Magnesium in PDB 1yxi: R-State Amp Complex Reveals Initial Steps of the Quaternary Transition of Fructose-1,6-Bisphosphatase

All present enzymatic activity of R-State Amp Complex Reveals Initial Steps of the Quaternary Transition of Fructose-1,6-Bisphosphatase:
3.1.3.11;

The structure of R-State Amp Complex Reveals Initial Steps of the Quaternary Transition of Fructose-1,6-Bisphosphatase, PDB code: 1yxi was solved by C.V.Iancu, S.Mukund, 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)	6.00 / 2.00
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	52.790, 82.800, 165.510, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 24.2

The binding sites of Magnesium atom in the R-State Amp Complex Reveals Initial Steps of the Quaternary Transition of Fructose-1,6-Bisphosphatase (pdb code 1yxi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the R-State Amp Complex Reveals Initial Steps of the Quaternary Transition of Fructose-1,6-Bisphosphatase, PDB code: 1yxi:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the R-State Amp Complex Reveals Initial Steps of the Quaternary Transition of Fructose-1,6-Bisphosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of R-State Amp Complex Reveals Initial Steps of the Quaternary Transition of Fructose-1,6-Bisphosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg340 b:33.9 occ:1.00 OE1 A:GLU97 2.1 37.1 1.0 OD2 A:ASP118 2.1 24.2 1.0 O A:LEU120 2.2 26.4 1.0 O2 A:PO4434 2.2 38.9 1.0 O4 A:PO4434 2.2 39.8 1.0 P A:PO4434 2.7 38.6 1.0 CD A:GLU97 3.0 34.5 1.0 CG A:ASP118 3.1 24.9 1.0 C A:LEU120 3.2 26.1 1.0 OE2 A:GLU97 3.3 37.2 1.0 OD1 A:ASP118 3.3 23.5 1.0 O3 A:PO4434 3.7 38.8 1.0 O1 A:PO4434 3.8 36.7 1.0 MG A:MG342 3.8 49.9 1.0 MG A:MG341 3.8 29.1 1.0 CA A:ASP121 3.9 27.0 1.0 N A:ASP121 3.9 26.1 1.0 N A:LEU120 4.1 23.5 1.0 OD2 A:ASP74 4.2 35.4 1.0 CA A:LEU120 4.2 25.6 1.0 OE2 A:GLU98 4.2 35.5 1.0 CG A:GLU97 4.4 32.1 1.0 CB A:ASP118 4.5 22.7 1.0 CB A:GLU97 4.7 27.7 1.0 CB A:LEU120 4.8 27.3 1.0 CB A:ASP121 4.8 27.3 1.0 O A:HOH593 4.8 58.3 1.0 CA A:ASP118 4.8 23.0 1.0 C A:ASP118 4.9 24.5 1.0 C A:ASP121 4.9 27.6 1.0

Magnesium binding site 2 out of 3 in the R-State Amp Complex Reveals Initial Steps of the Quaternary Transition of Fructose-1,6-Bisphosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of R-State Amp Complex Reveals Initial Steps of the Quaternary Transition of Fructose-1,6-Bisphosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg341 b:29.1 occ:1.00 OD1 A:ASP118 2.0 23.5 1.0 OE1 A:GLU280 2.0 27.9 1.0 OD1 A:ASP121 2.2 25.6 1.0 O2 A:PO4434 2.2 38.9 1.0 CG A:ASP121 3.0 28.2 1.0 CD A:GLU280 3.1 25.4 1.0 CG A:ASP118 3.2 24.9 1.0 CB A:ASP121 3.2 27.3 1.0 P A:PO4434 3.4 38.6 1.0 O A:HOH593 3.4 58.3 1.0 CA A:ASP121 3.5 27.0 1.0 CG A:GLU280 3.6 23.4 1.0 C1 A:F6P339 3.6 28.8 1.0 O1 A:PO4434 3.7 36.7 1.0 OD2 A:ASP118 3.8 24.2 1.0 MG A:MG340 3.8 33.9 1.0 OE1 A:GLU97 4.0 37.1 1.0 O3 A:PO4434 4.1 38.8 1.0 OE2 A:GLU280 4.2 24.4 1.0 O3 A:F6P339 4.2 22.7 1.0 OD2 A:ASP121 4.2 30.1 1.0 O1 A:F6P339 4.3 34.9 1.0 N A:GLY122 4.3 27.0 1.0 CB A:ASP118 4.3 22.7 1.0 C A:ASP121 4.5 27.6 1.0 O4 A:PO4434 4.5 39.8 1.0 CD1 A:ILE135 4.5 16.9 1.0 C2 A:F6P339 4.6 25.9 1.0 N A:ASP121 4.6 26.1 1.0 C3 A:F6P339 4.6 23.9 1.0 O A:LEU120 4.7 26.4 1.0 CD A:GLU97 4.9 34.5 1.0 CB A:GLU280 5.0 24.4 1.0 O2 A:F6P339 5.0 25.3 1.0

Magnesium binding site 3 out of 3 in the R-State Amp Complex Reveals Initial Steps of the Quaternary Transition of Fructose-1,6-Bisphosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of R-State Amp Complex Reveals Initial Steps of the Quaternary Transition of Fructose-1,6-Bisphosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg342 b:49.9 occ:1.00 O3 A:PO4434 2.1 38.8 1.0 OE2 A:GLU97 2.2 37.2 1.0 OD2 A:ASP68 2.2 62.1 1.0 O4 A:PO4434 2.5 39.8 1.0 P A:PO4434 2.8 38.6 1.0 CG A:ASP68 3.1 62.1 1.0 CB A:ASP68 3.3 61.7 1.0 CD A:GLU97 3.3 34.5 1.0 ND2 A:ASN64 3.5 62.5 1.0 O2 A:PO4434 3.7 38.9 1.0 OE1 A:GLU97 3.8 37.1 1.0 MG A:MG340 3.8 33.9 1.0 O1 A:PO4434 4.0 36.7 1.0 O A:HOH610 4.0 36.6 1.0 O A:HOH593 4.2 58.3 1.0 OD1 A:ASP68 4.3 62.5 1.0 OE2 A:GLU98 4.3 35.5 1.0 CB A:SER123 4.4 33.5 1.0 CG A:GLU97 4.5 32.1 1.0 OG A:SER123 4.7 40.1 1.0 CA A:ASP68 4.7 61.3 1.0 CG A:ASN64 4.8 62.1 1.0 O1 A:F6P339 4.8 34.9 1.0 OD1 A:ASP74 4.9 37.5 1.0

C.V.Iancu, S.Mukund, H.J.Fromm, R.B.Honzatko. R-State Amp Complex Reveals Initial Steps of the Quaternary Transition of Fructose-1,6-Bisphosphatase. J.Biol.Chem. V. 280 19737 2005.
ISSN: ISSN 0021-9258
PubMed: 15767255
DOI: 10.1074/JBC.M501011200