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Magnesium in PDB 3geb: Crystal Structure of EDEYA2

Enzymatic activity of Crystal Structure of EDEYA2

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

Protein crystallography data

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

Magnesium Binding Sites:

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 3geb

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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 3geb

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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 3geb

Go back to Magnesium Binding Sites List in 3geb
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 3geb

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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

Reference:

S.J.Kim, D.G.Jeong, S.K.Jung, E.R.Seong. Structure of EDEYA2 To Be Published.
Page generated: Mon Dec 14 08:11:16 2020

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