 OD1 B:ASP250 3.2 76.5 1.0 CB B:SER166 3.3 80.8 1.0 O1G B:ATP602 3.6 88.6 1.0 OD2 B:ASP250 3.6 78.3 1.0 PG B:ATP602 3.7 1.0 1.0 CG B:ASP250 3.7 71.1 1.0 PB B:ATP602 3.9 77.2 1.0 NZ B:LYS191 4.3 0.3 1.0 O3B B:ATP602 4.3 88.1 1.0 O2A B:ATP602 4.6 70.5 1.0 CB B:ASP251 4.6 57.0 1.0 CA B:SER166 4.7 84.2 1.0 O3A B:ATP602 4.7 71.8 1.0 OG1 B:THR271 4.9 64.4 1.0 CG B:ASP251 4.9 71.4 1.0 CE B:LYS191 5.0 0.4 1.0 O2B B:ATP602 5.0 77.6 1.0 N B:SER166 5.0 90.1 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:77.7 occ:1.00 O2G C:ATP602 2.3 0.5 1.0 O1B C:ATP602 2.4 80.2 1.0 OG C:SER166 2.8 0.0 1.0 NZ C:LYS191 3.2 0.7 1.0 CB C:SER166 3.4 0.5 1.0 PG C:ATP602 3.6 0.2 1.0 PB C:ATP602 3.7 90.1 1.0 O2A C:ATP602 3.7 81.2 1.0 OD1 C:ASP250 4.0 87.0 1.0 O3B C:ATP602 4.0 1.0 1.0 OD2 C:ASP250 4.0 80.4 1.0 O3A C:ATP602 4.1 95.7 1.0 O1G C:ATP602 4.1 92.0 1.0 PA C:ATP602 4.3 88.7 1.0 CE C:LYS191 4.4 0.5 1.0 CG C:ASP250 4.4 82.5 1.0 O1A C:ATP602 4.6 91.7 1.0 CE1 C:TYR369 4.7 95.0 1.0 CA C:SER166 4.8 0.1 1.0 O3G C:ATP602 4.8 81.8 1.0 N C:SER166 5.0 0.7 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:75.4 occ:1.00 OG D:SER166 2.6 0.1 1.0 OD1 D:ASP250 3.0 83.6 1.0 O2G D:ATP602 3.0 93.2 1.0 OG1 D:THR271 3.1 52.3 1.0 O1B D:ATP602 3.2 79.2 1.0 O1G D:ATP602 3.2 82.6 1.0 CB D:THR271 3.4 82.4 1.0 PG D:ATP602 3.6 0.9 1.0 CE D:LYS165 3.8 82.7 1.0 PB D:ATP602 3.8 91.6 1.0 N D:ASP251 3.9 98.1 1.0 CB D:SER166 4.0 0.8 1.0 CA D:ASP251 4.0 91.2 1.0 O2B D:ATP602 4.0 66.4 1.0 CG D:ASP250 4.1 80.3 1.0 O3B D:ATP602 4.1 0.8 1.0 CB D:ASP251 4.2 79.4 1.0 CG2 D:THR271 4.3 71.9 1.0 C D:THR271 4.3 84.9 1.0 NZ D:LYS165 4.3 82.2 1.0 N D:SER166 4.4 98.5 1.0 O D:THR271 4.4 87.1 1.0 CA D:THR271 4.5 77.8 1.0 OD1 D:ASP251 4.6 83.8 1.0 CG D:ASP251 4.6 81.4 1.0 CA D:SER166 4.6 94.7 1.0 N D:THR272 4.7 96.9 1.0 OD2 D:ASP250 4.7 72.7 1.0 CB D:LYS165 4.7 76.2 1.0 C D:ASP250 4.7 90.8 1.0 CD D:LYS165 4.9 93.9 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