Sodium 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:

Zinc

(Zn)

2 atoms

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Lacto-N-Biosidase From Treponema Denticola Atcc 35405, PDB code: 9fym:
Jump to Sodium binding site number: 1; 2;

Sodium 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 Sodium with other atoms in the Na 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:Na402 b:30.8 occ:1.00 HH11 A:ARG99 2.4 24.0 1.0 O A:VAL177 2.6 15.4 1.0 HG A:SER179 2.6 20.5 1.0 OG A:SER179 2.7 17.1 1.0 O A:HOH655 2.8 19.9 1.0 HG2 A:ARG99 3.0 19.1 1.0 NH1 A:ARG99 3.1 20.0 1.0 HD3 A:ARG99 3.3 23.1 1.0 HH12 A:ARG99 3.3 24.0 1.0 HH12 A:ARG106 3.4 26.4 1.0 HB2 A:SER179 3.4 20.4 1.0 HA A:ARG99 3.5 17.2 1.0 C A:VAL177 3.5 14.2 1.0 CB A:SER179 3.6 17.0 1.0 HA A:PHE178 3.6 17.3 1.0 HB3 A:ALA102 3.6 19.9 1.0 N A:SER179 3.7 13.8 1.0 H A:SER179 3.7 16.6 1.0 C A:PHE178 3.7 13.5 1.0 CG A:ARG99 3.8 15.9 1.0 HB3 A:ARG99 3.8 19.0 1.0 CD A:ARG99 3.9 19.2 1.0 O A:GLU176 4.0 16.1 1.0 CA A:PHE178 4.0 14.4 1.0 O A:HOH698 4.1 43.4 1.0 CZ A:ARG99 4.1 18.7 1.0 O A:PHE178 4.1 14.3 1.0 CB A:ARG99 4.1 15.8 1.0 N A:PHE178 4.2 13.5 1.0 NH1 A:ARG106 4.2 22.0 1.0 HB1 A:ALA102 4.2 19.9 1.0 CA A:SER179 4.2 13.7 1.0 CB A:ALA102 4.3 16.6 1.0 HA A:VAL177 4.3 17.7 1.0 CA A:ARG99 4.3 14.3 1.0 HH22 A:ARG106 4.3 32.7 1.0 HB3 A:SER179 4.4 20.4 1.0 HB2 A:ALA102 4.4 19.9 1.0 NE A:ARG99 4.5 16.8 1.0 O A:HOH815 4.5 45.4 1.0 CA A:VAL177 4.6 14.8 1.0 HH11 A:ARG106 4.6 26.4 1.0 HA A:SER179 4.6 16.4 1.0 HG3 A:ARG99 4.6 19.1 1.0 O A:ARG99 4.7 17.6 1.0 HD2 A:ARG99 4.8 23.1 1.0 NH2 A:ARG106 5.0 27.2 1.0 H A:PHE178 5.0 16.2 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na403 b:29.2 occ:1.00 HD22 A:ASN78 2.2 21.6 1.0 OE1 A:GLU74 2.7 21.1 0.5 O A:HOH786 2.8 35.3 1.0 O A:GLU74 2.8 16.6 0.5 ND2 A:ASN78 3.0 18.0 1.0 HB3 A:ASN48 3.0 21.7 1.0 O A:VAL47 3.0 17.5 1.0 HB3 A:SER46 3.2 23.2 1.0 HA A:ILE75 3.3 17.6 1.0 O A:GLU74 3.3 14.9 0.5 HD21 A:ASN78 3.3 21.6 1.0 O A:ILE75 3.3 14.5 1.0 HB2 A:ASN78 3.4 17.1 1.0 CD A:GLU74 3.6 21.0 0.5 O A:HOH512 3.6 32.2 1.0 H A:VAL47 3.6 18.7 1.0 C A:ILE75 3.7 15.1 1.0 C A:VAL47 3.7 16.3 1.0 C A:GLU74 3.7 16.5 0.5 OE2 A:GLU74 3.8 23.9 0.5 CA A:ILE75 3.8 14.6 1.0 HG2 A:GLU74 3.8 22.4 0.5 C A:GLU74 3.8 16.3 0.5 CB A:ASN48 3.9 18.1 1.0 HA A:ASN48 3.9 21.6 1.0 CG A:ASN78 4.0 16.4 1.0 N A:VAL47 4.0 15.6 1.0 CB A:SER46 4.1 19.4 1.0 CB A:ASN78 4.1 14.2 1.0 N A:ILE75 4.1 14.5 1.0 N A:ASN48 4.2 15.6 1.0 CA A:ASN48 4.2 18.0 1.0 HB2 A:ASN48 4.3 21.7 1.0 HB3 A:GLU74 4.3 19.8 0.5 HA A:SER46 4.4 18.9 1.0 OE2 A:GLU74 4.4 32.3 0.5 HB3 A:GLU74 4.4 19.4 0.5 N A:GLY76 4.5 15.4 1.0 HB3 A:ASN78 4.5 17.1 1.0 CA A:VAL47 4.6 17.0 1.0 CG A:GLU74 4.6 18.7 0.5 CA A:SER46 4.6 15.8 1.0 HA3 A:GLY76 4.6 18.7 1.0 HG A:SER46 4.7 38.0 1.0 C A:SER46 4.7 15.3 1.0 OG A:SER46 4.7 31.6 1.0 HB2 A:SER46 4.7 23.2 1.0 H A:ASN78 4.8 16.3 1.0 O A:HOH687 4.8 42.7 1.0 CG A:GLU74 4.8 18.8 0.5 HD22 A:ASN48 4.8 39.9 1.0 CB A:GLU74 4.8 16.5 0.5 H A:ILE75 4.9 17.4 0.5 CG A:ASN48 4.9 22.1 1.0 H A:ASN48 4.9 18.8 1.0 HD13 A:ILE75 4.9 24.6 1.0 H A:ILE75 4.9 17.4 0.5 CB A:GLU74 4.9 16.2 0.5 CD A:GLU74 4.9 26.1 0.5 CA A:GLU74 4.9 15.7 0.5 CA A:GLU74 5.0 15.7 0.5 H A:GLY76 5.0 18.5 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