Magnesium in PDB 3ct7: Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12

The structure of Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12, PDB code: 3ct7 was solved by A.A.Fedorov, E.V.Fedorov, K.K.Chan, J.A.Gerlt, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.90 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.462, 129.209, 154.451, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 24.9

The binding sites of Magnesium atom in the Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12 (pdb code 3ct7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12, PDB code: 3ct7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12


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 D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg232 b:36.3 occ:1.00 OD2 A:ASP32 2.3 34.9 1.0 ND1 A:HIS63 2.3 30.9 1.0 NE2 A:HIS30 2.4 31.9 1.0 OD1 A:ASP173 2.5 44.9 1.0 CE1 A:HIS63 3.0 31.8 1.0 CG A:ASP32 3.1 33.9 1.0 CE1 A:HIS30 3.3 32.3 1.0 CD2 A:HIS30 3.4 30.7 1.0 OD1 A:ASP32 3.4 35.6 1.0 CG A:HIS63 3.5 30.5 1.0 CG A:ASP173 3.5 45.1 1.0 CE A:MET65 3.9 31.7 1.0 OD2 A:ASP173 3.9 47.0 1.0 CB A:HIS63 3.9 29.6 1.0 NE2 A:HIS63 4.2 32.7 1.0 ND1 A:HIS30 4.4 33.0 1.0 CD2 A:HIS63 4.5 32.4 1.0 CB A:ASP32 4.5 30.1 1.0 CG A:HIS30 4.5 32.7 1.0 CB A:ASP173 4.8 45.0 1.0 CD1 A:ILE112 4.8 28.7 1.0 SD A:MET65 4.9 29.3 1.0 SD A:MET135 4.9 37.1 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12


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 D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg232 b:35.9 occ:1.00 OD2 B:ASP32 2.2 40.4 1.0 NE2 B:HIS30 2.4 28.3 1.0 OD1 B:ASP173 2.5 42.1 1.0 ND1 B:HIS63 2.5 29.5 1.0 CG B:ASP32 3.1 37.6 1.0 CE1 B:HIS63 3.1 30.9 1.0 OD1 B:ASP32 3.3 42.0 1.0 CD2 B:HIS30 3.4 30.0 1.0 CE1 B:HIS30 3.4 30.9 1.0 CG B:ASP173 3.5 45.1 1.0 CG B:HIS63 3.6 27.0 1.0 OD2 B:ASP173 3.8 44.6 1.0 CE B:MET65 3.9 28.9 1.0 CB B:HIS63 4.1 24.9 1.0 NE2 B:HIS63 4.4 29.7 1.0 CB B:ASP32 4.5 35.0 1.0 ND1 B:HIS30 4.5 30.4 1.0 CG B:HIS30 4.5 30.3 1.0 CD2 B:HIS63 4.6 29.4 1.0 CB B:ASP173 4.8 42.5 1.0 SD B:MET65 4.9 32.3 1.0 CD1 B:ILE112 4.9 24.6 1.0 CD1 B:ILE193 5.0 25.6 1.0 SD B:MET135 5.0 33.6 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12


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 D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:42.3 occ:1.00 OD1 C:ASP173 2.4 42.8 1.0 OD2 C:ASP32 2.4 34.9 1.0 NE2 C:HIS30 2.4 27.3 1.0 ND1 C:HIS63 2.5 36.4 1.0 CE1 C:HIS63 3.1 38.3 1.0 CG C:ASP32 3.2 33.2 1.0 OD1 C:ASP32 3.4 32.2 1.0 CD2 C:HIS30 3.4 29.7 1.0 CG C:ASP173 3.4 40.4 1.0 CE1 C:HIS30 3.4 27.2 1.0 CG C:HIS63 3.7 35.6 1.0 OD2 C:ASP173 3.7 40.5 1.0 CE C:MET65 3.9 31.8 1.0 CB C:HIS63 4.2 29.3 1.0 NE2 C:HIS63 4.4 39.3 1.0 ND1 C:HIS30 4.5 28.9 1.0 CG C:HIS30 4.5 29.4 1.0 CB C:ASP32 4.6 30.9 1.0 CD2 C:HIS63 4.6 36.7 1.0 CB C:ASP173 4.7 40.8 1.0 CD1 C:ILE112 4.9 29.1 1.0 SD C:MET135 4.9 39.5 1.0 CD1 C:ILE193 4.9 30.1 1.0 SD C:MET65 4.9 30.0 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12


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 D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:33.9 occ:1.00 OD2 D:ASP32 2.2 32.8 1.0 ND1 D:HIS63 2.3 34.0 1.0 NE2 D:HIS30 2.4 36.9 1.0 OD1 D:ASP173 2.5 43.0 1.0 CE1 D:HIS63 2.9 33.0 1.0 CG D:ASP32 3.1 30.1 1.0 CE1 D:HIS30 3.3 37.5 1.0 OD1 D:ASP32 3.4 32.1 1.0 CG D:HIS63 3.4 32.2 1.0 CD2 D:HIS30 3.4 36.3 1.0 CG D:ASP173 3.5 43.2 1.0 CE D:MET65 3.8 32.6 1.0 CB D:HIS63 4.0 30.4 1.0 OD2 D:ASP173 4.0 44.6 1.0 NE2 D:HIS63 4.2 33.9 1.0 O D:HOH806 4.3 38.5 1.0 CD2 D:HIS63 4.4 32.7 1.0 CB D:ASP32 4.5 27.0 1.0 ND1 D:HIS30 4.5 38.5 1.0 CG D:HIS30 4.6 36.5 1.0 CD1 D:ILE112 4.8 23.1 1.0 CB D:ASP173 4.8 41.5 1.0 SD D:MET65 4.8 36.2 1.0 SD D:MET135 4.9 32.6 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg501 b:29.8 occ:1.00 OD2 E:ASP32 2.3 40.0 1.0 OD1 E:ASP173 2.4 50.3 1.0 NE2 E:HIS30 2.4 37.5 1.0 ND1 E:HIS63 2.5 28.3 1.0 CG E:ASP32 3.1 40.5 1.0 CE1 E:HIS63 3.2 27.0 1.0 OD1 E:ASP32 3.3 40.0 1.0 CD2 E:HIS30 3.3 37.3 1.0 CE1 E:HIS30 3.4 37.7 1.0 CG E:ASP173 3.4 47.8 1.0 CG E:HIS63 3.7 27.5 1.0 OD2 E:ASP173 3.7 50.0 1.0 CE E:MET65 4.0 30.8 1.0 CB E:HIS63 4.2 25.5 1.0 O E:HOH826 4.3 37.6 1.0 NE2 E:HIS63 4.4 27.2 1.0 ND1 E:HIS30 4.5 38.7 1.0 CG E:HIS30 4.5 36.6 1.0 CB E:ASP32 4.5 36.6 1.0 CD2 E:HIS63 4.7 27.9 1.0 CB E:ASP173 4.7 46.0 1.0 SD E:MET135 4.9 34.0 1.0 SD E:MET65 4.9 28.5 1.0 CD1 E:ILE112 4.9 31.8 1.0 CD1 E:ILE193 5.0 28.2 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg601 b:42.7 occ:1.00 OD2 F:ASP32 2.3 39.9 1.0 OD1 F:ASP173 2.5 45.1 1.0 ND1 F:HIS63 2.7 32.0 1.0 NE2 F:HIS30 2.7 33.9 1.0 CG F:ASP32 3.0 38.4 1.0 OD1 F:ASP32 3.1 41.3 1.0 CE1 F:HIS63 3.2 31.1 1.0 CG F:ASP173 3.5 43.2 1.0 CD2 F:HIS30 3.6 32.4 1.0 CE F:MET65 3.7 21.9 1.0 OD2 F:ASP173 3.7 42.5 1.0 CE1 F:HIS30 3.8 33.4 1.0 CG F:HIS63 3.9 30.3 1.0 CB F:ASP32 4.4 34.8 1.0 CB F:HIS63 4.4 28.5 1.0 NE2 F:HIS63 4.5 31.5 1.0 O F:HOH816 4.6 40.4 1.0 SD F:MET65 4.7 26.4 1.0 CD2 F:HIS63 4.8 30.3 1.0 CG F:HIS30 4.8 34.0 1.0 CB F:ASP173 4.8 41.8 1.0 ND1 F:HIS30 4.9 33.5 1.0 SD F:MET135 4.9 34.6 1.0

K.K.Chan, A.A.Fedorov, E.V.Fedorov, S.C.Almo, J.A.Gerlt. Structural Basis For Substrate Specificity in Phosphate Binding (Beta/Alpha)8-Barrels: D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12. Biochemistry V. 47 9608 2008.
ISSN: ISSN 0006-2960
PubMed: 18700786
DOI: 10.1021/BI800821V