Sodium in PDB 7rg8: Crystal Structure of A Stable Heparanase Mutant

The structure of Crystal Structure of A Stable Heparanase Mutant, PDB code: 7rg8 was solved by C.Whitefield, N.S.Hong, C.J.Jackson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.01 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.785, 76.094, 124.432, 90, 90, 90
R / Rfree (%)	14.3 / 16.5

The binding sites of Sodium atom in the Crystal Structure of A Stable Heparanase Mutant (pdb code 7rg8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of A Stable Heparanase Mutant, PDB code: 7rg8:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of A Stable Heparanase Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of A Stable Heparanase Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:16.8 occ:1.00 H A:ALA388 2.5 25.0 1.0 O B:HOH340 3.1 37.2 1.0 HD13 B:LEU65 3.1 25.3 1.0 O A:HOH752 3.1 21.8 1.0 HA3 A:GLY387 3.2 23.4 1.0 HB2 B:LEU65 3.2 22.2 1.0 O B:HOH357 3.2 27.0 1.0 HB3 B:ASP62 3.2 20.7 1.0 O A:HOH851 3.2 21.0 1.0 N A:ALA388 3.3 20.8 1.0 HB3 A:ALA388 3.5 30.0 1.0 HA2 A:GLY387 3.6 23.4 1.0 CA A:GLY387 3.7 19.5 1.0 HA B:LEU65 3.8 21.2 1.0 HB3 B:ASN64 3.9 25.7 1.0 H B:LEU65 3.9 20.7 1.0 HB2 A:ALA388 3.9 30.0 1.0 CB B:LEU65 4.0 18.4 1.0 CD1 B:LEU65 4.0 21.1 1.0 N B:LEU65 4.0 17.3 1.0 C A:GLY387 4.1 20.8 1.0 CB A:ALA388 4.1 25.0 1.0 CB B:ASP62 4.1 17.2 1.0 CA B:LEU65 4.2 17.6 1.0 HD12 B:LEU65 4.2 25.3 1.0 H A:GLY389 4.2 24.6 1.0 HB2 B:ASP62 4.3 20.7 1.0 CA A:ALA388 4.3 22.5 1.0 HD21 B:ASN64 4.4 34.7 1.0 H B:ASP62 4.5 18.2 1.0 CG B:LEU65 4.6 19.3 1.0 C B:ASN64 4.7 17.7 1.0 HD22 B:LEU65 4.7 24.6 1.0 O B:ASP62 4.7 17.2 1.0 HD11 B:LEU65 4.7 25.3 1.0 HB3 B:LEU65 4.7 22.2 1.0 CB B:ASN64 4.8 21.4 1.0 O B:HOH343 4.8 41.6 1.0 HG11 A:VAL384 4.9 20.3 1.0 N A:GLY389 4.9 20.5 1.0 HG21 A:VAL384 4.9 19.2 1.0 O A:HOH831 5.0 27.2 1.0 O B:HOH353 5.0 39.8 1.0 CG B:ASP62 5.0 19.8 1.0 O A:PHE386 5.0 16.6 1.0 HB1 A:ALA388 5.0 30.0 1.0 O B:HOH313 5.0 26.1 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of A Stable Heparanase Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of A Stable Heparanase Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:23.8 occ:1.00 OE2 A:GLU221 2.5 16.7 1.0 HA3 A:GLY342 2.6 17.9 1.0 OD1 A:ASP267 2.7 16.8 1.0 HG3 B:ARG93 2.8 20.1 1.0 O A:GLY342 2.9 15.7 1.0 HA2 A:GLY342 3.1 17.9 1.0 CA A:GLY342 3.1 14.9 1.0 HE B:ARG93 3.2 21.2 1.0 HD2 B:ARG93 3.2 20.5 1.0 CD A:GLU221 3.2 15.9 1.0 HG21 A:THR294 3.3 19.3 1.0 OE1 A:GLU221 3.3 16.7 1.0 NE B:ARG93 3.3 17.6 1.0 C A:GLY342 3.4 14.9 1.0 CD B:ARG93 3.5 17.0 1.0 CG A:ASP267 3.5 15.8 1.0 HB A:THR294 3.6 18.2 1.0 CG B:ARG93 3.6 16.8 1.0 OD2 A:ASP267 3.6 16.9 1.0 SD A:MET381 3.8 17.4 1.0 CZ B:ARG93 3.8 18.1 1.0 HE2 A:HIS296 3.9 18.6 1.0 CG2 A:THR294 4.0 16.0 1.0 HG22 A:THR294 4.0 19.3 1.0 HG1 A:THR294 4.1 18.9 1.0 HH21 B:ARG93 4.1 22.7 1.0 CB A:THR294 4.2 15.2 1.0 NH2 B:ARG93 4.2 18.9 1.0 HE1 A:MET381 4.2 25.1 1.0 HG2 B:ARG93 4.3 20.1 1.0 HB2 B:ARG93 4.3 19.2 1.0 HD3 B:ARG93 4.5 20.5 1.0 N A:GLY342 4.5 14.9 1.0 CE A:MET381 4.5 20.9 1.0 CB B:ARG93 4.5 16.0 1.0 HE3 A:MET381 4.5 25.1 1.0 NH1 B:ARG93 4.5 18.5 1.0 HB2 A:GLU343 4.6 18.0 1.0 OG1 A:THR294 4.6 15.7 1.0 N A:GLU343 4.6 14.8 1.0 HH11 B:ARG93 4.6 22.2 1.0 CG A:GLU221 4.6 15.9 1.0 NE2 A:HIS296 4.6 15.5 1.0 HB3 B:ARG93 4.7 19.2 1.0 H A:GLY342 4.7 17.9 1.0 HG2 A:GLU221 4.8 19.1 1.0 HG23 A:THR294 4.8 19.3 1.0 HH22 B:ARG93 4.8 22.7 1.0 HG21 A:ILE185 4.9 19.3 1.0 CB A:ASP267 5.0 15.3 1.0 HD2 A:HIS296 5.0 17.0 1.0 HB2 A:MET381 5.0 18.1 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of A Stable Heparanase Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of A Stable Heparanase Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:26.0 occ:1.00 OH A:TYR299 2.7 19.5 1.0 OD2 A:ASP367 2.7 19.0 1.0 HD12 A:LEU371 2.8 24.8 1.0 O A:LEU316 2.8 19.1 1.0 HE2 A:TYR299 2.9 20.3 1.0 HB3 A:PHE319 2.9 21.7 1.0 HH A:TYR299 3.0 23.4 1.0 HB3 A:LEU316 3.0 22.9 1.0 HA A:LEU316 3.2 22.7 1.0 HD22 A:LEU316 3.3 26.4 1.0 HB3 A:ASP367 3.3 21.0 1.0 HD2 A:PHE319 3.4 21.2 1.0 HB2 A:PHE319 3.5 21.7 1.0 CZ A:TYR299 3.5 18.6 1.0 C A:LEU316 3.5 19.2 1.0 CE2 A:TYR299 3.5 16.9 1.0 CD1 A:LEU371 3.6 20.6 1.0 CB A:PHE319 3.6 18.0 1.0 CA A:LEU316 3.6 18.9 1.0 CG A:ASP367 3.7 18.0 1.0 CB A:LEU316 3.7 19.1 1.0 HD11 A:LEU371 3.8 24.8 1.0 HA A:LYS368 3.8 18.6 1.0 HD13 A:LEU371 3.8 24.8 1.0 CB A:ASP367 4.0 17.5 1.0 CD2 A:PHE319 4.0 17.7 1.0 HH21 A:ARG432 4.0 24.6 1.0 CD2 A:LEU316 4.1 22.0 1.0 CG A:PHE319 4.1 17.0 1.0 N A:LYS368 4.2 15.9 1.0 C A:ASP367 4.2 16.2 1.0 HD23 A:LEU316 4.3 26.4 1.0 H A:PHE319 4.3 21.7 1.0 O A:ASP367 4.4 17.3 1.0 HB2 A:LYS368 4.4 19.4 1.0 H A:LYS368 4.4 19.1 1.0 CA A:LYS368 4.4 15.4 1.0 HB2 A:LEU316 4.5 22.9 1.0 HB2 A:LEU371 4.5 21.2 1.0 CG A:LEU316 4.5 20.9 1.0 NH2 A:ARG432 4.6 20.5 1.0 HD13 A:LEU316 4.6 27.3 1.0 HH22 A:ARG432 4.7 24.6 1.0 HB2 A:ASP367 4.7 21.0 1.0 N A:ASP317 4.7 19.5 1.0 CA A:ASP367 4.8 16.3 1.0 CG A:LEU371 4.8 18.7 1.0 CE1 A:TYR299 4.8 18.2 1.0 OD1 A:ASP367 4.8 18.8 1.0 HA A:ASP317 4.8 25.1 1.0 CD2 A:TYR299 4.8 17.1 1.0 HG A:LEU371 4.9 22.5 1.0 HA A:MET364 4.9 21.8 1.0 HD21 A:LEU316 4.9 26.4 1.0 CA A:PHE319 4.9 18.3 1.0 CB A:LYS368 5.0 16.2 1.0 N A:PHE319 5.0 18.1 1.0 CE2 A:PHE319 5.0 17.3 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of A Stable Heparanase Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of A Stable Heparanase Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:25.3 occ:1.00 HH11 B:ARG93 2.2 22.2 1.0 HB B:THR60 2.6 18.0 1.0 HG1 B:THR60 2.7 19.6 1.0 O B:GLY95 2.7 16.1 1.0 OE1 A:GLN383 2.8 15.6 1.0 NH1 B:ARG93 2.8 18.5 1.0 HG21 B:THR60 2.9 19.3 1.0 HG3 A:GLU343 2.9 19.1 1.0 HH12 B:ARG93 3.1 22.2 1.0 CB B:THR60 3.2 15.0 1.0 HD3 B:ARG93 3.2 20.5 1.0 OG1 B:THR60 3.3 16.4 1.0 HA B:ASP62 3.4 19.2 1.0 CG2 B:THR60 3.5 16.1 1.0 C B:GLY95 3.5 14.7 1.0 H B:GLY95 3.6 17.4 1.0 HD2 B:ARG93 3.7 20.5 1.0 OE1 A:GLU343 3.7 18.7 1.0 CG A:GLU343 3.8 15.9 1.0 CD B:ARG93 3.8 17.0 1.0 CD A:GLN383 3.9 15.4 1.0 CZ B:ARG93 3.9 18.1 1.0 HB2 A:GLU343 4.0 18.0 1.0 HG22 B:THR60 4.0 19.3 1.0 CD A:GLU343 4.0 17.8 1.0 O B:ILE61 4.0 15.4 1.0 HE22 A:GLN383 4.0 19.5 1.0 HA2 B:GLY96 4.1 18.1 1.0 N B:GLY95 4.2 14.5 1.0 HG23 B:THR60 4.2 19.3 1.0 CA B:ASP62 4.3 16.0 1.0 HA3 B:GLY96 4.3 18.1 1.0 N B:GLY96 4.3 15.0 1.0 NE B:ARG93 4.3 17.6 1.0 CA B:GLY95 4.3 14.6 1.0 O B:ARG93 4.3 15.6 1.0 HG12 A:VAL384 4.3 20.3 1.0 C B:ILE61 4.4 14.8 1.0 NE2 A:GLN383 4.4 16.2 1.0 HA3 B:GLY95 4.4 17.6 1.0 CB A:GLU343 4.4 15.0 1.0 CA B:GLY96 4.5 15.1 1.0 N B:ASP62 4.5 15.2 1.0 HG2 A:GLU343 4.5 19.1 1.0 HB2 A:GLN383 4.5 17.3 1.0 OD2 B:ASP62 4.6 20.4 1.0 CA B:THR60 4.6 14.6 1.0 HA A:GLU343 4.6 17.5 1.0 HB2 B:ASP62 4.6 20.7 1.0 H B:ILE61 4.7 17.2 1.0 N B:ILE61 4.8 14.3 1.0 H B:ALA63 4.8 19.9 1.0 HB3 B:ARG93 4.8 19.2 1.0 HA B:THR60 4.8 17.6 1.0 HA A:GLN383 4.8 16.6 1.0 CB B:ASP62 4.9 17.2 1.0 CG B:ASP62 5.0 19.8 1.0 C B:THR60 5.0 14.6 1.0 H B:ASP62 5.0 18.2 1.0 H B:GLY96 5.0 18.1 1.0

C.Whitefield, N.Hong, J.A.Mitchell, C.J.Jackson. Computational Design and Experimental Characterisation of A Stable Human Heparanase Variant. Rsc Chem Biol V. 3 341 2022.
ISSN: ESSN 2633-0679
PubMed: 35382258
DOI: 10.1039/D1CB00239B