Sodium in PDB 5bwi: Crystallographic Structure of A Bacterial Heparanase

The structure of Crystallographic Structure of A Bacterial Heparanase, PDB code: 5bwi was solved by X.Yu, H.Blanchard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.29 / 1.60
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	125.030, 125.030, 125.160, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 19.2

The binding sites of Sodium atom in the Crystallographic Structure of A Bacterial Heparanase (pdb code 5bwi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystallographic Structure of A Bacterial Heparanase, PDB code: 5bwi:

Sodium binding site 1 out of 1 in the Crystallographic Structure of A Bacterial Heparanase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystallographic Structure of A Bacterial Heparanase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:13.1 occ:1.00 O A:CYS103 2.6 11.7 1.0 O A:GLY60 2.7 19.2 1.0 O A:HOH1145 2.7 33.0 1.0 OD1 A:ASN57 2.9 14.8 1.0 O A:HOH795 2.9 18.4 1.0 O B:HOH819 3.2 28.3 1.0 C A:GLY60 3.7 15.7 1.0 C A:CYS103 3.7 12.7 1.0 O A:HOH1019 3.7 36.5 1.0 CG A:ASN57 4.0 13.1 1.0 O A:HOH617 4.2 39.0 1.0 CA A:ASN57 4.3 12.1 1.0 CA A:GLY60 4.3 14.3 1.0 CA A:CYS103 4.4 12.2 1.0 O A:HOH941 4.4 37.7 1.0 CD1 A:TRP105 4.5 10.8 1.0 O A:HOH1140 4.5 39.9 1.0 CB A:ARG104 4.6 16.5 1.0 CB A:ASN57 4.6 12.8 1.0 NE1 A:TRP105 4.6 11.2 1.0 N A:ALA61 4.6 16.6 1.0 N A:ARG104 4.7 12.4 1.0 O A:PHE56 4.7 11.3 1.0 O A:ASN57 4.8 12.2 1.0 O B:HOH736 4.8 38.0 1.0 CB A:CYS103 4.8 12.2 1.0 CA A:ALA61 4.9 16.1 1.0 CA A:ARG104 5.0 14.3 1.0

L.Bohlmann, G.D.Tredwell, X.Yu, C.W.Chang, T.Haselhorst, M.Winger, J.C.Dyason, R.J.Thomson, J.Tiralongo, I.R.Beacham, H.Blanchard, M.Von Itzstein. Functional and Structural Characterization of A Heparanase. Nat.Chem.Biol. V. 11 955 2015.
ISSN: ESSN 1552-4469
PubMed: 26565989
DOI: 10.1038/NCHEMBIO.1956