Sodium in PDB 5z48: Crystal Structure of Pyrrolidone Carboxylate Peptidase I From Deinococcus Radiodurans R1 Bound to Pyroglutamate

All present enzymatic activity of Crystal Structure of Pyrrolidone Carboxylate Peptidase I From Deinococcus Radiodurans R1 Bound to Pyroglutamate:
3.4.19.3;

The structure of Crystal Structure of Pyrrolidone Carboxylate Peptidase I From Deinococcus Radiodurans R1 Bound to Pyroglutamate, PDB code: 5z48 was solved by R.Agrawal, A.Kumar, A.Kumar, R.D.Makde, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.22 / 1.55
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	89.069, 46.918, 105.584, 90.00, 105.51, 90.00
R / Rfree (%)	15.9 / 18.6

The binding sites of Sodium atom in the Crystal Structure of Pyrrolidone Carboxylate Peptidase I From Deinococcus Radiodurans R1 Bound to Pyroglutamate (pdb code 5z48). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Pyrrolidone Carboxylate Peptidase I From Deinococcus Radiodurans R1 Bound to Pyroglutamate, PDB code: 5z48:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Pyrrolidone Carboxylate Peptidase I From Deinococcus Radiodurans R1 Bound to Pyroglutamate


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 Pyrrolidone Carboxylate Peptidase I From Deinococcus Radiodurans R1 Bound to Pyroglutamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:20.5 occ:1.00 O A:HOH550 2.2 28.9 1.0 O A:HOH436 2.5 20.6 1.0 O A:HOH559 2.5 30.7 1.0 O A:HOH539 2.5 17.2 1.0 O A:MET1 2.5 20.6 1.0 O A:GLY-1 2.6 24.1 1.0 C A:MET1 3.4 20.6 1.0 C A:GLY-1 3.6 27.4 1.0 CA A:PRO2 3.9 19.2 1.0 N A:GLY-1 3.9 32.1 1.0 O A:HOH516 4.0 27.4 1.0 N A:PRO2 4.0 20.2 1.0 O A:ASP62 4.1 18.7 1.0 N A:MET1 4.1 23.4 1.0 C A:SER0 4.2 26.1 1.0 O A:HOH592 4.2 30.0 1.0 N A:THR3 4.2 13.5 1.0 CA A:GLY-1 4.3 28.4 1.0 OG1 A:THR3 4.4 18.6 1.0 CA A:MET1 4.4 23.7 1.0 C A:PRO2 4.4 18.1 1.0 O A:SER0 4.4 28.9 1.0 N A:SER0 4.5 24.5 1.0 O A:HOH511 4.6 21.7 1.0 CA A:SER0 4.7 25.2 1.0 CB A:THR3 4.9 15.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Pyrrolidone Carboxylate Peptidase I From Deinococcus Radiodurans R1 Bound to Pyroglutamate


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 Pyrrolidone Carboxylate Peptidase I From Deinococcus Radiodurans R1 Bound to Pyroglutamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:34.1 occ:1.00 OD2 A:ASP89 2.7 22.7 1.0 O B:HOH447 2.8 23.2 0.4 NH2 B:ARG120 2.9 14.6 1.0 NE2 A:GLN91 3.0 40.4 1.0 O B:HOH470 3.3 29.1 1.0 NH1 B:ARG120 3.4 16.7 1.0 NE A:ARG101 3.5 26.8 1.0 CZ B:ARG120 3.6 15.7 1.0 CG A:ASP89 3.6 15.1 1.0 NH2 A:ARG101 3.6 26.9 1.0 OD1 A:ASP89 3.7 14.6 1.0 CZ A:ARG101 3.8 28.2 1.0 O B:HOH504 4.1 12.9 1.0 CD A:GLN91 4.1 37.9 1.0 O A:HOH415 4.2 30.3 1.0 CD A:ARG101 4.4 25.8 1.0 OE1 A:GLN91 4.5 42.8 1.0 O B:HOH447 4.5 14.7 0.6 NH1 A:ARG101 4.8 30.5 1.0 OD1 B:ASP134 4.8 18.2 1.0 NE B:ARG120 4.9 15.2 1.0 NH2 B:ARG82 4.9 12.5 1.0 CB A:ASP89 5.0 12.2 1.0

R.Agrawal, R.Singh, A.Kumar, A.Kumar, R.D.Makde. Crystal Structures of Pyrrolidone-Carboxylate Peptidase I From Deinococcus Radiodurans Reveal the Mechanism of L-Pyroglutamate Recognition. Acta Crystallogr D Struct V. 75 308 2019BIOL.
ISSN: ISSN 2059-7983
PubMed: 30950401
DOI: 10.1107/S2059798319000676