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

Enzymatic activity of 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;

Protein crystallography data

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

Zinc Binding Sites:

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 8bal

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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 8bal

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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 8bal

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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 8bal

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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 8bal

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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

Reference:

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
Page generated: Sat Apr 8 07:46:02 2023

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