Sodium in PDB 3b3t: Crystal Structure of the D118N Mutant of the Aminopeptidase From Vibrio Proteolyticus

All present enzymatic activity of Crystal Structure of the D118N Mutant of the Aminopeptidase From Vibrio Proteolyticus:
3.4.11.10;

The structure of Crystal Structure of the D118N Mutant of the Aminopeptidase From Vibrio Proteolyticus, PDB code: 3b3t was solved by N.J.Ataie, Q.Q.Hoang, M.P.D.Zahniser, A.Milne, G.A.Petsko, D.Ringe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.00 / 1.17
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	109.294, 109.294, 91.009, 90.00, 90.00, 120.00
R / Rfree (%)	14.2 / 16.1

The structure of Crystal Structure of the D118N Mutant of the Aminopeptidase From Vibrio Proteolyticus also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of the D118N Mutant of the Aminopeptidase From Vibrio Proteolyticus (pdb code 3b3t). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the D118N Mutant of the Aminopeptidase From Vibrio Proteolyticus, PDB code: 3b3t:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the D118N Mutant of the Aminopeptidase From Vibrio Proteolyticus


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 the D118N Mutant of the Aminopeptidase From Vibrio Proteolyticus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na294 b:21.9 occ:1.00 O A:HOH385 2.3 22.3 1.0 O A:HOH540 2.4 27.3 1.0 O A:HOH506 2.4 21.8 1.0 OD1 A:ASN74 2.4 19.5 1.0 O A:HOH569 2.5 29.4 1.0 CG A:ASN74 3.4 18.3 1.0 O A:HOH478 4.0 30.6 1.0 O A:HOH441 4.1 20.7 1.0 CB A:ASN74 4.2 16.3 1.0 ND2 A:ASN74 4.2 19.7 1.0 O A:HOH454 4.3 23.5 1.0 CA A:ASN74 4.3 15.4 1.0 O A:HOH405 4.5 34.2 1.0 O A:HOH363 4.5 21.6 1.0 O A:HOH417 4.6 20.1 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the D118N Mutant of the Aminopeptidase From Vibrio Proteolyticus


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 the D118N Mutant of the Aminopeptidase From Vibrio Proteolyticus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na295 b:26.7 occ:1.00 CG A:GLN54 3.8 15.9 1.0 CA A:ALA55 3.9 14.5 1.0 CB A:ALA58 4.0 20.3 1.0 O A:GLN54 4.1 15.6 1.0 N A:ALA55 4.1 13.8 1.0 C A:GLN54 4.2 13.9 1.0 NE2 A:GLN54 4.4 25.8 1.0 CB A:ALA55 4.5 15.9 1.0 O A:HOH479 4.5 28.9 1.0 CB A:GLN54 4.7 14.5 1.0 CD A:GLN54 4.7 20.1 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the D118N Mutant of the Aminopeptidase From Vibrio Proteolyticus


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 the D118N Mutant of the Aminopeptidase From Vibrio Proteolyticus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na296 b:30.4 occ:1.00 N A:THR258 3.3 13.4 0.5 N A:THR258 3.3 12.7 0.5 CG2 A:THR258 3.3 12.4 0.5 O A:HOH558 3.3 32.2 1.0 OG1 A:THR258 3.7 14.1 0.5 CA A:THR257 3.7 11.8 1.0 O A:HOH424 3.9 21.8 0.5 CB A:THR258 3.9 12.7 0.5 CB A:THR257 4.0 11.9 1.0 C A:THR257 4.0 11.8 1.0 CB A:THR258 4.0 14.6 0.5 CA A:THR258 4.2 12.1 0.5 CD1 A:ILE102 4.2 18.5 1.0 CG2 A:THR258 4.2 14.2 0.5 CA A:THR258 4.2 13.5 0.5 CG2 A:ILE102 4.3 14.9 1.0 CB A:ILE102 4.4 14.7 1.0 CG2 A:THR257 4.7 13.2 1.0 O A:HIS256 4.8 12.8 1.0 CG1 A:ILE102 4.9 16.5 1.0 N A:THR257 5.0 10.5 1.0

N.J.Ataie, Q.Q.Hoang, M.P.Zahniser, Y.Tu, A.Milne, G.A.Petsko, D.Ringe. Zinc Coordination Geometry and Ligand Binding Affinity: the Structural and Kinetic Analysis of the Second-Shell Serine 228 Residue and the Methionine 180 Residue of the Aminopeptidase From Vibrio Proteolyticus. Biochemistry V. 47 7673 2008.
ISSN: ISSN 0006-2960
PubMed: 18576673
DOI: 10.1021/BI702188E