Magnesium in PDB 1umg: Crystal Structure of Fructose-1,6-Bisphosphatase

All present enzymatic activity of Crystal Structure of Fructose-1,6-Bisphosphatase:
3.1.3.11;

The structure of Crystal Structure of Fructose-1,6-Bisphosphatase, PDB code: 1umg was solved by H.Nishimasu, S.Fushinobu, H.Shoun, T.Wakagi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.23 / 1.80
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	111.778, 111.778, 153.174, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 19.7

The binding sites of Magnesium atom in the Crystal Structure of Fructose-1,6-Bisphosphatase (pdb code 1umg). 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 Fructose-1,6-Bisphosphatase, PDB code: 1umg:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure 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 Crystal Structure of Fructose-1,6-Bisphosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:17.0 occ:1.00 OD2 A:ASP233 1.9 25.5 1.0 O A:HOH409 2.1 16.4 1.0 O A:HOH408 2.2 18.2 1.0 O A:HOH410 2.2 15.4 1.0 O11 A:2FP400 2.2 20.2 1.0 O1 A:2FP400 2.7 19.4 1.0 CG A:ASP233 2.9 24.3 1.0 P1 A:2FP400 3.0 16.9 1.0 OD1 A:ASP233 3.4 21.4 1.0 MG A:MG402 3.6 18.3 1.0 O12 A:2FP400 3.7 14.1 1.0 OE1 A:GLU347 4.0 29.1 1.0 O A:HOH586 4.0 20.5 1.0 O A:HOH461 4.1 20.1 1.0 O2 A:2FP400 4.1 15.6 1.0 C1 A:2FP400 4.1 14.5 1.0 O A:HOH423 4.1 17.1 1.0 OD2 A:ASP234 4.2 12.6 1.0 CB A:ASP233 4.2 20.1 1.0 O A:HOH577 4.2 45.0 1.0 O13 A:2FP400 4.3 12.5 1.0 ND2 A:ASN105 4.3 24.7 1.0 OD1 A:ASP234 4.3 13.8 1.0 OE2 A:GLU347 4.4 21.9 1.0 O A:HOH411 4.5 19.4 1.0 CG A:ASP234 4.5 15.0 1.0 C2 A:2FP400 4.6 13.6 1.0 CD A:GLU347 4.6 25.3 1.0 O A:HOH495 4.9 29.5 1.0 O A:HOH406 5.0 15.5 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure 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 Crystal Structure of Fructose-1,6-Bisphosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:18.3 occ:1.00 OD1 A:ASP233 2.3 21.4 1.0 O11 A:2FP400 2.3 20.2 1.0 O A:HOH412 2.4 18.2 1.0 O A:HOH411 2.4 19.4 1.0 OD2 A:ASP234 2.4 12.6 1.0 O A:HOH406 2.4 15.5 1.0 CG A:ASP234 3.2 15.0 1.0 CG A:ASP233 3.3 24.3 1.0 MG A:MG403 3.5 7.8 1.0 P1 A:2FP400 3.5 16.9 1.0 OD2 A:ASP233 3.6 25.5 1.0 MG A:MG401 3.6 17.0 1.0 OD1 A:ASP54 3.7 17.1 1.0 O A:HOH477 3.7 20.8 1.0 CB A:ASP234 3.8 14.7 1.0 O12 A:2FP400 3.8 14.1 1.0 OD1 A:ASP234 4.0 13.8 1.0 O A:HOH410 4.0 15.4 1.0 NE2 A:GLN95 4.1 16.9 1.0 O13 A:2FP400 4.2 12.5 1.0 O A:HOH461 4.2 20.1 1.0 OD2 A:ASP96 4.3 17.4 1.0 OD2 A:ASP54 4.3 14.0 1.0 O A:HOH408 4.4 18.2 1.0 CG A:ASP54 4.4 20.2 1.0 C A:ASP233 4.5 20.7 1.0 OD1 A:ASP96 4.5 18.1 1.0 O A:ASP233 4.5 20.1 1.0 CB A:ASP233 4.6 20.1 1.0 N A:ASP234 4.7 17.3 1.0 CB A:ASP12 4.7 14.6 1.0 NZ A:LYS10 4.7 20.1 1.0 OD2 A:ASP12 4.7 17.8 1.0 O1 A:2FP400 4.7 19.4 1.0 CG A:ASP96 4.8 18.5 1.0 CA A:ASP234 4.9 13.0 1.0 CA A:ASP233 4.9 20.4 1.0 N A:ASP233 4.9 18.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure 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 Crystal Structure of Fructose-1,6-Bisphosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:7.8 occ:1.00 OD2 A:ASP234 2.0 12.6 1.0 OD1 A:ASP132 2.1 12.8 1.0 OD1 A:ASP53 2.1 12.0 1.0 O A:HOH406 2.1 15.5 1.0 OD2 A:ASP54 2.1 14.0 1.0 O12 A:2FP400 2.2 14.1 1.0 CG A:ASP234 3.0 15.0 1.0 CG A:ASP54 3.1 20.2 1.0 CG A:ASP132 3.1 12.1 1.0 CG A:ASP53 3.2 10.8 1.0 P1 A:2FP400 3.3 16.9 1.0 OD1 A:ASP54 3.4 17.1 1.0 MG A:MG402 3.5 18.3 1.0 O11 A:2FP400 3.6 20.2 1.0 OD2 A:ASP53 3.6 11.1 1.0 OD2 A:ASP132 3.7 13.1 1.0 OD1 A:ASP234 3.7 13.8 1.0 NZ A:LYS133 3.8 14.2 1.0 O13 A:2FP400 3.9 12.5 1.0 OD2 A:ASP12 4.0 17.8 1.0 O A:HOH410 4.0 15.4 1.0 CB A:ASP234 4.0 14.7 1.0 CB A:ASP132 4.2 9.4 1.0 CB A:ASP54 4.4 12.2 1.0 N A:LYS133 4.4 12.4 1.0 C A:ASP53 4.4 16.5 1.0 N A:ASP53 4.5 11.2 1.0 CB A:ASP53 4.5 10.1 1.0 O A:HOH412 4.5 18.2 1.0 N A:ASP54 4.5 14.5 1.0 CA A:ASP132 4.6 10.7 1.0 O1 A:2FP400 4.6 19.4 1.0 MG A:MG404 4.7 10.0 1.0 CA A:ASP53 4.7 12.1 1.0 O A:ASP53 4.8 13.7 1.0 CE A:LYS133 4.9 9.6 1.0 CD A:LYS133 4.9 9.8 1.0 CG A:ASP12 4.9 16.7 1.0 CA A:ASP54 4.9 12.4 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure 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 4 of Crystal Structure of Fructose-1,6-Bisphosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:10.0 occ:1.00 O13 A:2FP400 2.0 12.5 1.0 O A:HOH407 2.0 14.1 1.0 OD2 A:ASP12 2.1 17.8 1.0 OD2 A:ASP53 2.1 11.1 1.0 ND1 A:HIS19 2.2 19.1 1.0 OE1 A:GLN95 2.3 17.7 1.0 CE1 A:HIS19 3.0 19.6 1.0 CG A:ASP53 3.1 10.8 1.0 CG A:ASP12 3.1 16.7 1.0 CD A:GLN95 3.2 20.6 1.0 CG A:HIS19 3.3 18.3 1.0 P1 A:2FP400 3.5 16.9 1.0 NE2 A:GLN95 3.5 16.9 1.0 OD1 A:ASP12 3.5 15.2 1.0 CB A:HIS19 3.7 14.1 1.0 OD1 A:ASP53 3.9 12.0 1.0 CB A:ASP53 3.9 10.1 1.0 O A:HOH406 3.9 15.5 1.0 O12 A:2FP400 3.9 14.1 1.0 CA A:HIS19 4.2 12.9 1.0 C1 A:2FP400 4.2 14.5 1.0 NE2 A:HIS19 4.2 18.2 1.0 CB A:ASP12 4.3 14.6 1.0 CD2 A:HIS19 4.4 15.9 1.0 O1 A:2FP400 4.4 19.4 1.0 OG A:SER15 4.4 17.4 1.0 ND2 A:ASN105 4.4 24.7 1.0 O11 A:2FP400 4.4 20.2 1.0 CG A:GLN95 4.6 18.3 1.0 CB A:ALA92 4.6 16.2 1.0 MG A:MG403 4.7 7.8 1.0 CB A:GLN95 4.9 18.3 1.0 O A:ASP53 5.0 13.7 1.0

H.Nishimasu, S.Fushinobu, H.Shoun, T.Wakagi. The First Crystal Structure of the Novel Class of Fructose-1,6-Bisphosphatase Present in Thermophilic Archaea. Structure V. 12 949 2004.
ISSN: ISSN 0969-2126
PubMed: 15274916
DOI: 10.1016/J.STR.2004.03.026