Zinc 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:

Magnesium

(Mg)

5 atoms

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 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 Zinc with other atoms in the Zn 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:Zn901 b:11.7 occ:1.00 ND1 A:HIS91 2.1 11.5 1.0 SG A:CYS97 2.3 10.0 1.0 SG A:CYS99 2.3 11.6 1.0 SG A:CYS89 2.4 11.3 1.0 CE1 A:HIS91 3.0 13.2 1.0 CG A:HIS91 3.1 13.1 1.0 CB A:CYS97 3.1 12.1 1.0 CB A:CYS89 3.4 10.6 1.0 CB A:CYS99 3.4 10.5 1.0 CB A:HIS91 3.5 14.0 1.0 N A:ARG100 3.5 10.3 1.0 C A:CYS99 3.7 10.8 1.0 N A:CYS99 3.8 8.8 1.0 CA A:CYS99 3.8 10.6 1.0 CA A:CYS89 3.9 9.7 1.0 NE2 A:HIS91 4.1 16.4 1.0 N A:HIS91 4.2 12.5 1.0 CD2 A:HIS91 4.2 15.7 1.0 CA A:ARG100 4.2 11.4 1.0 CB A:ARG100 4.2 11.6 1.0 CD A:PRO90 4.3 11.3 1.0 C A:CYS89 4.4 9.5 1.0 N A:PRO90 4.4 9.4 1.0 CA A:HIS91 4.5 13.0 1.0 O A:CYS99 4.5 10.2 1.0 CA A:CYS97 4.5 12.2 1.0 N A:ALA98 4.8 11.0 1.0 C A:CYS97 4.9 11.5 1.0 O A:HOH610 4.9 13.2 1.0 O A:HOH313 4.9 24.1 1.0

Zinc binding site 2 out of 4 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 Zinc with other atoms in the Zn 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 B:Zn902 b:14.2 occ:1.00 ND1 B:HIS91 2.0 15.4 1.0 SG B:CYS89 2.2 11.6 1.0 SG B:CYS99 2.3 13.9 1.0 SG B:CYS97 2.4 14.9 1.0 CE1 B:HIS91 3.0 18.3 1.0 CG B:HIS91 3.1 16.0 1.0 CB B:CYS97 3.2 18.1 1.0 CB B:CYS89 3.3 12.1 1.0 CB B:HIS91 3.4 16.0 1.0 CB B:CYS99 3.5 13.8 1.0 N B:ARG100 3.5 11.9 1.0 C B:CYS99 3.7 12.6 1.0 CA B:CYS99 3.8 13.8 1.0 N B:CYS99 3.9 15.1 1.0 CA B:CYS89 3.9 13.5 1.0 NE2 B:HIS91 4.1 18.8 1.0 N B:HIS91 4.2 14.6 1.0 CD2 B:HIS91 4.2 20.1 1.0 CA B:ARG100 4.2 11.3 1.0 CB B:ARG100 4.2 11.8 1.0 CD B:PRO90 4.2 16.6 1.0 C B:CYS89 4.4 13.7 1.0 CA B:HIS91 4.4 15.5 1.0 O B:CYS99 4.5 13.5 1.0 N B:PRO90 4.5 14.3 1.0 CA B:CYS97 4.6 18.2 1.0 N B:ALA98 4.9 16.0 1.0 C B:CYS97 4.9 16.9 1.0 O B:HOH390 4.9 25.6 1.0

Zinc binding site 3 out of 4 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 Zinc with other atoms in the Zn 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 C:Zn903 b:27.6 occ:1.00 ND1 C:HIS91 2.2 29.2 1.0 SG C:CYS89 2.3 24.1 1.0 SG C:CYS99 2.4 28.6 1.0 SG C:CYS97 2.4 24.2 1.0 CG C:HIS91 3.2 31.1 1.0 CB C:CYS97 3.2 29.0 1.0 CE1 C:HIS91 3.2 31.3 1.0 CB C:CYS89 3.3 23.1 1.0 CB C:HIS91 3.4 29.6 1.0 N C:ARG100 3.5 22.6 1.0 CB C:CYS99 3.6 24.3 1.0 C C:CYS99 3.7 21.7 1.0 N C:CYS99 3.8 24.2 1.0 CA C:CYS99 3.9 25.2 1.0 CA C:CYS89 4.0 24.8 1.0 N C:HIS91 4.2 29.0 1.0 CA C:ARG100 4.2 22.3 1.0 CB C:ARG100 4.2 23.3 1.0 CD C:PRO90 4.3 27.2 1.0 NE2 C:HIS91 4.3 30.3 1.0 CD2 C:HIS91 4.3 32.1 1.0 CA C:HIS91 4.4 30.3 1.0 C C:CYS89 4.4 25.7 1.0 O C:CYS99 4.4 22.4 1.0 N C:PRO90 4.5 27.3 1.0 CA C:CYS97 4.6 29.1 1.0 O C:HOH570 4.8 34.0 1.0 N C:ALA98 4.8 27.2 1.0 C C:CYS97 4.9 28.2 1.0

Zinc binding site 4 out of 4 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 Zinc with other atoms in the Zn 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 D:Zn904 b:26.3 occ:1.00 ND1 D:HIS91 2.2 27.9 1.0 SG D:CYS97 2.3 25.7 1.0 SG D:CYS89 2.3 24.6 1.0 SG D:CYS99 2.4 26.7 1.0 CE1 D:HIS91 3.1 29.4 1.0 CB D:CYS97 3.1 30.6 1.0 CG D:HIS91 3.2 30.2 1.0 CB D:CYS89 3.3 24.5 1.0 CB D:CYS99 3.5 23.9 1.0 CB D:HIS91 3.5 29.6 1.0 N D:ARG100 3.5 23.3 1.0 C D:CYS99 3.8 22.7 1.0 CA D:CYS99 3.8 24.9 1.0 N D:CYS99 3.8 25.5 1.0 CA D:CYS89 3.9 24.8 1.0 N D:HIS91 4.2 29.1 1.0 CB D:ARG100 4.2 23.8 1.0 CA D:ARG100 4.2 21.5 1.0 NE2 D:HIS91 4.2 30.4 1.0 CD2 D:HIS91 4.3 31.3 1.0 CD D:PRO90 4.3 27.3 1.0 C D:CYS89 4.4 25.5 1.0 CA D:HIS91 4.5 29.9 1.0 N D:PRO90 4.5 27.0 1.0 O D:CYS99 4.5 22.0 1.0 CA D:CYS97 4.6 32.6 1.0 O D:HOH443 4.8 32.9 1.0 C D:CYS97 4.9 31.6 1.0 N D:ALA98 4.9 29.5 1.0 O D:HOH264 4.9 31.0 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