Magnesium in PDB 3ctl: Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K12 Complexed with D-Glucitol 6- Phosphate and Magnesium

The structure of Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K12 Complexed with D-Glucitol 6- Phosphate and Magnesium, PDB code: 3ctl 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)	24.96 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.706, 129.040, 154.874, 90.00, 90.00, 90.00
R / Rfree (%)	24.3 / 26.5

The binding sites of Magnesium atom in the Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K12 Complexed with D-Glucitol 6- Phosphate and Magnesium (pdb code 3ctl). 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 K12 Complexed with D-Glucitol 6- Phosphate and Magnesium, PDB code: 3ctl:
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 K12 Complexed with D-Glucitol 6- Phosphate and Magnesium


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 K12 Complexed with D-Glucitol 6- Phosphate and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:35.2 occ:1.00 ND1 A:HIS63 2.0 34.7 1.0 O2 A:S6P501 2.0 53.8 1.0 OD2 A:ASP32 2.1 34.9 1.0 NE2 A:HIS30 2.1 33.9 1.0 OD1 A:ASP173 2.6 40.8 1.0 CE1 A:HIS63 2.9 33.6 1.0 CE1 A:HIS30 3.0 34.3 1.0 CG A:HIS63 3.1 34.5 1.0 CG A:ASP32 3.2 33.7 1.0 CD2 A:HIS30 3.2 33.3 1.0 O3 A:S6P501 3.3 55.0 1.0 C2 A:S6P501 3.3 54.9 1.0 CB A:HIS63 3.6 32.9 1.0 CG A:ASP173 3.7 39.0 1.0 OD1 A:ASP32 3.7 36.5 1.0 C3 A:S6P501 3.7 55.8 1.0 CE A:MET65 4.0 34.0 1.0 NE2 A:HIS63 4.1 34.3 1.0 ND1 A:HIS30 4.2 33.0 1.0 OD2 A:ASP173 4.2 40.4 1.0 CD2 A:HIS63 4.2 34.2 1.0 CG A:HIS30 4.3 33.6 1.0 C1 A:S6P501 4.4 54.9 1.0 CB A:ASP32 4.4 31.7 1.0 O A:HOH612 4.6 35.2 1.0 CD1 A:ILE112 4.6 23.4 1.0 O1 A:S6P501 4.8 53.5 1.0 CA A:ASP32 4.9 29.3 1.0 CD1 A:ILE193 4.9 35.2 1.0 CB A:ASP173 4.9 36.9 1.0 SD A:MET65 5.0 34.0 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K12 Complexed with D-Glucitol 6- Phosphate and Magnesium


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 K12 Complexed with D-Glucitol 6- Phosphate and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:41.6 occ:1.00 O2 B:S6P502 2.0 47.4 1.0 NE2 B:HIS30 2.0 36.0 1.0 OD2 B:ASP32 2.1 43.3 1.0 ND1 B:HIS63 2.2 29.9 1.0 OD1 B:ASP173 2.5 48.9 1.0 CE1 B:HIS30 2.9 36.1 1.0 CE1 B:HIS63 3.0 27.6 1.0 CD2 B:HIS30 3.1 36.0 1.0 CG B:ASP32 3.2 43.2 1.0 O3 B:S6P502 3.2 52.0 1.0 C2 B:S6P502 3.2 52.0 1.0 CG B:HIS63 3.3 30.2 1.0 CG B:ASP173 3.6 47.5 1.0 CB B:HIS63 3.6 29.9 1.0 C3 B:S6P502 3.7 51.7 1.0 OD1 B:ASP32 3.7 43.7 1.0 CE B:MET65 4.1 27.8 1.0 ND1 B:HIS30 4.1 36.0 1.0 OD2 B:ASP173 4.1 50.5 1.0 CG B:HIS30 4.2 35.3 1.0 NE2 B:HIS63 4.2 28.3 1.0 CD2 B:HIS63 4.3 30.5 1.0 C1 B:S6P502 4.3 51.5 1.0 CB B:ASP32 4.5 39.5 1.0 CD1 B:ILE112 4.7 33.1 1.0 O1 B:S6P502 4.7 52.2 1.0 CD1 B:ILE193 4.7 28.7 1.0 CB B:ASP173 4.8 45.5 1.0 CA B:ASP32 4.9 37.8 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K12 Complexed with D-Glucitol 6- Phosphate and Magnesium


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 K12 Complexed with D-Glucitol 6- Phosphate and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg603 b:45.3 occ:1.00 ND1 C:HIS63 2.0 35.3 1.0 O2 C:S6P503 2.0 59.4 1.0 NE2 C:HIS30 2.1 29.4 1.0 OD2 C:ASP32 2.2 37.5 1.0 OD1 C:ASP173 2.4 34.6 1.0 CE1 C:HIS63 2.8 36.5 1.0 CE1 C:HIS30 3.0 29.4 1.0 CG C:HIS63 3.2 33.2 1.0 CD2 C:HIS30 3.2 30.1 1.0 O3 C:S6P503 3.3 61.3 1.0 C2 C:S6P503 3.3 60.1 1.0 CG C:ASP32 3.3 37.6 1.0 CG C:ASP173 3.6 35.7 1.0 CB C:HIS63 3.7 28.3 1.0 C3 C:S6P503 3.7 61.0 1.0 OD1 C:ASP32 3.8 38.5 1.0 CE C:MET65 4.0 31.6 1.0 NE2 C:HIS63 4.0 35.0 1.0 OD2 C:ASP173 4.0 40.0 1.0 ND1 C:HIS30 4.2 29.4 1.0 CD2 C:HIS63 4.2 34.0 1.0 CG C:HIS30 4.3 29.3 1.0 C1 C:S6P503 4.4 59.6 1.0 CD1 C:ILE112 4.6 31.0 1.0 CB C:ASP32 4.6 34.3 1.0 CB C:ASP173 4.8 36.2 1.0 CD1 C:ILE193 4.8 28.8 1.0 O1 C:S6P503 4.8 58.3 1.0 SD C:MET65 4.9 30.3 1.0 SD C:MET135 5.0 37.5 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K12 Complexed with D-Glucitol 6- Phosphate and Magnesium


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 K12 Complexed with D-Glucitol 6- Phosphate and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg604 b:41.6 occ:1.00 O2 D:S6P504 2.0 57.0 1.0 OD2 D:ASP32 2.1 37.5 1.0 NE2 D:HIS30 2.1 32.2 1.0 ND1 D:HIS63 2.2 33.8 1.0 OD1 D:ASP173 2.5 40.1 1.0 CE1 D:HIS63 3.0 35.8 1.0 CE1 D:HIS30 3.0 31.6 1.0 CD2 D:HIS30 3.1 32.2 1.0 CG D:ASP32 3.2 35.9 1.0 CG D:HIS63 3.3 33.7 1.0 O3 D:S6P504 3.3 59.2 1.0 C2 D:S6P504 3.3 59.0 1.0 CG D:ASP173 3.6 40.6 1.0 OD1 D:ASP32 3.7 37.0 1.0 CB D:HIS63 3.7 31.3 1.0 C3 D:S6P504 3.7 59.6 1.0 CE D:MET65 4.0 31.6 1.0 OD2 D:ASP173 4.1 41.7 1.0 ND1 D:HIS30 4.2 31.8 1.0 NE2 D:HIS63 4.2 34.7 1.0 CG D:HIS30 4.2 32.9 1.0 CD2 D:HIS63 4.3 34.1 1.0 C1 D:S6P504 4.4 58.9 1.0 CB D:ASP32 4.4 33.6 1.0 CD1 D:ILE112 4.7 27.5 1.0 O1 D:S6P504 4.8 59.2 1.0 CB D:ASP173 4.8 40.2 1.0 CD1 D:ILE193 4.9 37.5 1.0 CA D:ASP32 4.9 33.0 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K12 Complexed with D-Glucitol 6- Phosphate and Magnesium


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 K12 Complexed with D-Glucitol 6- Phosphate and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg605 b:45.8 occ:1.00 O2 E:S6P505 2.0 58.0 1.0 NE2 E:HIS30 2.1 33.8 1.0 OD2 E:ASP32 2.1 34.1 1.0 ND1 E:HIS63 2.2 31.7 1.0 OD1 E:ASP173 2.5 37.2 1.0 CE1 E:HIS30 3.0 33.6 1.0 CE1 E:HIS63 3.0 30.3 1.0 CD2 E:HIS30 3.2 33.2 1.0 CG E:ASP32 3.2 33.8 1.0 O3 E:S6P505 3.2 61.2 1.0 C2 E:S6P505 3.3 60.3 1.0 CG E:HIS63 3.3 29.7 1.0 CG E:ASP173 3.6 39.2 1.0 C3 E:S6P505 3.7 61.7 1.0 OD1 E:ASP32 3.7 38.0 1.0 CB E:HIS63 3.7 27.1 1.0 CE E:MET65 4.0 30.5 1.0 OD2 E:ASP173 4.1 41.4 1.0 ND1 E:HIS30 4.1 34.2 1.0 NE2 E:HIS63 4.2 32.1 1.0 CG E:HIS30 4.3 33.7 1.0 CD2 E:HIS63 4.3 29.8 1.0 C1 E:S6P505 4.4 60.1 1.0 CB E:ASP32 4.5 32.7 1.0 CD1 E:ILE112 4.6 24.5 1.0 O1 E:S6P505 4.8 57.8 1.0 CD1 E:ILE193 4.8 28.9 1.0 CB E:ASP173 4.8 38.5 1.0 CA E:ASP32 4.9 31.6 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K12 Complexed with D-Glucitol 6- Phosphate and Magnesium


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 K12 Complexed with D-Glucitol 6- Phosphate and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg606 b:46.4 occ:1.00 O2 F:S6P506 2.0 53.6 1.0 OD2 F:ASP32 2.0 38.4 1.0 ND1 F:HIS63 2.0 28.9 1.0 NE2 F:HIS30 2.2 33.6 1.0 OD1 F:ASP173 2.6 44.0 1.0 CE1 F:HIS63 2.8 28.1 1.0 CE1 F:HIS30 3.1 33.4 1.0 CG F:ASP32 3.1 38.5 1.0 CG F:HIS63 3.2 26.8 1.0 O3 F:S6P506 3.2 53.7 1.0 C2 F:S6P506 3.3 54.2 1.0 CD2 F:HIS30 3.3 33.2 1.0 CB F:HIS63 3.7 25.9 1.0 OD1 F:ASP32 3.7 41.7 1.0 C3 F:S6P506 3.7 55.3 1.0 CG F:ASP173 3.7 42.6 1.0 CE F:MET65 3.8 23.0 1.0 NE2 F:HIS63 4.0 30.6 1.0 OD2 F:ASP173 4.2 41.7 1.0 CD2 F:HIS63 4.2 27.3 1.0 ND1 F:HIS30 4.3 31.9 1.0 C1 F:S6P506 4.4 53.1 1.0 CB F:ASP32 4.4 35.6 1.0 CG F:HIS30 4.4 34.5 1.0 CD1 F:ILE112 4.7 22.0 1.0 O1 F:S6P506 4.7 52.1 1.0 SD F:MET65 4.8 26.6 1.0 CA F:ASP32 4.8 33.1 1.0 CB F:ASP173 4.9 40.2 1.0 CD1 F:ILE193 5.0 32.0 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