Magnesium in PDB 3l8h: Crystal Structure of D,D-Heptose 1.7-Bisphosphate Phosphatase From B. Bronchiseptica Complexed with Magnesium and Phosphate

The structure of Crystal Structure of D,D-Heptose 1.7-Bisphosphate Phosphatase From B. Bronchiseptica Complexed with Magnesium and Phosphate, PDB code: 3l8h was solved by H.Nguyen, E.Peisach, K.N.Allen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.17 / 1.68
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	38.072, 58.389, 85.724, 90.48, 97.54, 92.02
R / Rfree (%)	17.2 / 20

The structure of Crystal Structure of D,D-Heptose 1.7-Bisphosphate Phosphatase From B. Bronchiseptica Complexed with Magnesium and Phosphate also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of D,D-Heptose 1.7-Bisphosphate Phosphatase From B. Bronchiseptica Complexed with Magnesium and Phosphate (pdb code 3l8h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of D,D-Heptose 1.7-Bisphosphate Phosphatase From B. Bronchiseptica Complexed with Magnesium and Phosphate, PDB code: 3l8h:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of D,D-Heptose 1.7-Bisphosphate Phosphatase From B. Bronchiseptica Complexed with Magnesium and Phosphate


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,D-Heptose 1.7-Bisphosphate Phosphatase From B. Bronchiseptica Complexed with Magnesium and Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:10.9 occ:1.00 OD2 A:ASP7 2.1 11.2 1.0 O1 A:PO42001 2.1 11.8 1.0 O A:ASP9 2.2 10.0 1.0 O A:HOH181 2.2 11.0 1.0 O A:HOH188 2.2 11.2 1.0 OD1 A:ASP126 2.2 10.0 1.0 CG A:ASP126 3.2 9.4 1.0 CG A:ASP7 3.2 12.5 1.0 C A:ASP9 3.3 10.5 1.0 OD2 A:ASP126 3.4 11.3 1.0 P A:PO42001 3.4 14.6 1.0 OD1 A:ASP7 3.8 14.4 1.0 OD2 A:ASP130 3.9 12.0 1.0 O2 A:PO42001 4.0 13.1 1.0 O4 A:PO42001 4.0 12.7 1.0 O A:HOH587 4.0 23.9 1.0 CA A:ASP9 4.1 10.7 1.0 CB A:ASP9 4.1 11.2 1.0 OG A:SER127 4.2 12.4 1.0 N A:ASP9 4.2 10.7 1.0 O A:HOH199 4.3 14.9 1.0 N A:GLY10 4.3 10.0 1.0 O A:HOH635 4.4 23.4 1.0 CB A:ASP7 4.4 9.3 1.0 CA A:GLY10 4.4 9.5 1.0 CB A:ASP126 4.5 9.6 1.0 O3 A:PO42001 4.6 15.5 1.0 N A:ASP126 4.7 8.6 1.0 CG A:ASP130 4.8 12.7 1.0 OD1 A:ASP130 4.8 14.0 1.0 C A:ARG8 4.9 10.3 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of D,D-Heptose 1.7-Bisphosphate Phosphatase From B. Bronchiseptica Complexed with Magnesium and Phosphate


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,D-Heptose 1.7-Bisphosphate Phosphatase From B. Bronchiseptica Complexed with Magnesium and Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg180 b:29.0 occ:1.00 OD2 A:ASP167 2.2 14.0 1.0 O A:HOH184 2.3 23.1 1.0 O A:HOH200 2.5 17.0 1.0 O A:HOH637 2.7 26.9 1.0 CG A:ASP167 3.2 12.8 1.0 O A:HOH363 3.5 29.1 1.0 OD1 A:ASP167 3.5 11.8 1.0 O A:HOH237 4.2 17.2 1.0 CB A:ASP167 4.5 9.4 1.0 O C:HOH338 4.5 29.2 1.0 O A:PRO30 4.7 10.8 1.0 O A:HOH664 4.9 21.4 1.0 CB A:ALA169 4.9 12.5 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of D,D-Heptose 1.7-Bisphosphate Phosphatase From B. Bronchiseptica Complexed with Magnesium and Phosphate


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,D-Heptose 1.7-Bisphosphate Phosphatase From B. Bronchiseptica Complexed with Magnesium and Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:11.9 occ:1.00 OD2 B:ASP7 2.1 11.6 1.0 O3 B:PO42002 2.1 13.4 1.0 O B:ASP9 2.1 10.6 1.0 OD1 B:ASP126 2.2 11.3 1.0 O B:HOH194 2.2 12.4 1.0 O B:HOH186 2.2 12.7 1.0 CG B:ASP126 3.1 11.3 1.0 CG B:ASP7 3.2 12.4 1.0 C B:ASP9 3.3 11.0 1.0 P B:PO42002 3.4 15.2 1.0 OD2 B:ASP126 3.4 12.2 1.0 OD1 B:ASP7 3.8 13.7 1.0 O B:HOH560 3.8 23.6 1.0 OD2 B:ASP130 3.9 12.0 1.0 O2 B:PO42002 4.0 15.5 1.0 CB B:ASP9 4.0 12.5 1.0 O1 B:PO42002 4.0 13.3 1.0 CA B:ASP9 4.0 12.2 1.0 OG B:SER127 4.1 14.1 1.0 N B:ASP9 4.2 11.1 1.0 N B:GLY10 4.3 9.2 1.0 O B:HOH349 4.4 18.7 1.0 CB B:ASP7 4.4 10.7 1.0 CA B:GLY10 4.5 10.2 1.0 CB B:ASP126 4.5 10.2 1.0 O4 B:PO42002 4.5 15.5 1.0 O B:HOH636 4.6 23.0 1.0 N B:ASP126 4.7 10.1 1.0 CG B:ASP130 4.8 13.6 1.0 OD1 B:ASP130 4.8 14.4 1.0 C B:ARG8 4.8 10.7 1.0 N B:SER127 5.0 9.7 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of D,D-Heptose 1.7-Bisphosphate Phosphatase From B. Bronchiseptica Complexed with Magnesium and Phosphate


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,D-Heptose 1.7-Bisphosphate Phosphatase From B. Bronchiseptica Complexed with Magnesium and Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg803 b:15.6 occ:1.00 OD2 C:ASP7 2.1 15.7 1.0 O C:ASP9 2.1 16.0 1.0 O2 C:PO42003 2.1 18.7 1.0 OD1 C:ASP126 2.2 13.4 1.0 O C:HOH180 2.2 16.1 1.0 O C:HOH185 2.2 16.5 1.0 CG C:ASP126 3.1 13.7 1.0 CG C:ASP7 3.2 17.3 1.0 C C:ASP9 3.3 16.9 1.0 OD2 C:ASP126 3.4 15.0 1.0 P C:PO42003 3.4 23.9 1.0 OD1 C:ASP7 3.8 20.4 1.0 OD2 C:ASP130 3.8 14.1 1.0 O C:HOH622 3.9 28.4 1.0 O4 C:PO42003 4.0 19.1 1.0 O3 C:PO42003 4.0 22.7 1.0 CA C:ASP9 4.1 18.9 1.0 CB C:ASP9 4.1 19.1 1.0 OG C:SER127 4.1 16.4 1.0 O C:HOH203 4.2 20.7 1.0 N C:GLY10 4.2 15.4 1.0 N C:ASP9 4.3 16.6 1.0 CA C:GLY10 4.4 15.3 1.0 CB C:ASP7 4.4 15.7 1.0 CB C:ASP126 4.5 12.5 1.0 O1 C:PO42003 4.6 23.4 1.0 OD1 C:ASP15 4.6 25.7 1.0 N C:ASP126 4.7 11.7 1.0 CG C:ASP130 4.7 15.6 1.0 OD1 C:ASP130 4.7 18.7 1.0 C C:ARG8 4.9 16.7 1.0 C C:GLY10 4.9 15.8 1.0 CG2 C:VAL11 5.0 13.6 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of D,D-Heptose 1.7-Bisphosphate Phosphatase From B. Bronchiseptica Complexed with Magnesium and Phosphate


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,D-Heptose 1.7-Bisphosphate Phosphatase From B. Bronchiseptica Complexed with Magnesium and Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg804 b:19.2 occ:1.00 OD2 D:ASP7 2.1 19.5 1.0 O D:ASP9 2.1 19.5 1.0 O D:HOH181 2.1 17.0 1.0 OD1 D:ASP126 2.2 15.6 1.0 O4 D:PO42004 2.2 21.4 1.0 O D:HOH200 2.3 19.2 1.0 CG D:ASP126 3.2 17.2 1.0 C D:ASP9 3.3 19.5 1.0 CG D:ASP7 3.3 19.3 1.0 OD2 D:ASP126 3.4 16.1 1.0 P D:PO42004 3.5 25.6 1.0 O D:HOH574 3.8 29.8 1.0 OD1 D:ASP7 3.8 21.0 1.0 OD2 D:ASP130 3.9 16.6 1.0 O2 D:PO42004 4.0 21.9 1.0 CB D:ASP9 4.0 22.5 1.0 CA D:ASP9 4.0 21.1 1.0 O1 D:PO42004 4.1 24.1 1.0 OG D:SER127 4.1 17.0 1.0 O D:HOH547 4.2 22.8 1.0 N D:ASP9 4.2 20.1 1.0 N D:GLY10 4.2 18.3 1.0 CA D:GLY10 4.4 18.8 1.0 CB D:ASP7 4.4 18.2 1.0 CB D:ASP126 4.5 14.8 1.0 OD1 D:ASP15 4.6 26.6 1.0 O3 D:PO42004 4.7 26.5 1.0 OD1 D:ASP130 4.7 20.0 1.0 CG D:ASP130 4.7 18.4 1.0 N D:ASP126 4.7 15.0 1.0 C D:ARG8 4.9 19.6 1.0 C D:GLY10 5.0 17.4 1.0

H.H.Nguyen, L.Wang, H.Huang, E.Peisach, D.Dunaway-Mariano, K.N.Allen. Structural Determinants of Substrate Recognition in the Had Superfamily Member D-Glycero-D-Manno-Heptose-1,7-Bisphosphate Phosphatase (Gmhb) . Biochemistry V. 49 1082 2010.
ISSN: ISSN 0006-2960
PubMed: 20050614
DOI: 10.1021/BI902019Q