Sodium in PDB 4bym: Structure of PHAZ7 Phb Depolymerase Y105E Mutant

All present enzymatic activity of Structure of PHAZ7 Phb Depolymerase Y105E Mutant:
3.1.1.75;

The structure of Structure of PHAZ7 Phb Depolymerase Y105E Mutant, PDB code: 4bym was solved by S.Hermawan, B.Subedi, A.C.Papageorgiou, D.Jendrossek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.843 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.560, 200.340, 44.520, 90.00, 114.57, 90.00
R / Rfree (%)	14.84 / 17.43

The structure of Structure of PHAZ7 Phb Depolymerase Y105E Mutant also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Structure of PHAZ7 Phb Depolymerase Y105E Mutant (pdb code 4bym). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of PHAZ7 Phb Depolymerase Y105E Mutant, PDB code: 4bym:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of PHAZ7 Phb Depolymerase Y105E Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of PHAZ7 Phb Depolymerase Y105E Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1343 b:46.9 occ:1.00 O A:HOH2329 2.0 37.4 1.0 O A:HOH2574 2.5 36.8 1.0 NZ A:LYS122 2.7 13.9 1.0 O A:HOH2311 2.9 41.2 1.0 O A:SER128 3.0 10.5 1.0 CE A:LYS122 3.1 13.9 1.0 C A:SER128 3.9 10.7 1.0 CA A:SER128 4.0 11.2 1.0 CB A:SER128 4.1 13.6 1.0 OG A:SER154 4.2 13.9 1.0 CD A:LYS122 4.5 9.8 1.0 O A:HOH2162 4.5 27.0 1.0 O A:HOH2353 4.9 19.1 1.0

Sodium binding site 2 out of 2 in the Structure of PHAZ7 Phb Depolymerase Y105E Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of PHAZ7 Phb Depolymerase Y105E Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1344 b:31.6 occ:1.00 O B:HOH2418 2.7 20.1 1.0 CE1 B:TYR169 2.7 17.4 1.0 O B:HOH2416 2.9 18.2 1.0 CD1 B:TYR169 3.0 16.5 1.0 O B:GLY167 3.1 11.2 1.0 CA B:ALA258 3.3 8.0 1.0 CB B:ALA258 3.3 11.6 1.0 O B:ARG166 3.4 8.2 1.0 CZ B:TYR169 3.5 15.8 1.0 N B:ALA258 3.8 8.8 1.0 CB B:ARG166 3.8 6.9 1.0 C B:ARG166 3.8 8.6 1.0 CG B:TYR169 3.9 12.5 1.0 C B:GLY167 3.9 12.0 1.0 OH B:TYR169 4.0 18.9 1.0 CE2 B:TYR169 4.2 11.6 1.0 O B:GLY254 4.2 10.9 1.0 O B:CYS255 4.3 9.2 1.0 CA B:ARG166 4.4 5.7 1.0 CD2 B:TYR169 4.4 12.6 1.0 N B:TYR169 4.4 9.9 1.0 N B:GLY167 4.5 7.6 1.0 C B:SER257 4.5 8.5 1.0 C B:ALA258 4.5 4.6 1.0 CA B:CYS255 4.5 9.5 1.0 CA B:GLY167 4.6 7.0 1.0 N B:LEU168 4.6 8.4 1.0 O B:HOH2411 4.7 12.1 1.0 CA B:LEU168 4.8 8.2 1.0 C B:CYS255 4.8 10.3 1.0 O B:ALA258 4.8 5.4 1.0 CB B:TYR169 4.8 11.3 1.0 N B:ARG166 4.9 6.9 1.0 O B:SER257 4.9 8.8 1.0 CG B:ARG166 4.9 5.7 1.0 C B:LEU168 4.9 10.8 1.0

D.Jendrossek, S.Hermawan, B.Subedi, A.C.Papageorgiou. Biochemical Analysis and Structure Determination of Paucimonas Lemoignei Poly(3-Hydroxybutyrate) (Phb) Depolymerase PHAZ7 Muteins Reveal the Phb Binding Site and Details of Substrate-Enzyme Interactions. Mol.Microbiol. V. 90 649 2013.
ISSN: ISSN 0950-382X
PubMed: 24007310
DOI: 10.1111/MMI.12391