Zinc in PDB 9fym: Lacto-N-Biosidase From Treponema Denticola Atcc 35405

The structure of Lacto-N-Biosidase From Treponema Denticola Atcc 35405, PDB code: 9fym 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)	48.15 / 1.34
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.954, 50.701, 153.656, 90, 90, 90
R / Rfree (%)	16.9 / 19.7

The structure of Lacto-N-Biosidase From Treponema Denticola Atcc 35405 also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Zinc atom in the Lacto-N-Biosidase From Treponema Denticola Atcc 35405 (pdb code 9fym). 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, PDB code: 9fym:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:30.6 occ:1.00 OE1 A:GLU140 2.0 26.1 1.0 SG A:CYS201 2.3 31.7 1.0 SG A:CYS157 2.3 26.8 1.0 SG A:CYS198 2.3 35.6 1.0 HB2 A:CYS201 2.8 41.4 1.0 CD A:GLU140 2.9 29.0 1.0 CB A:CYS201 3.2 34.5 1.0 HA A:CYS157 3.2 28.9 1.0 OE2 A:GLU140 3.2 32.8 1.0 HB2 A:CYS157 3.3 30.1 1.0 CB A:CYS157 3.3 25.1 1.0 CB A:CYS198 3.4 39.8 1.0 HB2 A:CYS198 3.4 47.8 1.0 HB2 A:LEU200 3.5 47.6 1.0 H A:CYS201 3.5 45.0 1.0 HB3 A:CYS198 3.5 47.8 1.0 HA A:GLU140 3.7 33.4 1.0 CA A:CYS157 3.7 24.1 1.0 H A:SER159 3.8 31.2 1.0 O A:HOH580 3.8 32.0 1.0 HB3 A:CYS201 3.9 41.4 1.0 H A:SER158 3.9 29.7 1.0 N A:CYS201 3.9 37.5 1.0 HB2 A:SER159 4.0 38.5 1.0 CA A:CYS201 4.2 36.1 1.0 HB3 A:CYS157 4.2 30.1 1.0 O A:HOH556 4.2 37.8 1.0 N A:SER158 4.3 24.8 1.0 C A:CYS157 4.3 26.5 1.0 CG A:GLU140 4.3 28.1 1.0 CB A:LEU200 4.4 39.7 1.0 HG A:SER159 4.4 37.4 1.0 H A:LEU200 4.4 49.0 1.0 HB2 A:GLU140 4.5 32.7 1.0 CA A:GLU140 4.5 27.9 1.0 HB3 A:LEU200 4.5 47.6 1.0 N A:SER159 4.6 26.0 1.0 CB A:GLU140 4.7 27.2 1.0 HA A:CYS201 4.7 43.3 1.0 HD13 A:LEU200 4.7 75.5 1.0 CA A:CYS198 4.7 43.4 1.0 HG A:SER158 4.7 36.6 1.0 H A:GLY194 4.7 33.3 1.0 C A:LEU200 4.7 41.5 1.0 HD22 A:LEU200 4.7 54.9 1.0 O A:HOH730 4.7 35.3 1.0 O A:GLU140 4.8 36.3 1.0 CB A:SER159 4.8 32.0 1.0 HG3 A:GLU140 4.8 33.6 1.0 OG A:SER159 4.9 31.1 1.0 HG2 A:GLU140 4.9 33.6 1.0 HA A:CYS198 4.9 52.1 1.0 CA A:LEU200 5.0 34.3 1.0 N A:LEU200 5.0 40.8 1.0 N A:CYS157 5.0 20.9 1.0

Zinc binding site 2 out of 2 in the Lacto-N-Biosidase From Treponema Denticola Atcc 35405


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:33.9 occ:1.00 OE1 A:GLU189 2.1 56.4 1.0 ND1 A:HIS121 2.3 34.9 1.0 SG A:CYS153 2.4 27.3 1.0 N3 A:IMD401 2.5 53.8 1.0 HB3 A:GLU189 2.8 32.9 1.0 HB3 A:CYS153 2.9 31.0 1.0 HA A:HIS121 3.1 24.4 1.0 HG3 A:GLU189 3.1 39.9 1.0 CD A:GLU189 3.1 52.5 1.0 CB A:CYS153 3.2 25.8 1.0 CE1 A:HIS121 3.2 32.1 1.0 C2 A:IMD401 3.3 56.5 1.0 CG A:HIS121 3.3 25.6 1.0 HE1 A:HIS121 3.3 38.5 1.0 HB2 A:HIS121 3.4 27.2 1.0 CG A:GLU189 3.4 33.2 1.0 HB2 A:CYS153 3.5 31.0 1.0 CB A:GLU189 3.5 27.4 1.0 C4 A:IMD401 3.6 70.3 1.0 CB A:HIS121 3.7 22.7 1.0 CA A:HIS121 3.8 20.3 1.0 HE2 A:PHE191 3.8 36.8 1.0 HB2 A:GLU189 3.9 32.9 1.0 H4 A:IMD401 3.9 84.4 1.0 H A:HIS121 4.2 24.6 1.0 O A:SER123 4.3 24.5 1.0 OE2 A:GLU189 4.3 76.1 1.0 HG2 A:GLU189 4.4 39.9 1.0 NE2 A:HIS121 4.4 28.6 1.0 HB3 A:TYR152 4.4 47.5 1.0 CD2 A:HIS121 4.4 28.2 1.0 N A:HIS121 4.5 20.5 1.0 N1 A:IMD401 4.5 63.6 1.0 CA A:CYS153 4.6 23.4 1.0 HB3 A:HIS121 4.6 27.2 1.0 C5 A:IMD401 4.7 68.7 1.0 CE2 A:PHE191 4.7 30.7 1.0 O A:TYR152 4.8 27.2 1.0 HA A:GLU189 4.8 28.2 1.0 N A:CYS153 4.8 26.8 1.0 CA A:GLU189 4.8 23.5 1.0 C A:TYR152 4.9 28.8 1.0 O A:GLU189 4.9 21.4 1.0 C A:HIS121 4.9 18.6 1.0 HD2 A:PHE191 5.0 33.7 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