Zinc in PDB 8bal: NIAKO3494, A Bacterial Protein Structure in Glycoside Hydrolase Family 20

All present enzymatic activity of NIAKO3494, A Bacterial Protein Structure in Glycoside Hydrolase Family 20:
3.2.1.52;

The structure of NIAKO3494, A Bacterial Protein Structure in Glycoside Hydrolase Family 20, PDB code: 8bal was solved by M.D.Dong, C.R.Roth, Y.J.Jin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	73.49 / 2.27
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	146.987, 254.589, 139.58, 90, 90, 90
R / Rfree (%)	28.3 / 35.6

The binding sites of Zinc atom in the NIAKO3494, A Bacterial Protein Structure in Glycoside Hydrolase Family 20 (pdb code 8bal). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the NIAKO3494, A Bacterial Protein Structure in Glycoside Hydrolase Family 20, PDB code: 8bal:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the NIAKO3494, A Bacterial Protein Structure in Glycoside Hydrolase Family 20


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of NIAKO3494, A Bacterial Protein Structure in Glycoside Hydrolase Family 20 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:31.8 occ:1.00 OE2 A:GLU141 1.6 12.5 1.0 SG A:CYS206 1.9 16.4 1.0 CD A:GLU141 2.1 13.7 1.0 SG A:CYS165 2.2 23.4 1.0 OE1 A:GLU141 2.2 12.4 1.0 SG A:CYS209 2.5 27.4 1.0 CB A:CYS209 3.1 22.6 1.0 CB A:CYS165 3.4 19.9 1.0 CB A:CYS206 3.5 17.1 1.0 CG A:GLU141 3.6 12.8 1.0 N A:CYS209 3.9 21.9 1.0 CA A:CYS165 3.9 19.1 1.0 CA A:CYS209 4.1 22.6 1.0 CD A:PRO166 4.3 16.3 1.0 OG A:SER167 4.3 17.8 1.0 CB A:GLU141 4.4 13.5 1.0 C A:CYS165 4.4 18.2 1.0 CB A:ARG208 4.5 18.3 1.0 N A:PRO166 4.6 18.7 1.0 CB A:SER167 4.7 18.6 1.0 CA A:GLU141 4.7 13.2 1.0 CA A:CYS206 4.8 19.3 1.0 C A:ARG208 4.8 19.6 1.0 N A:SER167 4.8 17.5 1.0 CG A:ARG208 4.9 17.2 1.0

Zinc binding site 2 out of 5 in the NIAKO3494, A Bacterial Protein Structure in Glycoside Hydrolase Family 20


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of NIAKO3494, A Bacterial Protein Structure in Glycoside Hydrolase Family 20 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:42.6 occ:1.00 SG C:CYS206 2.0 36.0 1.0 OE2 C:GLU141 2.2 30.1 1.0 SG C:CYS209 2.7 34.2 1.0 CB C:CYS209 3.0 30.4 1.0 CD C:GLU141 3.1 32.0 1.0 CB C:CYS165 3.2 26.7 1.0 CB C:CYS206 3.2 41.8 1.0 OE1 C:GLU141 3.3 31.3 1.0 SG C:CYS165 3.4 31.3 1.0 CA C:CYS165 3.6 27.6 1.0 N C:CYS209 3.6 38.1 1.0 CA C:CYS209 3.9 32.0 1.0 CB C:ARG208 4.3 35.5 1.0 C C:CYS165 4.3 26.5 1.0 CG C:GLU141 4.5 33.9 1.0 CA C:CYS206 4.6 42.6 1.0 CA C:GLU141 4.6 39.9 1.0 C C:ARG208 4.7 38.5 1.0 CD C:PRO166 4.7 24.0 1.0 N C:PRO166 4.8 25.3 1.0 O C:CYS165 4.8 26.4 1.0 N C:CYS165 4.9 28.4 1.0 CA C:ARG208 4.9 38.3 1.0 CB C:SER167 4.9 24.4 1.0 CB C:GLU141 5.0 37.2 1.0 N C:SER167 5.0 23.3 1.0

Zinc binding site 3 out of 5 in the NIAKO3494, A Bacterial Protein Structure in Glycoside Hydrolase Family 20


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of NIAKO3494, A Bacterial Protein Structure in Glycoside Hydrolase Family 20 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:39.1 occ:0.80 OE2 D:GLU141 1.7 18.0 1.0 SG D:CYS209 1.9 25.4 1.0 CD D:GLU141 2.4 19.9 1.0 SG D:CYS165 2.5 25.0 1.0 OE1 D:GLU141 2.5 21.1 1.0 SG D:CYS206 2.8 29.1 1.0 CB D:CYS209 3.3 24.4 1.0 CB D:CYS165 3.3 26.3 1.0 CA D:CYS165 3.7 25.8 1.0 CG D:GLU141 3.8 20.5 1.0 CB D:CYS206 3.9 26.5 1.0 N D:CYS209 4.0 24.8 1.0 CD D:PRO166 4.1 18.1 1.0 O D:HOH501 4.1 29.6 1.0 CA D:GLU141 4.3 21.9 1.0 CA D:CYS209 4.3 25.2 1.0 CB D:GLU141 4.3 20.6 1.0 C D:CYS165 4.4 22.8 1.0 N D:PRO166 4.5 19.6 1.0 CB D:ARG208 4.7 23.6 1.0 O D:GLU141 4.8 22.8 1.0 N D:CYS165 5.0 27.8 1.0 CD D:ARG208 5.0 22.5 1.0

Zinc binding site 4 out of 5 in the NIAKO3494, A Bacterial Protein Structure in Glycoside Hydrolase Family 20


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of NIAKO3494, A Bacterial Protein Structure in Glycoside Hydrolase Family 20 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn401 b:52.9 occ:1.00 SG E:CYS165 2.2 49.4 1.0 SG E:CYS209 2.4 27.8 1.0 SG E:CYS206 2.6 48.5 1.0 OE2 E:GLU141 2.7 58.9 1.0 CB E:CYS209 2.8 31.3 1.0 CB E:CYS165 3.5 44.7 1.0 N E:CYS209 3.6 35.2 1.0 CD E:GLU141 3.7 58.8 1.0 CB E:CYS206 3.7 42.8 1.0 CA E:CYS209 3.8 34.0 1.0 NH1 E:ARG208 3.8 32.9 1.0 CB E:ARG208 3.9 36.6 1.0 CA E:CYS165 3.9 41.1 1.0 CD E:PRO166 4.0 37.1 1.0 OE1 E:GLU141 4.0 61.1 1.0 N E:ARG208 4.2 36.1 1.0 C E:ARG208 4.2 33.1 1.0 CA E:ARG208 4.3 36.1 1.0 O E:CYS206 4.6 43.9 1.0 C E:CYS206 4.6 40.3 1.0 C E:CYS165 4.6 37.7 1.0 N E:PRO166 4.7 36.3 1.0 CA E:CYS206 4.8 41.1 1.0 CD E:ARG208 4.9 35.1 1.0 C E:CYS209 4.9 34.7 1.0 CG E:ARG208 4.9 38.1 1.0 CZ E:ARG208 5.0 33.6 1.0 N E:PRO207 5.0 39.8 1.0 CG E:GLU141 5.0 55.5 1.0

Zinc binding site 5 out of 5 in the NIAKO3494, A Bacterial Protein Structure in Glycoside Hydrolase Family 20


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of NIAKO3494, A Bacterial Protein Structure in Glycoside Hydrolase Family 20 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn401 b:44.5 occ:1.00 OE2 F:GLU141 1.9 39.4 1.0 SG F:CYS206 2.2 49.1 1.0 SG F:CYS165 2.3 36.8 1.0 SG F:CYS209 2.5 37.1 1.0 CD F:GLU141 2.5 37.2 1.0 OE1 F:GLU141 2.6 33.3 1.0 CB F:CYS209 3.0 42.0 1.0 CB F:CYS165 3.5 37.6 1.0 N F:CYS209 3.6 41.2 1.0 CB F:CYS206 3.7 49.6 1.0 CA F:CYS209 3.9 40.8 1.0 CG F:GLU141 3.9 36.4 1.0 CD F:PRO166 3.9 39.7 1.0 CA F:CYS165 4.0 38.5 1.0 N F:PRO166 4.4 38.2 1.0 C F:CYS165 4.5 35.6 1.0 CB F:GLU141 4.5 36.9 1.0 C F:ARG208 4.6 40.1 1.0 NH1 F:ARG208 4.6 27.6 1.0 O F:CYS206 4.6 44.8 1.0 CA F:GLU141 4.7 36.9 1.0 CB F:ARG208 4.8 34.9 1.0 CG F:PRO166 4.9 36.5 1.0 CA F:CYS206 4.9 52.2 1.0 N F:SER167 5.0 35.6 1.0

Z.Zhang, M.Dong, R.Zallot, G.M.Blackburn, N.Wang, C.Wang, L.Chen, P.Baumann, Z.Wu, Z.Wang, H.Fan, C.Roth, Y.Jin, Y.He. Mechanistic and Structural Insights Into the Specificity and Biological Functions of Bacterial Sulfoglycosidases Acs Catalysis 2022.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.2C05405