Magnesium in PDB 3hb0: Structure of EDEYA2 Complexed with BEF3

All present enzymatic activity of Structure of EDEYA2 Complexed with BEF3:
3.1.3.48;

The structure of Structure of EDEYA2 Complexed with BEF3, PDB code: 3hb0 was solved by S.K.Jung, D.G.Jeong, S.E.Ryu, S.J.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.50
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	184.002, 184.002, 119.954, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 25.4

The structure of Structure of EDEYA2 Complexed with BEF3 also contains other interesting chemical elements:

Fluorine

(F)

12 atoms

The binding sites of Magnesium atom in the Structure of EDEYA2 Complexed with BEF3 (pdb code 3hb0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of EDEYA2 Complexed with BEF3, PDB code: 3hb0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of EDEYA2 Complexed with BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of EDEYA2 Complexed with BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:36.5 occ:1.00 OD1 A:ASP502 2.1 36.0 1.0 O A:HOH126 2.1 28.2 1.0 F2 A:BEF801 2.1 36.3 1.0 OD2 A:ASP274 2.1 30.1 1.0 O A:ASP276 2.3 34.4 1.0 CG A:ASP274 3.0 29.6 1.0 CG A:ASP502 3.1 31.2 1.0 BE A:BEF801 3.2 33.9 1.0 OE2 A:GLU506 3.2 44.3 1.0 OD1 A:ASP274 3.3 31.1 1.0 OD2 A:ASP502 3.4 31.8 1.0 C A:ASP276 3.5 31.6 1.0 OG1 A:THR278 4.0 29.1 1.0 F1 A:BEF801 4.1 33.9 1.0 F3 A:BEF801 4.2 34.7 1.0 CA A:ASP276 4.2 30.3 1.0 N A:GLY503 4.3 31.1 1.0 CB A:ASP274 4.3 26.6 1.0 O A:HOH111 4.3 42.1 1.0 CB A:ASP276 4.3 29.0 1.0 CD A:GLU506 4.3 38.7 1.0 N A:ASP276 4.4 29.6 1.0 CB A:GLU277 4.4 28.5 1.0 CB A:ASP502 4.4 30.3 1.0 O A:HOH133 4.4 27.7 1.0 O A:HOH71 4.5 29.7 1.0 N A:GLU277 4.5 30.2 1.0 N A:ASP502 4.6 30.1 1.0 OE1 A:GLU506 4.7 40.0 1.0 C A:GLU277 4.7 28.5 1.0 CA A:GLU277 4.7 29.1 1.0 CA A:GLY503 4.9 31.6 1.0 N A:THR278 4.9 27.7 1.0 C A:ASP502 4.9 29.9 1.0 CA A:ASP502 4.9 30.3 1.0

Magnesium binding site 2 out of 4 in the Structure of EDEYA2 Complexed with BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of EDEYA2 Complexed with BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:44.1 occ:1.00 O B:HOH132 1.9 64.9 1.0 F2 B:BEF802 1.9 44.4 1.0 O B:ASP276 2.1 36.1 1.0 O B:HOH135 2.2 51.1 1.0 OD1 B:ASP502 2.2 36.4 1.0 OD2 B:ASP274 2.3 39.9 1.0 CG B:ASP502 3.1 34.5 1.0 BE B:BEF802 3.2 43.5 1.0 CG B:ASP274 3.2 39.7 1.0 C B:ASP276 3.3 37.4 1.0 OD2 B:ASP502 3.4 38.2 1.0 OD1 B:ASP274 3.5 42.3 1.0 O B:HOH134 4.0 40.4 1.0 O B:HOH60 4.0 36.9 1.0 F1 B:BEF802 4.0 44.7 1.0 F3 B:BEF802 4.1 43.0 1.0 CA B:ASP276 4.1 37.7 1.0 CB B:ASP276 4.2 40.3 1.0 OE2 B:GLU506 4.2 57.4 1.0 OG1 B:THR278 4.2 30.8 1.0 N B:GLU277 4.4 36.5 1.0 CB B:GLU277 4.4 35.8 1.0 N B:ASP276 4.4 35.6 1.0 CB B:ASP502 4.5 36.6 1.0 N B:GLY503 4.5 39.8 1.0 CB B:ASP274 4.5 36.5 1.0 CA B:GLU277 4.7 35.6 1.0 C B:GLU277 4.8 34.9 1.0 OE1 B:GLU506 4.8 57.4 1.0 N B:ASP502 4.8 37.7 1.0 CD B:GLU506 4.8 55.7 1.0 N B:THR278 4.9 33.7 1.0 C B:ASP502 4.9 39.0 1.0

Magnesium binding site 3 out of 4 in the Structure of EDEYA2 Complexed with BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of EDEYA2 Complexed with BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg703 b:39.3 occ:1.00 O C:HOH129 1.9 29.8 1.0 OD1 C:ASP502 2.1 38.7 1.0 F2 C:BEF803 2.1 41.3 1.0 OD2 C:ASP274 2.3 37.8 1.0 O C:ASP276 2.3 38.7 1.0 CG C:ASP502 3.0 37.2 1.0 CG C:ASP274 3.1 36.2 1.0 BE C:BEF803 3.2 40.5 1.0 OD2 C:ASP502 3.3 36.1 1.0 OE2 C:GLU506 3.4 53.9 1.0 OD1 C:ASP274 3.4 38.8 1.0 C C:ASP276 3.5 38.6 1.0 F1 C:BEF803 4.1 41.6 1.0 F3 C:BEF803 4.2 40.1 1.0 OG1 C:THR278 4.3 35.8 1.0 CA C:ASP276 4.3 38.3 1.0 CD C:GLU506 4.3 50.4 1.0 CB C:ASP276 4.3 38.9 1.0 N C:GLY503 4.3 38.3 1.0 CB C:ASP502 4.4 35.3 1.0 CB C:ASP274 4.4 36.3 1.0 O C:HOH137 4.4 36.5 1.0 N C:ASP276 4.5 38.9 1.0 CB C:GLU277 4.5 36.3 1.0 N C:GLU277 4.5 37.4 1.0 OE1 C:GLU506 4.6 52.6 1.0 N C:ASP502 4.7 37.1 1.0 CA C:GLU277 4.8 36.9 1.0 C C:GLU277 4.8 36.4 1.0 CA C:GLY503 4.9 39.8 1.0 C C:ASP502 4.9 37.0 1.0 CA C:ASP502 5.0 36.5 1.0 N C:THR278 5.0 36.0 1.0

Magnesium binding site 4 out of 4 in the Structure of EDEYA2 Complexed with BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of EDEYA2 Complexed with BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg704 b:43.9 occ:1.00 O D:HOH138 1.9 45.2 1.0 F2 D:BEF804 1.9 37.3 1.0 OD1 D:ASP502 2.1 38.3 1.0 OD2 D:ASP274 2.2 37.2 1.0 O D:ASP276 2.2 35.2 1.0 CG D:ASP502 3.0 35.8 1.0 OE2 D:GLU506 3.1 49.0 1.0 CG D:ASP274 3.1 34.3 1.0 BE D:BEF804 3.1 36.5 1.0 OD2 D:ASP502 3.3 36.1 1.0 OD1 D:ASP274 3.4 35.5 1.0 C D:ASP276 3.4 35.5 1.0 O D:HOH139 4.0 45.7 1.0 F1 D:BEF804 4.0 39.1 1.0 F3 D:BEF804 4.0 35.7 1.0 O D:HOH131 4.1 49.6 1.0 CA D:ASP276 4.1 36.3 1.0 CD D:GLU506 4.2 46.0 1.0 CB D:ASP276 4.2 38.3 1.0 OG1 D:THR278 4.3 29.4 1.0 O D:HOH130 4.3 42.9 1.0 N D:ASP276 4.4 35.7 1.0 CB D:ASP274 4.4 29.8 1.0 CB D:ASP502 4.4 34.2 1.0 N D:GLY503 4.4 34.9 1.0 N D:GLU277 4.5 33.3 1.0 CB D:GLU277 4.5 32.2 1.0 OE1 D:GLU506 4.5 45.9 1.0 N D:ASP502 4.7 34.5 1.0 C D:GLU277 4.7 30.6 1.0 CA D:GLU277 4.7 31.5 1.0 C D:ASP502 4.9 35.0 1.0 CA D:ASP502 4.9 35.4 1.0 N D:THR278 4.9 29.5 1.0 NZ D:LYS480 5.0 31.2 1.0

S.K.Jung, D.G.Jeong, S.J.Chung, J.H.Kim, B.C.Park, N.K.Tonks, S.E.Ryu, S.J.Kim. Crystal Structure of Ed-EYA2: Insight Into Dual Roles As A Protein Tyrosine Phosphatase and A Transcription Factor Faseb J. V. 24 560 2010.
ISSN: ISSN 0892-6638
PubMed: 19858093
DOI: 10.1096/FJ.09-143891