Magnesium in PDB 4u8d: X-Ray Structure of Mg-Bound Human Sorcin

The structure of X-Ray Structure of Mg-Bound Human Sorcin, PDB code: 4u8d was solved by A.Fiorillo, A.Ilari, G.Colotti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.76 / 2.30
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	117.832, 117.832, 86.880, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 24.9

The binding sites of Magnesium atom in the X-Ray Structure of Mg-Bound Human Sorcin (pdb code 4u8d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the X-Ray Structure of Mg-Bound Human Sorcin, PDB code: 4u8d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the X-Ray Structure of Mg-Bound Human Sorcin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of Mg-Bound Human Sorcin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:40.7 occ:1.00 OG A:SER87 2.1 45.6 1.0 O A:THR89 2.2 36.3 1.0 OD1 A:ASP85 2.2 49.9 1.0 OD1 A:ASP83 2.2 42.8 1.0 O A:HOH343 2.5 37.4 1.0 O A:HOH353 2.7 39.3 1.0 CG A:ASP85 3.3 49.1 1.0 CB A:SER87 3.3 43.7 1.0 C A:THR89 3.3 35.8 1.0 CG A:ASP83 3.4 41.6 1.0 OD2 A:ASP85 3.7 53.1 1.0 N A:SER87 3.8 47.5 1.0 N A:THR89 3.9 38.3 1.0 O A:HOH365 4.0 61.2 1.0 OG1 A:THR89 4.0 35.6 1.0 CA A:ASP83 4.0 41.4 1.0 CA A:SER87 4.0 44.6 1.0 CA A:THR89 4.2 36.6 1.0 O A:HOH334 4.2 39.3 1.0 CB A:ASP83 4.2 41.9 1.0 OD2 A:ASP83 4.3 38.6 1.0 N A:MET90 4.3 35.7 1.0 OE1 A:GLN48 4.3 42.0 1.0 CA A:MET90 4.3 39.7 1.0 C A:ASP83 4.5 40.4 1.0 N A:GLY88 4.5 41.4 1.0 N A:ASP85 4.5 48.2 1.0 C A:SER87 4.5 43.7 1.0 CB A:ASP85 4.6 50.2 1.0 N A:ARG84 4.7 40.9 1.0 N A:MET86 4.7 49.8 1.0 CB A:THR89 4.7 36.5 1.0 C A:ASP85 4.9 49.3 1.0 CA A:ASP85 4.9 48.8 1.0 O A:LEU82 4.9 38.5 1.0 C A:MET86 5.0 49.8 1.0

Magnesium binding site 2 out of 7 in the X-Ray Structure of Mg-Bound Human Sorcin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of Mg-Bound Human Sorcin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:75.4 occ:1.00 O A:HOH366 1.9 71.0 1.0 OG A:SER117 2.1 75.0 1.0 OD1 A:ASP115 2.2 81.3 1.0 OD1 A:ASP113 2.2 69.0 1.0 O A:THR119 2.8 52.9 1.0 CG A:ASP115 3.0 85.4 1.0 OD2 A:ASP115 3.3 83.5 1.0 CG A:ASP113 3.4 60.3 1.0 CB A:SER117 3.5 76.6 1.0 N A:ASP115 3.7 84.6 1.0 CA A:ASP113 3.9 60.4 1.0 N A:SER117 3.9 82.5 1.0 C A:THR119 4.0 48.2 1.0 C A:ASP113 4.1 67.0 1.0 N A:THR114 4.1 77.8 1.0 CB A:ASP115 4.1 81.7 1.0 CA A:ASP115 4.2 81.1 1.0 CB A:ASP113 4.2 56.4 1.0 OD2 A:ASP113 4.3 54.8 1.0 CA A:SER117 4.3 75.3 1.0 N A:ARG116 4.3 84.9 1.0 OE2 A:GLU124 4.3 65.1 1.0 C A:ASP115 4.4 82.1 1.0 OG1 A:THR119 4.4 59.0 1.0 OE1 A:GLU124 4.5 68.7 1.0 O A:ASP113 4.7 66.7 1.0 O A:PHE112 4.7 65.8 1.0 N A:THR119 4.7 52.4 1.0 C A:THR114 4.8 82.2 1.0 CA A:VAL120 4.8 52.7 1.0 CD A:GLU124 4.8 60.7 1.0 N A:VAL120 4.9 49.4 1.0 OG1 A:THR114 4.9 84.8 1.0 CA A:THR119 4.9 50.7 1.0 CA A:THR114 4.9 82.5 1.0

Magnesium binding site 3 out of 7 in the X-Ray Structure of Mg-Bound Human Sorcin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Structure of Mg-Bound Human Sorcin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:39.4 occ:1.00 OG B:SER87 2.1 42.1 1.0 OD1 B:ASP85 2.2 41.8 1.0 OD1 B:ASP83 2.2 37.1 1.0 O B:THR89 2.2 34.5 1.0 O B:HOH333 2.3 40.5 1.0 O B:HOH341 2.5 42.3 1.0 CB B:SER87 3.2 40.1 1.0 CG B:ASP85 3.3 41.6 1.0 C B:THR89 3.4 33.5 1.0 CG B:ASP83 3.4 36.0 1.0 OD2 B:ASP85 3.7 43.4 1.0 N B:SER87 3.8 42.2 1.0 N B:THR89 4.0 37.3 1.0 CA B:ASP83 4.0 38.0 1.0 O B:HOH366 4.0 54.8 1.0 CA B:SER87 4.0 40.0 1.0 O B:HOH332 4.1 43.6 1.0 CB B:ASP83 4.2 35.5 1.0 OG1 B:THR89 4.2 32.7 1.0 CA B:THR89 4.2 34.8 1.0 O B:HOH346 4.2 36.6 1.0 OE1 B:GLN48 4.3 47.6 1.0 OD2 B:ASP83 4.3 34.4 1.0 N B:MET90 4.3 34.5 1.0 C B:ASP83 4.4 38.4 1.0 N B:ASP85 4.4 40.1 1.0 N B:GLY88 4.5 40.9 1.0 C B:SER87 4.6 39.7 1.0 CB B:ASP85 4.6 39.6 1.0 N B:MET86 4.6 46.5 1.0 CA B:MET90 4.6 35.1 1.0 N B:ARG84 4.6 38.0 1.0 OE2 B:GLU94 4.7 52.5 1.0 C B:ASP85 4.8 41.9 1.0 CA B:ASP85 4.8 39.9 1.0 CB B:THR89 4.9 37.4 1.0 O B:ASP83 4.9 42.0 1.0 C B:MET86 4.9 40.8 1.0 O B:LEU82 5.0 36.9 1.0

Magnesium binding site 4 out of 7 in the X-Ray Structure of Mg-Bound Human Sorcin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of X-Ray Structure of Mg-Bound Human Sorcin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:54.6 occ:1.00 O B:SER61 2.6 37.0 1.0 C B:SER61 3.8 34.9 1.0 OH B:TYR38 3.9 30.9 1.0 CA B:GLY62 4.2 34.0 1.0 CH2 B:TRP99 4.2 36.3 1.0 N B:GLY62 4.4 34.8 1.0 C B:GLY62 4.5 34.7 1.0 O B:GLY62 4.7 32.2 1.0 CZ B:TYR38 4.8 34.0 1.0 CA B:SER61 4.9 33.5 1.0 CZ2 B:TRP99 4.9 37.2 1.0

Magnesium binding site 5 out of 7 in the X-Ray Structure of Mg-Bound Human Sorcin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of X-Ray Structure of Mg-Bound Human Sorcin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:48.8 occ:1.00 OG1 B:THR31 2.1 38.1 1.0 O B:GLN32 2.2 35.0 1.0 CG2 B:THR31 3.0 37.5 1.0 CB B:THR31 3.1 36.2 1.0 C B:GLN32 3.3 35.4 1.0 N B:GLN32 3.4 31.8 1.0 CA B:GLN32 3.9 34.8 1.0 C B:THR31 3.9 32.8 1.0 CA B:THR31 4.0 35.8 1.0 CD B:PRO34 4.3 33.6 1.0 CB B:GLN32 4.4 35.6 1.0 N B:ASP33 4.4 34.7 1.0 O B:THR31 4.7 32.5 1.0 CA B:ASP33 4.8 34.2 1.0 N B:PRO34 4.9 32.6 1.0

Magnesium binding site 6 out of 7 in the X-Ray Structure of Mg-Bound Human Sorcin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of X-Ray Structure of Mg-Bound Human Sorcin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg204 b:58.3 occ:1.00 O B:HOH360 2.1 51.6 1.0 O B:HOH364 2.1 60.0 1.0 O B:HOH361 2.1 46.6 1.0 O B:HOH363 2.1 54.2 1.0 O B:HOH362 2.1 56.5 1.0 OE1 B:GLU124 4.2 71.6 1.0 OE2 B:GLU124 4.3 73.2 1.0 OD1 B:ASP113 4.3 54.3 1.0 O B:PHE112 4.3 64.6 1.0 O B:THR119 4.3 54.4 1.0 OG B:SER117 4.4 59.7 1.0 OD1 B:ASP115 4.5 80.7 1.0 CD B:GLU124 4.7 68.2 1.0

Magnesium binding site 7 out of 7 in the X-Ray Structure of Mg-Bound Human Sorcin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of X-Ray Structure of Mg-Bound Human Sorcin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg205 b:71.7 occ:1.00 OD2 B:ASP50 2.7 50.4 1.0 CG B:ASP50 3.5 42.3 1.0 OD1 B:ASP50 3.5 40.0 1.0 OD1 B:ASP52 3.6 79.2 1.0 ND2 A:ASN151 3.8 0.4 1.0 OD1 A:ASN151 3.9 0.4 1.0 CB B:ASP52 4.2 50.2 1.0 CG B:ASP52 4.2 60.9 1.0 CG A:ASN151 4.3 0.6 1.0 OE1 B:GLU53 4.6 43.3 1.0 CD B:GLU53 4.8 38.3 1.0 CB B:ASP50 4.9 40.8 1.0

A.Ilari, A.Fiorillo, G.Colotti. Investigating the Conformational Changes of Sorcin to Shed Light on Signal Transduction in the Apoptotic Process To Be Published.