Zinc in PDB 9fyl: Lacto-N-Biosidase From Treponema Denticola Atcc 35405, Histag Bound in Active Site

The structure of Lacto-N-Biosidase From Treponema Denticola Atcc 35405, Histag Bound in Active Site, PDB code: 9fyl was solved by M.Vuillemin, S.Siebenhaar, B.Zeuner, J.P.Morth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.31 / 2.24
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	128.917, 89.471, 93.757, 90, 127, 90
R / Rfree (%)	23.2 / 26.9

The binding sites of Zinc atom in the Lacto-N-Biosidase From Treponema Denticola Atcc 35405, Histag Bound in Active Site (pdb code 9fyl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Lacto-N-Biosidase From Treponema Denticola Atcc 35405, Histag Bound in Active Site, PDB code: 9fyl:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Lacto-N-Biosidase From Treponema Denticola Atcc 35405, Histag Bound in Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Lacto-N-Biosidase From Treponema Denticola Atcc 35405, Histag Bound in Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:75.6 occ:1.00 OE1 A:GLU140 2.0 67.9 1.0 SG A:CYS198 2.2 86.2 1.0 SG A:CYS201 2.2 295.0 1.0 SG A:CYS157 2.4 83.7 1.0 HB2 A:CYS201 2.9 124.0 1.0 CD A:GLU140 2.9 77.3 1.0 HA A:CYS157 3.1 91.0 1.0 CB A:CYS201 3.1 103.0 1.0 OE2 A:GLU140 3.2 69.9 1.0 HB2 A:CYS157 3.3 100.3 1.0 CB A:CYS157 3.3 83.3 1.0 HB3 A:LEU200 3.3 114.6 1.0 CB A:CYS198 3.4 76.4 1.0 HB2 A:CYS198 3.4 92.1 1.0 H A:CYS201 3.5 95.6 1.0 HB3 A:CYS198 3.5 92.1 1.0 HB2 A:LEU200 3.6 114.6 1.0 CA A:CYS157 3.6 75.5 1.0 HA A:GLU140 3.7 87.7 1.0 H A:SER159 3.8 97.7 1.0 N A:CYS201 3.8 79.3 1.0 H A:SER158 3.8 96.4 1.0 HB2 A:SER159 3.8 88.9 1.0 HB3 A:CYS201 3.9 124.0 1.0 CB A:LEU200 3.9 95.1 1.0 CA A:CYS201 4.1 90.3 1.0 HB3 A:CYS157 4.2 100.3 1.0 N A:SER158 4.2 80.0 1.0 C A:CYS157 4.3 70.4 1.0 CG A:GLU140 4.3 80.0 1.0 HB2 A:GLU140 4.4 90.7 1.0 C A:LEU200 4.5 83.0 1.0 H A:LEU200 4.5 95.7 1.0 HG A:LEU200 4.6 111.2 1.0 CA A:GLU140 4.6 72.7 1.0 HA A:CYS201 4.6 108.8 1.0 N A:SER159 4.6 81.1 1.0 CB A:GLU140 4.6 75.2 1.0 HG A:SER159 4.7 85.4 1.0 HG3 A:GLU140 4.7 96.4 1.0 CB A:SER159 4.7 73.7 1.0 H A:GLY194 4.7 96.4 1.0 CA A:CYS198 4.8 81.9 1.0 CG A:LEU200 4.8 92.3 1.0 CA A:LEU200 4.8 84.0 1.0 O A:GLU140 4.8 74.4 1.0 HG2 A:GLU140 4.9 96.4 1.0 HA A:CYS198 4.9 98.7 1.0 N A:CYS157 4.9 69.8 1.0

Zinc binding site 2 out of 2 in the Lacto-N-Biosidase From Treponema Denticola Atcc 35405, Histag Bound in Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Lacto-N-Biosidase From Treponema Denticola Atcc 35405, Histag Bound in Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:183.3 occ:1.00 SG B:CYS157 1.8 179.4 1.0 OE1 B:GLU140 1.9 81.2 1.0 SG B:CYS198 2.1 95.4 1.0 SG B:CYS201 2.1 81.5 1.0 CD B:GLU140 2.8 77.6 1.0 HB2 B:CYS201 2.9 85.6 1.0 OE2 B:GLU140 3.0 78.6 1.0 CB B:CYS201 3.1 71.0 1.0 CB B:CYS198 3.1 76.8 1.0 HB2 B:CYS198 3.2 92.6 1.0 CB B:CYS157 3.2 67.8 1.0 HB3 B:CYS198 3.3 92.6 1.0 H B:CYS201 3.3 88.7 1.0 HA B:CYS157 3.3 87.1 1.0 HB2 B:CYS157 3.4 81.8 1.0 HB2 B:LEU200 3.5 109.3 1.0 O B:HOH512 3.7 78.8 1.0 HA B:GLU140 3.7 93.6 1.0 N B:CYS201 3.7 73.5 1.0 CA B:CYS157 3.8 72.2 1.0 HB3 B:CYS201 3.8 85.6 1.0 H B:SER158 4.0 83.7 1.0 H B:SER159 4.0 91.5 1.0 HB3 B:CYS157 4.0 81.8 1.0 CA B:CYS201 4.0 77.1 1.0 CG B:GLU140 4.1 76.8 1.0 HB2 B:SER159 4.2 105.0 1.0 H B:LEU200 4.2 106.7 1.0 HB2 B:GLU140 4.3 94.3 1.0 N B:SER158 4.4 69.4 1.0 C B:CYS157 4.4 65.4 1.0 CB B:LEU200 4.4 90.7 1.0 CA B:GLU140 4.5 77.6 1.0 CA B:CYS198 4.5 82.1 1.0 HG3 B:GLU140 4.6 92.6 1.0 CB B:GLU140 4.6 78.3 1.0 H B:GLY194 4.6 90.1 1.0 O B:GLU140 4.6 74.6 1.0 HB3 B:LEU200 4.6 109.3 1.0 C B:LEU200 4.6 84.7 1.0 HA B:CYS201 4.6 93.0 1.0 HA B:CYS198 4.7 98.9 1.0 HG2 B:GLU140 4.7 92.6 1.0 HD11 B:LEU200 4.8 122.1 1.0 N B:SER159 4.8 75.9 1.0 N B:LEU200 4.9 88.6 1.0 CA B:LEU200 4.9 89.3 1.0 HD2 B:PRO199 4.9 104.1 1.0 H B:GLU195 4.9 78.1 1.0 HG B:SER159 4.9 102.9 1.0 CB B:SER159 5.0 87.2 1.0 OG B:SER159 5.0 85.4 1.0

M.Vuillemin, J.Muschiol, Y.Zhang, J.Holck, K.Barrett, J.P.Morth, A.S.Meyer, B.Zeuner. Discovery of Lacto-N-Biosidases and A Novel N-Acetyllactosaminidase Activity in the Cazy Family GH20: Functional Diversity and Structural Insights. Chembiochem 00710 2024.
ISSN: ESSN 1439-7633
PubMed: 39239753
DOI: 10.1002/CBIC.202400710