Magnesium in PDB 4hgo: 2-Keto-3-Deoxy-D-Glycero-D-Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron in Complex with Transition State Mimic

The structure of 2-Keto-3-Deoxy-D-Glycero-D-Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron in Complex with Transition State Mimic, PDB code: 4hgo was solved by K.D.Daughtry, K.N.Allen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.48 / 2.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	81.296, 106.324, 74.147, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 24.6

The structure of 2-Keto-3-Deoxy-D-Glycero-D-Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron in Complex with Transition State Mimic also contains other interesting chemical elements:

Vanadium

(V)

4 atoms

The binding sites of Magnesium atom in the 2-Keto-3-Deoxy-D-Glycero-D-Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron in Complex with Transition State Mimic (pdb code 4hgo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the 2-Keto-3-Deoxy-D-Glycero-D-Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron in Complex with Transition State Mimic, PDB code: 4hgo:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the 2-Keto-3-Deoxy-D-Glycero-D-Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron in Complex with Transition State Mimic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 2-Keto-3-Deoxy-D-Glycero-D-Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron in Complex with Transition State Mimic within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg200 b:21.3 occ:1.00 O1 A:VN4201 2.0 22.1 1.0 O A:ASP12 2.0 14.0 1.0 O A:HOH337 2.1 17.2 1.0 OD1 A:ASP103 2.1 16.3 1.0 O A:HOH338 2.2 19.7 1.0 OD1 A:ASP10 2.2 15.6 1.0 CG A:ASP103 3.1 18.5 1.0 CG A:ASP10 3.2 17.2 1.0 C A:ASP12 3.2 15.9 1.0 OD2 A:ASP103 3.4 18.8 1.0 V A:VN4201 3.5 45.0 1.0 OD2 A:ASP10 3.6 17.3 1.0 CA A:ASP12 4.0 15.8 1.0 OD2 A:ASP107 4.0 15.6 1.0 N A:ASP12 4.1 13.9 1.0 CB A:ASP12 4.1 13.4 1.0 N A:GLY13 4.3 12.6 1.0 CB A:ASP103 4.4 16.9 1.0 C9 A:KDN202 4.4 38.0 1.0 CA A:GLY13 4.5 13.3 1.0 CB A:ASP10 4.5 16.4 1.0 O2 A:VN4201 4.5 26.5 1.0 N A:ASP103 4.5 12.2 1.0 O10 A:KDN202 4.6 33.2 1.0 CB A:ASP104 4.6 15.3 1.0 O3 A:VN4201 4.6 24.1 1.0 N A:ASP104 4.7 10.6 1.0 C A:ILE11 4.8 13.8 1.0 CA A:ASP103 4.8 14.6 1.0 C A:ASP103 4.9 15.7 1.0

Magnesium binding site 2 out of 4 in the 2-Keto-3-Deoxy-D-Glycero-D-Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron in Complex with Transition State Mimic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 2-Keto-3-Deoxy-D-Glycero-D-Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron in Complex with Transition State Mimic within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg200 b:19.9 occ:1.00 O2 B:VN4201 1.8 21.1 1.0 O B:ASP12 2.0 9.6 1.0 OD1 B:ASP10 2.0 16.8 1.0 OD1 B:ASP103 2.0 17.1 1.0 O B:HOH347 2.1 16.7 1.0 O B:HOH348 2.2 14.8 1.0 CG B:ASP103 3.0 14.9 1.0 CG B:ASP10 3.1 15.3 1.0 C B:ASP12 3.2 10.1 1.0 V B:VN4201 3.3 36.2 1.0 OD2 B:ASP103 3.4 20.0 1.0 OD2 B:ASP10 3.6 20.2 1.0 CA B:ASP12 4.0 15.9 1.0 OD2 B:ASP107 4.0 19.2 1.0 CB B:ASP12 4.1 14.4 1.0 O D:HOH328 4.1 23.1 1.0 N B:ASP12 4.2 11.6 1.0 N B:GLY13 4.2 11.7 1.0 CB B:ASP103 4.3 15.2 1.0 O1 B:VN4201 4.3 23.9 1.0 CB B:ASP10 4.3 12.0 1.0 CA B:GLY13 4.4 10.1 1.0 N B:ASP103 4.5 13.3 1.0 O3 B:VN4201 4.5 28.8 1.0 C9 D:KDN203 4.5 32.3 1.0 CB B:ASP104 4.7 18.9 1.0 O10 D:KDN203 4.7 31.9 1.0 N B:ASP104 4.7 15.8 1.0 CA B:ASP103 4.8 14.7 1.0 C B:ILE11 4.8 12.3 1.0 C B:GLY13 4.8 11.6 1.0 C B:ASP103 4.9 19.0 1.0 N B:VAL14 4.9 10.0 1.0

Magnesium binding site 3 out of 4 in the 2-Keto-3-Deoxy-D-Glycero-D-Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron in Complex with Transition State Mimic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 2-Keto-3-Deoxy-D-Glycero-D-Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron in Complex with Transition State Mimic within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg200 b:27.3 occ:1.00 O1 C:VN4201 2.0 27.8 1.0 O C:ASP12 2.1 16.9 1.0 O C:HOH329 2.1 18.7 1.0 OD1 C:ASP103 2.1 17.0 1.0 OD1 C:ASP10 2.2 16.2 1.0 O C:HOH330 2.3 23.4 1.0 CG C:ASP103 3.0 18.8 1.0 C C:ASP12 3.2 12.9 1.0 CG C:ASP10 3.2 19.7 1.0 V C:VN4201 3.3 46.4 1.0 OD2 C:ASP103 3.3 23.1 1.0 OD2 C:ASP10 3.6 19.3 1.0 CA C:ASP12 4.0 14.6 1.0 CB C:ASP12 4.0 14.9 1.0 N C:ASP12 4.1 11.6 1.0 OD2 C:ASP107 4.2 18.4 1.0 N C:GLY13 4.3 11.2 1.0 O2 C:VN4201 4.3 30.4 1.0 CB C:ASP103 4.4 14.3 1.0 O3 C:VN4201 4.4 33.5 1.0 O C:HOH334 4.4 28.6 1.0 CA C:GLY13 4.4 10.6 1.0 CB C:ASP104 4.5 22.0 1.0 CB C:ASP10 4.6 11.4 1.0 N C:ASP103 4.6 15.0 1.0 N C:ASP104 4.7 16.6 1.0 C C:ILE11 4.8 16.0 1.0 CA C:ASP103 4.9 12.7 1.0 C C:ASP103 4.9 14.0 1.0 C C:GLY13 5.0 16.9 1.0

Magnesium binding site 4 out of 4 in the 2-Keto-3-Deoxy-D-Glycero-D-Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron in Complex with Transition State Mimic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 2-Keto-3-Deoxy-D-Glycero-D-Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron in Complex with Transition State Mimic within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:21.1 occ:1.00 O2 D:VN4202 2.0 32.8 1.0 OD2 D:ASP10 2.0 21.9 1.0 OD1 D:ASP103 2.1 20.7 1.0 O D:ASP12 2.1 19.7 1.0 O D:HOH325 2.1 19.9 1.0 O D:HOH326 2.2 19.9 1.0 CG D:ASP103 3.0 20.4 1.0 CG D:ASP10 3.0 20.6 1.0 C D:ASP12 3.3 16.6 1.0 OD2 D:ASP103 3.3 17.4 1.0 V D:VN4202 3.4 48.1 1.0 OD1 D:ASP10 3.5 21.1 1.0 CA D:ASP12 4.0 14.1 1.0 N D:ASP12 4.0 15.3 1.0 CB D:ASP12 4.1 13.2 1.0 OD2 D:ASP107 4.3 23.1 1.0 N D:GLY13 4.3 13.5 1.0 O3 D:VN4202 4.3 30.8 1.0 CB D:ASP10 4.3 21.5 1.0 CB D:ASP103 4.3 15.8 1.0 CA D:GLY13 4.5 15.9 1.0 N D:ASP103 4.6 17.3 1.0 O1 D:VN4202 4.6 32.1 1.0 C D:ILE11 4.6 14.8 1.0 CB D:ASP104 4.8 19.9 1.0 N D:ASP104 4.9 17.8 1.0 CA D:ASP103 4.9 19.1 1.0 N D:ILE11 4.9 16.4 1.0 C D:GLY13 5.0 14.3 1.0 CG2 D:VAL14 5.0 13.0 1.0

K.D.Daughtry, H.Huang, V.Malashkevich, Y.Patskovsky, W.Liu, U.Ramagopal, J.M.Sauder, S.K.Burley, S.C.Almo, D.Dunaway-Mariano, K.N.Allen. Structural Basis For the Divergence of Substrate Specificity and Biological Function Within Had Phosphatases in Lipopolysaccharide and Sialic Acid Biosynthesis. Biochemistry V. 52 5372 2013.
ISSN: ISSN 0006-2960
PubMed: 23848398
DOI: 10.1021/BI400659K