Magnesium in PDB 7f9f: Thrombocorticin

The structure of Thrombocorticin, PDB code: 7f9f was solved by H.Kageyama, K.Onodera, R.Sakai, Y.Tanaka, D.M.Freymann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.47 / 1.41
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.458, 92.445, 58.536, 90, 102.76, 90
R / Rfree (%)	16.9 / 19.4

The binding sites of Magnesium atom in the Thrombocorticin (pdb code 7f9f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Thrombocorticin, PDB code: 7f9f:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Thrombocorticin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thrombocorticin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:8.5 occ:1.00 O A:HOH432 2.4 9.0 1.0 O C:HOH380 2.4 7.8 1.0 O A:HOH398 2.4 9.8 1.0 O D:HOH252 2.4 8.4 1.0 O B:GLU88 2.4 7.5 1.0 O A:GLU88 2.4 7.0 1.0 C B:GLU88 3.6 7.4 1.0 C A:GLU88 3.6 7.7 1.0 N A:GLU88 4.0 7.5 1.0 N B:GLU88 4.0 7.4 1.0 OE1 A:GLU88 4.1 15.3 1.0 OE1 B:GLU88 4.2 13.9 1.0 OG D:SER89 4.2 12.9 1.0 OG C:SER89 4.2 11.9 1.0 O A:HOH380 4.3 7.8 1.0 O D:HOH255 4.3 10.4 1.0 CA B:GLU88 4.3 6.8 1.0 CA A:GLU88 4.3 7.7 1.0 O B:HOH249 4.3 8.1 1.0 O C:HOH353 4.3 9.8 1.0 O B:HOH337 4.6 25.2 1.0 O A:HOH457 4.6 24.6 1.0 CB A:GLU88 4.7 12.3 1.0 N B:SER89 4.7 8.3 1.0 N A:SER89 4.7 6.7 1.0 CB B:GLU88 4.7 10.0 1.0 CA B:SER89 4.9 8.1 1.0 CA A:SER89 4.9 7.2 1.0 OG A:SER89 5.0 10.0 1.0

Magnesium binding site 2 out of 2 in the Thrombocorticin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thrombocorticin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:7.4 occ:1.00 O D:GLU88 2.3 5.8 1.0 O C:GLU88 2.3 6.1 1.0 O A:HOH380 2.4 7.8 1.0 O B:HOH249 2.4 8.1 1.0 O D:HOH319 2.5 7.9 1.0 O C:HOH421 2.5 8.1 1.0 C D:GLU88 3.5 5.9 1.0 C C:GLU88 3.5 5.2 1.0 N C:GLU88 3.9 5.7 1.0 N D:GLU88 3.9 5.7 1.0 OE1 D:GLU88 4.2 8.4 1.0 CA D:GLU88 4.2 5.9 1.0 OE1 C:GLU88 4.2 9.2 1.0 O C:HOH380 4.2 7.8 1.0 CA C:GLU88 4.2 4.9 1.0 O D:HOH252 4.3 8.4 1.0 OG B:SER89 4.3 12.3 1.0 OG A:SER89 4.3 10.0 1.0 O D:HOH281 4.4 7.3 1.0 O B:HOH253 4.4 8.4 1.0 N D:SER89 4.5 5.7 1.0 N C:SER89 4.5 5.9 1.0 CB D:GLU88 4.6 7.2 1.0 CB C:GLU88 4.6 6.6 1.0 O C:HOH420 4.7 19.0 1.0 O D:HOH378 4.7 21.2 1.0 CA D:SER89 4.8 5.8 1.0 CA C:SER89 4.8 6.1 1.0 OG D:SER89 4.8 12.9 1.0 OG C:SER89 4.9 11.9 1.0

H.Kageyama, K.Onodera, R.Sakai, Y.Tanaka. Crystal Structure of Thrombocorticin To Be Published.