Zinc in PDB 5lu7: Heptose Isomerase Gmha Mutant - D61A

All present enzymatic activity of Heptose Isomerase Gmha Mutant - D61A:
5.3.1.28;

The structure of Heptose Isomerase Gmha Mutant - D61A, PDB code: 5lu7 was solved by M.Vivoli, N.J.Harmer, J.Pang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.54 / 1.92
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.200, 83.680, 126.100, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 21.5

The binding sites of Zinc atom in the Heptose Isomerase Gmha Mutant - D61A (pdb code 5lu7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Heptose Isomerase Gmha Mutant - D61A, PDB code: 5lu7:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Heptose Isomerase Gmha Mutant - D61A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Heptose Isomerase Gmha Mutant - D61A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:20.8 occ:0.23 OE2 A:GLU68 1.9 29.3 1.0 NE2 A:HIS64 1.9 21.2 1.0 NE2 A:HIS183 1.9 19.6 1.0 OE1 D:GLN175 2.1 19.6 1.0 CE1 A:HIS64 2.8 24.4 1.0 CD A:GLU68 2.8 28.9 1.0 CD2 A:HIS183 2.8 20.1 1.0 CE1 A:HIS183 3.0 17.2 1.0 CD2 A:HIS64 3.0 20.2 1.0 OE1 A:GLU68 3.2 34.9 1.0 CD D:GLN175 3.3 23.1 1.0 O3 D:M7P201 3.6 27.8 1.0 NE2 D:GLN175 3.8 15.7 1.0 ND1 A:HIS64 4.0 22.6 1.0 CG A:HIS183 4.0 21.5 1.0 ND1 A:HIS183 4.1 18.5 1.0 CG A:GLU68 4.1 21.6 1.0 CG A:HIS64 4.1 20.9 1.0 CD1 A:LEU179 4.4 18.5 1.0 CG D:GLN175 4.5 18.7 1.0 O D:HOH352 4.6 34.6 1.0 CB D:GLN175 4.6 17.2 1.0 CA D:GLY57 4.8 17.5 1.0 CE1 A:PHE73 5.0 25.2 1.0 CA D:PRO172 5.0 17.2 1.0 C3 D:M7P201 5.0 21.1 1.0

Zinc binding site 2 out of 4 in the Heptose Isomerase Gmha Mutant - D61A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Heptose Isomerase Gmha Mutant - D61A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:26.3 occ:0.28 OE2 D:GLU68 1.9 32.3 1.0 OE1 A:GLN175 1.9 20.9 1.0 NE2 D:HIS183 2.0 16.6 1.0 NE2 D:HIS64 2.1 26.0 1.0 CE1 D:HIS183 2.9 19.3 1.0 CD D:GLU68 3.0 29.6 1.0 CD2 D:HIS64 3.0 24.8 1.0 CE1 D:HIS64 3.1 22.3 1.0 CD A:GLN175 3.1 20.5 1.0 CD2 D:HIS183 3.1 20.9 1.0 OE1 D:GLU68 3.6 33.0 1.0 NE2 A:GLN175 3.7 18.8 1.0 O3 A:M7P202 3.8 30.1 1.0 ND1 D:HIS183 4.1 15.6 1.0 ND1 D:HIS64 4.1 24.8 1.0 CG D:HIS64 4.2 25.0 1.0 CG D:HIS183 4.2 20.2 1.0 CG D:GLU68 4.2 24.4 1.0 CG A:GLN175 4.3 17.0 1.0 CB A:GLN175 4.4 18.6 1.0 CA A:PRO172 4.6 18.3 1.0 CD1 D:LEU179 4.6 20.6 1.0 CE1 D:PHE73 4.8 21.5 1.0 CA A:GLY57 4.8 18.5 1.0 CB A:PRO172 4.8 25.4 1.0

Zinc binding site 3 out of 4 in the Heptose Isomerase Gmha Mutant - D61A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Heptose Isomerase Gmha Mutant - D61A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:25.8 occ:0.21 OE1 B:GLU68 1.9 33.7 1.0 OE1 C:GLN175 1.9 19.8 1.0 NE2 B:HIS183 2.0 27.7 1.0 NE2 B:HIS64 2.1 24.5 1.0 O B:HOH302 2.6 33.4 1.0 O C:HOH301 3.0 30.9 1.0 CD2 B:HIS183 3.0 27.3 1.0 CD B:GLU68 3.0 37.1 1.0 CE1 B:HIS183 3.0 19.4 1.0 CE1 B:HIS64 3.0 27.6 1.0 CD C:GLN175 3.0 24.2 1.0 CD2 B:HIS64 3.1 22.8 1.0 OE2 B:GLU68 3.5 40.1 1.0 NE2 C:GLN175 3.6 20.6 1.0 O3 C:M7P201 3.9 26.0 1.0 ND1 B:HIS183 4.1 25.9 1.0 CG B:HIS183 4.1 27.9 1.0 ND1 B:HIS64 4.1 24.8 1.0 CG B:HIS64 4.2 27.0 1.0 CG B:GLU68 4.2 26.6 1.0 CG C:GLN175 4.3 20.0 1.0 CB C:GLN175 4.4 18.4 1.0 CA C:PRO172 4.5 22.4 1.0 CD1 B:LEU179 4.6 22.1 1.0 CB C:PRO172 4.6 29.4 1.0 CA C:GLY57 4.8 19.7 1.0 CE1 B:PHE73 4.8 28.5 1.0

Zinc binding site 4 out of 4 in the Heptose Isomerase Gmha Mutant - D61A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Heptose Isomerase Gmha Mutant - D61A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:31.3 occ:0.31 OE2 C:GLU68 1.9 33.9 1.0 NE2 C:HIS183 2.0 26.9 1.0 OE1 B:GLN175 2.1 22.7 1.0 NE2 C:HIS64 2.1 23.6 1.0 O C:HOH304 2.7 31.1 1.0 CD C:GLU68 2.8 30.1 1.0 CD2 C:HIS183 2.9 17.7 1.0 CD2 C:HIS64 3.0 22.3 1.0 CE1 C:HIS64 3.1 28.4 1.0 CD B:GLN175 3.1 23.2 1.0 CE1 C:HIS183 3.1 25.1 1.0 OE1 C:GLU68 3.2 38.2 1.0 NE2 B:GLN175 3.6 23.7 1.0 O3 B:M7P202 3.7 27.1 1.0 CG C:GLU68 4.0 24.3 1.0 CG C:HIS183 4.1 22.4 1.0 CG C:HIS64 4.1 25.2 1.0 ND1 C:HIS64 4.1 27.8 1.0 ND1 C:HIS183 4.2 18.7 1.0 CG B:GLN175 4.4 19.8 1.0 CB B:GLN175 4.6 20.7 1.0 CD1 C:LEU179 4.7 23.8 1.0 CA B:GLY57 4.7 19.8 1.0 CE1 C:PHE73 4.7 26.1 1.0 CA B:PRO172 4.9 22.1 1.0

M.Vivoli, J.Pang, N.J.Harmer. A Half-Site Multimeric Enzyme Achieves Its Cooperativity Without Conformational Changes. Sci Rep V. 7 16529 2017.
ISSN: ESSN 2045-2322
PubMed: 29184087
DOI: 10.1038/S41598-017-16421-2