Zinc in PDB 5i01: Structure of Phosphoheptose Isomerase Gmha From Neisseria Gonorrhoeae

All present enzymatic activity of Structure of Phosphoheptose Isomerase Gmha From Neisseria Gonorrhoeae:
5.3.1.28;

The structure of Structure of Phosphoheptose Isomerase Gmha From Neisseria Gonorrhoeae, PDB code: 5i01 was solved by I.H.Wierzbicki, A.E.Sikora, K.V.Korotkov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	85.91 / 2.37
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	114.360, 130.150, 47.150, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 26.7

The binding sites of Zinc atom in the Structure of Phosphoheptose Isomerase Gmha From Neisseria Gonorrhoeae (pdb code 5i01). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Phosphoheptose Isomerase Gmha From Neisseria Gonorrhoeae, PDB code: 5i01:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Phosphoheptose Isomerase Gmha From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Phosphoheptose Isomerase Gmha From Neisseria Gonorrhoeae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:58.7 occ:1.00 OE1 D:GLN175 2.0 40.9 1.0 OE2 A:GLU65 2.0 55.8 1.0 NE2 A:HIS61 2.2 44.0 1.0 NE2 A:HIS183 2.2 41.5 1.0 CD A:GLU65 2.8 51.0 1.0 CD D:GLN175 3.0 34.3 1.0 CE1 A:HIS61 3.1 42.5 1.0 CE1 A:HIS183 3.2 39.7 1.0 CD2 A:HIS183 3.2 39.1 1.0 CD2 A:HIS61 3.2 40.9 1.0 OE1 A:GLU65 3.2 54.1 1.0 NE2 D:GLN175 3.4 34.7 1.0 CG A:GLU65 4.1 48.2 1.0 ND1 A:HIS61 4.2 41.0 1.0 ND1 A:HIS183 4.3 37.4 1.0 CG A:HIS183 4.3 37.2 1.0 CG A:HIS61 4.3 38.4 1.0 CG D:GLN175 4.4 32.0 1.0 CB D:GLN175 4.7 29.7 1.0 CA D:GLY54 5.0 28.6 1.0

Zinc binding site 2 out of 4 in the Structure of Phosphoheptose Isomerase Gmha From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Phosphoheptose Isomerase Gmha From Neisseria Gonorrhoeae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:57.9 occ:1.00 OE1 C:GLN175 2.0 43.5 1.0 OE2 B:GLU65 2.0 59.7 1.0 NE2 B:HIS61 2.1 44.3 1.0 NE2 B:HIS183 2.2 44.0 1.0 CD B:GLU65 2.8 52.4 1.0 CD C:GLN175 3.0 36.9 1.0 OE1 B:GLU65 3.0 53.1 1.0 CE1 B:HIS61 3.0 42.6 1.0 CD2 B:HIS61 3.1 40.0 1.0 CE1 B:HIS183 3.1 42.2 1.0 CD2 B:HIS183 3.2 41.0 1.0 NE2 C:GLN175 3.3 37.9 1.0 ND1 B:HIS61 4.2 41.4 1.0 CG B:GLU65 4.2 48.1 1.0 CG B:HIS61 4.2 37.6 1.0 ND1 B:HIS183 4.3 40.7 1.0 CG B:HIS183 4.3 39.2 1.0 CG C:GLN175 4.4 34.1 1.0 CB C:GLN175 4.8 31.6 1.0 CA C:GLY54 4.9 25.7 1.0

Zinc binding site 3 out of 4 in the Structure of Phosphoheptose Isomerase Gmha From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Phosphoheptose Isomerase Gmha From Neisseria Gonorrhoeae within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:53.9 occ:1.00 OE1 B:GLN175 2.0 37.3 1.0 OE1 C:GLU65 2.0 45.8 1.0 NE2 C:HIS61 2.1 42.4 1.0 NE2 C:HIS183 2.1 40.1 1.0 CD B:GLN175 3.0 35.9 1.0 CE1 C:HIS61 3.0 41.1 1.0 CE1 C:HIS183 3.1 37.4 1.0 CD2 C:HIS61 3.1 40.1 1.0 CD2 C:HIS183 3.1 37.8 1.0 CD C:GLU65 3.3 42.8 1.0 NE2 B:GLN175 3.5 38.1 1.0 OE2 C:GLU65 4.0 44.0 1.0 ND1 C:HIS61 4.2 40.2 1.0 ND1 C:HIS183 4.2 36.1 1.0 CG C:HIS61 4.2 37.0 1.0 CG C:HIS183 4.2 35.7 1.0 CG C:GLU65 4.3 42.2 1.0 CG B:GLN175 4.4 34.1 1.0 CB B:GLN175 4.7 32.2 1.0 CA B:GLY54 4.9 25.5 1.0

Zinc binding site 4 out of 4 in the Structure of Phosphoheptose Isomerase Gmha From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Phosphoheptose Isomerase Gmha From Neisseria Gonorrhoeae within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:49.1 occ:1.00 OE1 A:GLN175 2.0 40.0 1.0 OE2 D:GLU65 2.0 52.0 1.0 NE2 D:HIS61 2.1 39.3 1.0 NE2 D:HIS183 2.1 38.4 1.0 CD D:GLU65 2.9 46.0 1.0 CD A:GLN175 3.1 39.3 1.0 CE1 D:HIS61 3.1 36.9 1.0 CE1 D:HIS183 3.1 36.3 1.0 CD2 D:HIS183 3.1 36.5 1.0 CD2 D:HIS61 3.2 36.3 1.0 OE1 D:GLU65 3.2 48.0 1.0 NE2 A:GLN175 3.5 39.9 1.0 CG D:GLU65 4.2 43.2 1.0 ND1 D:HIS61 4.2 35.8 1.0 ND1 D:HIS183 4.2 35.1 1.0 CG D:HIS183 4.3 34.4 1.0 CG D:HIS61 4.3 34.4 1.0 CG A:GLN175 4.4 36.3 1.0 CB A:GLN175 4.7 33.4 1.0 CA A:GLY54 4.9 25.6 1.0

I.H.Wierzbicki, R.A.Zielke, K.V.Korotkov, A.E.Sikora. Functional and Structural Studies on the Neisseria Gonorrhoeae Gmha, the First Enzyme in the Glycero-Manno-Heptose Biosynthesis Pathways, Demonstrate A Critical Role in Lipooligosaccharide Synthesis and Gonococcal Viability. Microbiologyopen V. 6 2017.
ISSN: ESSN 2045-8827
PubMed: 28063198
DOI: 10.1002/MBO3.432