Magnesium in PDB 1nuy: Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6- Phosphate, and Phosphate

All present enzymatic activity of Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6- Phosphate, and Phosphate:
3.1.3.11;

The structure of Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6- Phosphate, and Phosphate, PDB code: 1nuy was solved by J.Choe, C.V.Iancu, H.J.Fromm, R.B.Honzatko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.30
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	53.086, 82.849, 165.334, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 20.6

The binding sites of Magnesium atom in the Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6- Phosphate, and Phosphate (pdb code 1nuy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6- Phosphate, and Phosphate, PDB code: 1nuy:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6- Phosphate, and Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6- Phosphate, and Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2341 b:19.4 occ:1.00 OE1 A:GLU1097 1.9 20.9 1.0 OD2 A:ASP1118 2.0 18.8 1.0 O A:LEU1120 2.1 19.0 1.0 O A:HOH3073 2.1 20.0 1.0 O4 A:PO42340 2.3 24.4 1.0 O2 A:PO42340 2.3 21.2 1.0 P A:PO42340 2.8 20.8 1.0 CD A:GLU1097 3.0 21.4 1.0 CG A:ASP1118 3.0 18.9 1.0 C A:LEU1120 3.2 16.0 1.0 OE2 A:GLU1097 3.4 23.8 1.0 OD1 A:ASP1118 3.5 21.8 1.0 MG A:MG2343 3.7 25.9 1.0 O3 A:PO42340 3.8 24.5 1.0 MG A:MG2342 3.8 16.6 1.0 CA A:ASP1121 3.9 17.8 1.0 O1 A:PO42340 3.9 20.7 1.0 N A:ASP1121 3.9 15.8 1.0 OE2 A:GLU1098 4.0 25.4 1.0 O A:HOH3168 4.0 35.7 1.0 N A:LEU1120 4.0 17.4 1.0 OD2 A:ASP1074 4.1 29.9 1.0 CA A:LEU1120 4.2 18.2 1.0 O A:HOH3085 4.2 28.8 1.0 CG A:GLU1097 4.3 18.9 1.0 CB A:ASP1118 4.4 16.1 1.0 CB A:GLU1097 4.6 16.3 1.0 CD A:PRO1119 4.6 16.6 1.0 CA A:ASP1118 4.7 15.1 1.0 C A:ASP1118 4.7 14.7 1.0 N A:PRO1119 4.7 15.9 1.0 CB A:LEU1120 4.8 19.3 1.0 CB A:ASP1121 4.8 19.6 1.0 O1 A:F6P2339 4.9 14.0 0.5 NH2 A:ARG1276 5.0 29.5 1.0

Magnesium binding site 2 out of 3 in the Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6- Phosphate, and Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6- Phosphate, and Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2342 b:16.6 occ:1.00 OD1 A:ASP1121 2.0 19.9 1.0 O2 A:PO42340 2.0 21.2 1.0 OE1 A:GLU1280 2.0 20.2 1.0 OD1 A:ASP1118 2.0 21.8 1.0 O1 A:F6P2339 2.3 14.0 0.5 CG A:ASP1121 3.0 18.6 1.0 CD A:GLU1280 3.1 19.7 1.0 CG A:ASP1118 3.1 18.9 1.0 CB A:ASP1121 3.2 19.6 1.0 P A:PO42340 3.3 20.8 1.0 CA A:ASP1121 3.4 17.8 1.0 CG A:GLU1280 3.6 19.7 1.0 OD2 A:ASP1118 3.6 18.8 1.0 C1 A:F6P2339 3.7 18.3 0.5 O1 A:PO42340 3.7 20.7 1.0 C1 A:F6P2339 3.7 19.6 0.5 NH2 A:ARG1276 3.8 29.5 1.0 MG A:MG2341 3.8 19.4 1.0 O3 A:PO42340 3.9 24.5 1.0 OD2 A:ASP1121 4.1 19.7 1.0 O3 A:F6P2339 4.1 15.6 1.0 OE2 A:GLU1280 4.1 18.4 1.0 N A:GLY1122 4.2 17.2 1.0 CB A:ASP1118 4.3 16.1 1.0 C A:ASP1121 4.4 20.2 1.0 OE1 A:GLU1097 4.4 20.9 1.0 O4 A:PO42340 4.4 24.4 1.0 C3 A:F6P2339 4.5 15.5 1.0 C2 A:F6P2339 4.5 17.6 1.0 O A:LEU1120 4.5 19.0 1.0 CD1 A:ILE1135 4.6 15.6 1.0 N A:ASP1121 4.6 15.8 1.0 O1 A:F6P2339 4.6 26.4 0.5 O2 A:F6P2339 4.8 22.2 1.0 CZ A:ARG1276 4.9 27.5 1.0 C A:LEU1120 5.0 16.0 1.0 CB A:GLU1280 5.0 16.4 1.0

Magnesium binding site 3 out of 3 in the Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6- Phosphate, and Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6- Phosphate, and Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2343 b:25.9 occ:1.00 O A:HOH3167 2.0 31.4 1.0 O A:HOH3085 2.0 28.8 1.0 O3 A:PO42340 2.1 24.5 1.0 OD2 A:ASP1068 2.1 32.0 1.0 OE2 A:GLU1097 2.1 23.8 1.0 O4 A:PO42340 2.2 24.4 1.0 P A:PO42340 2.6 20.8 1.0 CG A:ASP1068 3.1 32.5 1.0 CD A:GLU1097 3.2 21.4 1.0 OE1 A:GLU1097 3.5 20.9 1.0 CB A:ASP1068 3.6 29.8 1.0 O2 A:PO42340 3.6 21.2 1.0 MG A:MG2341 3.7 19.4 1.0 O1 A:PO42340 3.7 20.7 1.0 O A:HOH3169 3.8 48.5 1.0 ND2 A:ASN1064 4.0 29.8 1.0 NH2 A:ARG1276 4.1 29.5 1.0 O A:HOH3168 4.1 35.7 1.0 OD1 A:ASP1068 4.2 34.0 1.0 NH1 A:ARG1276 4.2 25.8 1.0 OE2 A:GLU1098 4.2 25.4 1.0 O A:HOH3073 4.4 20.0 1.0 CB A:SER1123 4.4 30.6 1.0 CG A:GLU1097 4.5 18.9 1.0 CZ A:ARG1276 4.6 27.5 1.0 O1 A:F6P2339 4.7 26.4 0.5 OG A:SER1123 4.8 37.7 1.0 O1 A:F6P2339 4.8 14.0 0.5 OD2 A:ASP1074 5.0 29.9 1.0

J.Y.Choe, C.V.Iancu, H.J.Fromm, R.B.Honzatko. Metaphosphate in the Active Site of Fructose-1,6-Bisphosphatase J.Biol.Chem. V. 278 16015 2003.
ISSN: ISSN 0021-9258
PubMed: 12595528
DOI: 10.1074/JBC.M212395200