Sodium in PDB 3o4h: Structure and Catalysis of Acylaminoacyl Peptidase

All present enzymatic activity of Structure and Catalysis of Acylaminoacyl Peptidase:
3.4.19.1;

The structure of Structure and Catalysis of Acylaminoacyl Peptidase, PDB code: 3o4h was solved by V.Harmat, K.Domokos, D.K.Menyhard, A.Pallo, Z.Szeltner, I.Szamosi, T.Beke-Somfai, G.Naray-Szabo, L.Polgar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.62 / 1.82
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	71.405, 97.979, 98.797, 105.69, 103.52, 100.36
R / Rfree (%)	20.3 / 23.4

The binding sites of Sodium atom in the Structure and Catalysis of Acylaminoacyl Peptidase (pdb code 3o4h). 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 and Catalysis of Acylaminoacyl Peptidase, PDB code: 3o4h:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure and Catalysis of Acylaminoacyl Peptidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure and Catalysis of Acylaminoacyl Peptidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na583 b:43.4 occ:1.00 O B:HOH690 2.3 45.2 1.0 O B:HOH907 2.4 42.5 1.0 O B:HOH655 2.4 41.7 1.0 OD1 B:ASP374 2.5 45.9 1.0 O B:HOH687 2.6 41.0 1.0 O B:HOH717 2.8 42.1 1.0 CG B:ASP374 3.5 44.0 1.0 CA B:ASP374 3.8 42.0 1.0 CB B:ASP374 4.0 43.1 1.0 O B:HOH606 4.2 38.5 1.0 N B:SER375 4.3 41.3 1.0 O B:SER375 4.4 39.6 1.0 OD2 B:ASP374 4.4 47.8 1.0 CB B:ASP379 4.4 38.1 1.0 OD2 B:ASP379 4.4 43.0 1.0 SD B:MET394 4.5 40.1 1.0 O B:HOH672 4.5 47.2 1.0 C B:ASP374 4.5 42.8 1.0 O B:GLU373 4.6 41.0 1.0 CG B:ASP379 4.6 39.5 1.0 O B:HOH633 4.9 47.0 1.0 N B:ASP374 4.9 42.4 1.0 CD2 B:LEU302 4.9 40.4 1.0

Sodium binding site 2 out of 2 in the Structure and Catalysis of Acylaminoacyl Peptidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure and Catalysis of Acylaminoacyl Peptidase within 5.0Å range: probe atom residue distance (Å) B Occ D:Na583 b:39.3 occ:1.00 O D:HOH667 2.2 38.1 1.0 O D:HOH691 2.3 42.4 1.0 O D:HOH587 2.5 32.8 1.0 OD1 D:ASP374 2.6 35.0 1.0 O D:HOH604 2.7 37.3 1.0 O D:HOH608 2.7 31.9 1.0 CG D:ASP374 3.6 32.1 1.0 CA D:ASP374 3.9 29.5 1.0 O D:HOH688 3.9 43.1 1.0 CB D:ASP374 4.1 29.0 1.0 O D:HOH597 4.3 28.3 1.0 CB D:ASP379 4.3 30.2 1.0 O D:HOH666 4.3 47.1 1.0 SD D:MET394 4.4 29.0 1.0 N D:SER375 4.4 29.7 1.0 OD2 D:ASP379 4.5 34.5 1.0 O D:SER375 4.5 28.6 1.0 CG D:ASP379 4.5 32.4 1.0 OD2 D:ASP374 4.6 34.6 1.0 C D:ASP374 4.6 29.9 1.0 O D:GLU373 4.7 29.9 1.0 CD2 D:LEU302 4.9 34.5 1.0 N D:ASP374 5.0 29.6 1.0 O D:SER377 5.0 30.0 1.0

V.Harmat, K.Domokos, D.K.Menyhard, A.Pallo, Z.Szeltner, I.Szamosi, T.Beke-Somfai, G.Naray-Szabo, L.Polgar. Structure and Catalysis of Acylaminoacyl Peptidase: Closed and Open Subunits of A Dimer Oligopeptidase. J.Biol.Chem. V. 286 1987 2011.
ISSN: ISSN 0021-9258
PubMed: 21084296
DOI: 10.1074/JBC.M110.169862