Sodium in PDB 8jfs: Phosphate Bound Acylphosphatase From Deinococcus Radiodurans at 1 Angstrom Resolution

All present enzymatic activity of Phosphate Bound Acylphosphatase From Deinococcus Radiodurans at 1 Angstrom Resolution:
3.6.1.7;

The structure of Phosphate Bound Acylphosphatase From Deinococcus Radiodurans at 1 Angstrom Resolution, PDB code: 8jfs was solved by Z.Khakerwala, A.Kumar, R.D.Makde, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.00 / 1.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	33.003, 28.472, 83.604, 90, 90.43, 90
R / Rfree (%)	19.3 / 20.5

The binding sites of Sodium atom in the Phosphate Bound Acylphosphatase From Deinococcus Radiodurans at 1 Angstrom Resolution (pdb code 8jfs). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Phosphate Bound Acylphosphatase From Deinococcus Radiodurans at 1 Angstrom Resolution, PDB code: 8jfs:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Phosphate Bound Acylphosphatase From Deinococcus Radiodurans at 1 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Phosphate Bound Acylphosphatase From Deinococcus Radiodurans at 1 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:32.7 occ:1.00 NH1 A:ARG17 2.2 13.4 1.0 O A:HOH246 2.3 17.6 1.0 O A:TYR87 2.5 12.3 1.0 CB A:ASN35 2.7 8.8 1.0 N A:ASN35 2.8 6.8 1.0 OXT A:TYR87 3.0 17.7 1.0 C A:TYR87 3.1 12.3 1.0 CA A:ASN35 3.2 7.1 1.0 CG A:ASN35 3.3 7.7 1.0 CZ A:ARG17 3.3 11.8 1.0 O A:HOH285 3.5 28.8 1.0 ND2 A:ASN35 3.6 10.0 1.0 CD A:ARG17 3.8 8.7 1.0 O A:ASN35 3.8 9.9 1.0 O A:HOH271 3.8 17.7 1.0 NE A:ARG17 3.9 9.6 1.0 C A:GLU34 3.9 6.8 1.0 OD1 A:ASN35 4.0 8.4 1.0 C A:ASN35 4.0 7.6 1.0 NH2 A:ARG17 4.2 15.2 1.0 CA A:GLU34 4.3 8.9 1.0 CA A:TYR87 4.6 11.0 1.0 CG A:GLU34 4.7 13.4 1.0 O A:HOH289 4.8 20.1 1.0

Sodium binding site 2 out of 3 in the Phosphate Bound Acylphosphatase From Deinococcus Radiodurans at 1 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Phosphate Bound Acylphosphatase From Deinococcus Radiodurans at 1 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:14.7 occ:1.00 O2 A:PO4101 2.7 7.8 1.0 O A:HOH301 2.8 14.8 0.6 O A:HOH301 2.9 19.4 0.4 N A:LEU18 3.0 7.3 1.0 CA A:GLY15 3.3 9.3 1.0 C A:GLY15 3.3 7.8 1.0 N A:ARG17 3.3 6.6 1.0 CG A:LEU18 3.5 12.0 1.0 O A:GLY15 3.6 9.1 1.0 CB A:ARG17 3.6 6.9 1.0 CB A:LEU18 3.6 9.7 1.0 N A:TYR16 3.7 7.1 1.0 CA A:ARG17 3.7 6.6 1.0 CD1 A:LEU18 3.8 14.8 1.0 C A:ARG17 3.8 6.6 1.0 CA A:LEU18 3.9 8.6 1.0 O A:HOH253 4.0 15.5 1.0 NE A:ARG17 4.1 9.6 1.0 N A:GLY15 4.1 8.7 1.0 C A:TYR16 4.2 6.7 1.0 P A:PO4101 4.2 7.3 1.0 CG A:ARG17 4.5 8.6 1.0 CA A:TYR16 4.6 6.4 1.0 NH2 A:ARG17 4.6 15.2 1.0 O3 A:PO4101 4.6 7.1 1.0 CD1 A:ILE86 4.8 14.4 0.7 CZ A:ARG17 4.8 11.8 1.0 CD2 A:LEU18 4.8 14.1 1.0 O1 A:PO4101 4.9 7.7 1.0 CD A:ARG17 4.9 8.7 1.0 O A:ARG17 5.0 7.0 1.0

Sodium binding site 3 out of 3 in the Phosphate Bound Acylphosphatase From Deinococcus Radiodurans at 1 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Phosphate Bound Acylphosphatase From Deinococcus Radiodurans at 1 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na103 b:14.7 occ:1.00 O4 B:PO4101 2.8 7.3 0.9 O B:HOH282 2.8 15.8 0.4 N B:LEU18 2.9 7.4 1.0 C B:GLY15 3.3 7.3 1.0 CA B:GLY15 3.3 8.6 1.0 N B:ARG17 3.3 6.9 0.5 N B:ARG17 3.3 6.8 0.5 CG B:LEU18 3.4 11.6 1.0 CB B:LEU18 3.6 8.5 1.0 CB B:ARG17 3.6 7.8 0.5 O B:GLY15 3.6 7.9 1.0 CB B:ARG17 3.7 7.8 0.5 N B:TYR16 3.7 6.9 1.0 CA B:ARG17 3.7 7.4 0.5 CD1 B:LEU18 3.7 12.8 1.0 CA B:ARG17 3.7 7.4 0.5 C B:ARG17 3.7 7.4 0.5 C B:ARG17 3.8 7.4 0.5 CA B:LEU18 3.8 8.0 1.0 NE B:ARG17 4.0 9.8 0.5 N B:GLY15 4.1 8.2 1.0 C B:TYR16 4.1 6.3 1.0 O B:HOH201 4.2 22.4 1.0 NH2 B:ARG17 4.2 12.3 0.5 P B:PO4101 4.2 6.5 0.9 NE B:ARG17 4.2 10.3 0.5 CG B:ARG17 4.5 7.7 0.5 CZ B:ARG17 4.5 12.5 0.5 CA B:TYR16 4.5 7.1 1.0 CG B:ARG17 4.6 7.7 0.5 O1 B:PO4101 4.7 7.4 0.9 NH2 B:ARG17 4.8 13.6 0.5 CD2 B:LEU18 4.8 12.3 1.0 CD1 B:ILE86 4.9 15.2 0.6 CD B:ARG17 4.9 9.2 0.5 O B:ARG17 4.9 7.8 0.5 O2 B:PO4101 4.9 8.4 0.9 O B:ARG17 4.9 7.6 0.5 CZ B:ARG17 5.0 12.2 0.5 O B:TYR16 5.0 7.5 1.0 CD B:ARG17 5.0 8.9 0.5

Z.Khakerwala, A.Kumar, R.D.Makde. Crystal Structure of Phosphate Bound Acyl Phosphatase Mini-Enzyme From Deinococcus Radiodurans at 1A Resolution. Biochem.Biophys.Res.Commun. 2023.
ISSN: ESSN 1090-2104
DOI: 10.1016/J.BBRC.2023.06.003