Magnesium in PDB 3geb: Crystal Structure of EDEYA2

All present enzymatic activity of Crystal Structure of EDEYA2:
3.1.3.48;

The structure of Crystal Structure of EDEYA2, PDB code: 3geb was solved by S.J.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.40
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	183.612, 183.612, 120.150, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 21.8

The binding sites of Magnesium atom in the Crystal Structure of EDEYA2 (pdb code 3geb). 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 EDEYA2, PDB code: 3geb:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of EDEYA2


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 EDEYA2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:44.7 occ:1.00 OD1 A:ASP502 2.4 35.6 1.0 O A:ASP276 2.5 29.2 1.0 OD2 A:ASP274 2.6 24.0 1.0 CG A:ASP502 3.2 32.9 1.0 OD2 A:ASP502 3.3 33.2 1.0 O A:HOH63 3.4 22.1 1.0 CG A:ASP274 3.5 25.0 1.0 C A:ASP276 3.6 28.8 1.0 OD1 A:ASP274 3.7 27.6 1.0 CB A:GLU277 4.2 24.8 1.0 CB A:ASP276 4.3 32.6 1.0 OE2 A:GLU506 4.3 30.7 1.0 CA A:ASP276 4.4 29.5 1.0 N A:GLU277 4.6 26.5 1.0 N A:GLY503 4.6 32.3 1.0 CB A:ASP502 4.7 31.2 1.0 N A:ASP276 4.7 27.4 1.0 OG1 A:THR278 4.7 16.2 1.0 OE1 A:GLU277 4.7 33.5 1.0 CA A:GLU277 4.8 24.0 1.0 CB A:ASP274 4.9 22.6 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of EDEYA2


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 EDEYA2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:49.9 occ:1.00 OD2 B:ASP274 2.4 44.3 1.0 O B:ASP276 2.6 39.0 1.0 O B:HOH206 2.7 37.3 1.0 OD1 B:ASP274 2.8 45.0 1.0 CG B:ASP274 2.9 44.1 1.0 OD1 B:ASP502 3.5 55.2 1.0 C B:ASP276 3.7 37.6 1.0 OD2 B:ASP502 3.9 54.5 1.0 CG B:ASP502 4.0 54.2 1.0 CB B:ASP276 4.2 38.1 1.0 CA B:ASP276 4.3 36.9 1.0 OE1 B:GLU506 4.3 63.8 1.0 N B:ASP276 4.3 36.3 1.0 CB B:ASP274 4.4 41.0 1.0 OE2 B:GLU506 4.4 64.5 1.0 O B:HOH103 4.4 34.2 1.0 CB B:GLU277 4.5 36.6 1.0 CD B:GLU506 4.7 65.1 1.0 OG1 B:THR278 4.7 36.2 1.0 N B:GLY503 4.8 53.6 1.0 N B:GLU277 4.8 35.9 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of EDEYA2


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 EDEYA2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg703 b:29.9 occ:1.00 OD1 C:ASP502 2.5 36.3 1.0 OD2 C:ASP274 2.6 30.2 1.0 O C:ASP276 2.6 34.6 1.0 CG C:ASP274 3.5 29.3 1.0 CG C:ASP502 3.5 34.4 1.0 OD1 C:ASP274 3.6 31.0 1.0 OD2 C:ASP502 3.7 34.1 1.0 C C:ASP276 3.7 32.6 1.0 CB C:ASP276 4.2 34.9 1.0 N C:GLY503 4.3 36.0 1.0 CA C:ASP276 4.3 33.1 1.0 OG1 C:THR278 4.5 21.9 1.0 CB C:GLU277 4.6 30.9 1.0 N C:ASP276 4.6 31.1 1.0 OE2 C:GLU506 4.6 42.0 1.0 OE1 C:GLU506 4.7 39.0 1.0 CA C:GLY503 4.7 36.5 1.0 N C:GLU277 4.8 32.2 1.0 OE1 C:GLU277 4.8 44.5 1.0 CB C:ASP502 4.9 34.4 1.0 CB C:ASP274 4.9 28.9 1.0 O C:HOH16 4.9 16.6 1.0 CD C:GLU506 4.9 40.0 1.0 N C:ASP502 5.0 33.1 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of EDEYA2


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 EDEYA2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg704 b:46.3 occ:1.00 OD2 D:ASP274 2.5 38.5 1.0 OD1 D:ASP502 2.7 43.8 1.0 O D:ASP276 3.0 32.7 1.0 CG D:ASP274 3.2 35.4 1.0 OD1 D:ASP274 3.2 37.5 1.0 CG D:ASP502 3.6 45.6 1.0 OD2 D:ASP502 3.6 45.9 1.0 C D:ASP276 4.1 31.1 1.0 OE1 D:GLU506 4.1 47.9 1.0 CB D:ASP276 4.5 33.6 1.0 O D:HOH23 4.5 20.2 1.0 CB D:ASP274 4.6 31.2 1.0 CA D:ASP276 4.6 31.3 1.0 NZ D:LYS480 4.6 43.2 1.0 N D:ASP276 4.7 30.5 1.0 CD D:GLU506 4.7 46.3 1.0 OE2 D:GLU506 4.8 44.7 1.0 N D:GLY503 4.8 47.3 1.0 OG1 D:THR278 4.9 27.8 1.0

S.J.Kim, D.G.Jeong, S.K.Jung, E.R.Seong. Structure of EDEYA2 To Be Published.