Sodium in PDB 4ufq: Structure of A Novel Hyaluronidase (HYAL_SK) From Streptomyces Koganeiensis.

The structure of Structure of A Novel Hyaluronidase (HYAL_SK) From Streptomyces Koganeiensis., PDB code: 4ufq was solved by J.A.Gavira, L.Messina, S.Pernagallo, J.D.Unciti-Broceta, M.Conejero-Muriel, J.J.Diaz-Mochon, S.Vaccaro, S.Caruso, L.Musumeci, S.Bisicchia, R.Di Pasquale, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.24 / 1.45
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	66.884, 66.884, 483.942, 90.00, 90.00, 120.00
R / Rfree (%)	15 / 17.4

The structure of Structure of A Novel Hyaluronidase (HYAL_SK) From Streptomyces Koganeiensis. also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Structure of A Novel Hyaluronidase (HYAL_SK) From Streptomyces Koganeiensis. (pdb code 4ufq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Structure of A Novel Hyaluronidase (HYAL_SK) From Streptomyces Koganeiensis., PDB code: 4ufq:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Structure of A Novel Hyaluronidase (HYAL_SK) From Streptomyces Koganeiensis.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of A Novel Hyaluronidase (HYAL_SK) From Streptomyces Koganeiensis. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1221 b:46.2 occ:1.00 H A:THR24 2.3 25.3 1.0 HA A:THR23 3.1 24.3 1.0 OG1 A:THR23 3.2 22.5 1.0 N A:THR24 3.2 21.1 1.0 OG1 A:THR24 3.2 27.8 1.0 O A:HOH2017 3.4 33.4 1.0 HG1 A:THR24 3.6 33.3 1.0 HG21 A:THR24 3.7 38.7 1.0 HG1 A:THR23 3.7 27.0 1.0 H A:LEU25 3.7 25.3 1.0 O A:HOH2018 3.7 49.7 1.0 CA A:THR23 3.8 20.3 1.0 HG A:LEU25 3.8 33.1 1.0 C A:THR23 3.9 19.9 1.0 CB A:THR23 4.0 20.8 1.0 CB A:THR24 4.1 26.9 1.0 CA A:THR24 4.1 21.5 1.0 HB A:THR23 4.2 24.9 1.0 CG2 A:THR24 4.3 32.2 1.0 N A:LEU25 4.4 21.1 1.0 HG22 A:THR24 4.7 38.7 1.0 C A:THR24 4.7 24.4 1.0 CG A:LEU25 4.7 27.6 1.0 HA A:THR24 4.9 25.8 1.0 HB A:THR24 5.0 32.3 1.0 O A:ASP22 5.0 24.8 1.0

Sodium binding site 2 out of 5 in the Structure of A Novel Hyaluronidase (HYAL_SK) From Streptomyces Koganeiensis.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of A Novel Hyaluronidase (HYAL_SK) From Streptomyces Koganeiensis. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1222 b:60.0 occ:1.00 O A:THR213 2.6 23.3 1.0 O A:HOH2222 2.8 59.2 1.0 HA A:ILE214 3.2 23.1 1.0 HG23 A:THR212 3.3 27.9 1.0 HG21 A:THR212 3.4 27.9 1.0 CG2 A:THR212 3.7 23.3 1.0 C A:THR213 3.7 20.7 1.0 HG22 A:THR212 3.7 27.9 1.0 CA A:ILE214 4.0 19.2 1.0 O A:HOH2213 4.2 40.8 1.0 O A:ILE214 4.2 23.7 1.0 N A:ILE214 4.3 19.6 1.0 O A:HOH2210 4.3 53.3 1.0 C A:ILE214 4.5 23.9 1.0 O A:HOH2214 4.5 61.1 1.0 O A:HOH2209 4.6 32.5 1.0 H A:THR213 4.8 24.9 1.0 N A:THR213 4.8 20.8 1.0 CA A:THR213 4.8 22.0 1.0 HB A:THR213 4.9 28.6 1.0 HG12 A:ILE214 4.9 22.9 1.0

Sodium binding site 3 out of 5 in the Structure of A Novel Hyaluronidase (HYAL_SK) From Streptomyces Koganeiensis.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of A Novel Hyaluronidase (HYAL_SK) From Streptomyces Koganeiensis. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1223 b:34.2 occ:1.00 HG1 A:THR47 2.5 26.8 1.0 O A:HOH2223 2.7 38.0 1.0 OG1 A:THR47 3.0 22.3 1.0 HG22 A:THR47 3.2 28.2 1.0 HG21 A:THR47 3.3 28.2 1.0 CG2 A:THR47 3.6 23.5 1.0 CB A:THR47 3.9 20.6 1.0 H A:THR47 4.3 21.9 1.0 HB A:THR47 4.5 24.8 1.0 HG23 A:THR47 4.5 28.2 1.0 N A:THR47 4.8 18.3 1.0 O A:HOH2053 4.9 26.3 1.0 HA2 A:GLY46 4.9 22.5 1.0 CA A:THR47 5.0 17.3 1.0

Sodium binding site 4 out of 5 in the Structure of A Novel Hyaluronidase (HYAL_SK) From Streptomyces Koganeiensis.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of A Novel Hyaluronidase (HYAL_SK) From Streptomyces Koganeiensis. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1230 b:59.3 occ:1.00 O A:HOH2230 2.5 56.4 1.0 O A:HOH2231 3.1 46.9 1.0 O A:HOH2082 4.7 31.2 1.0

Sodium binding site 5 out of 5 in the Structure of A Novel Hyaluronidase (HYAL_SK) From Streptomyces Koganeiensis.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of A Novel Hyaluronidase (HYAL_SK) From Streptomyces Koganeiensis. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1220 b:43.5 occ:1.00 H B:ASP164 2.6 30.1 1.0 OD1 B:ASP164 2.6 31.5 1.0 O B:HOH2124 2.8 40.0 1.0 O B:HOH2122 3.1 47.6 1.0 HA3 B:GLY163 3.1 32.4 1.0 N B:ASP164 3.3 25.1 1.0 H B:ALA165 3.5 26.4 1.0 CG B:ASP164 3.7 33.6 1.0 N B:ALA165 3.9 22.0 1.0 CA B:GLY163 4.0 27.0 1.0 O B:ARG162 4.0 22.9 1.0 C B:GLY163 4.1 21.9 1.0 CA B:ASP164 4.1 24.9 1.0 HB3 B:ALA165 4.1 25.0 1.0 C B:ASP164 4.2 23.1 1.0 CB B:ASP164 4.5 29.1 1.0 HA2 B:GLY163 4.6 32.4 1.0 OD2 B:ASP164 4.6 48.4 1.0 C B:ARG162 4.7 22.0 1.0 CA B:ALA165 4.7 19.1 1.0 HA B:ALA165 4.7 22.9 1.0 N B:GLY163 4.8 23.9 1.0 HB3 B:ASP164 4.8 35.0 1.0 CB B:ALA165 4.9 20.9 1.0 O B:HOH2123 5.0 62.2 1.0

L.Messina, J.A.Gavira, S.Pernagallo, J.D.Unciti-Broceta, R.M.Sanchez Martin, J.J.Diaz-Mochon, S.Vaccaro, M.Conejero-Muriel, E.Pineda-Molina, S.Caruso, L.Musumeci, R.Di Pasquale, A.Pontillo, F.Sincinelli, M.Pavan, C.Secchieri. Identification and Characterization of A Bacterial Hyaluronidase and Its Production in Recombinant Form. Febs Lett. V. 590 2180 2016.
ISSN: ISSN 0014-5793
PubMed: 27311405
DOI: 10.1002/1873-3468.12258