Sodium in PDB 6xwd: 14-3-3 Sigma Bound to Canonical Mono-Phosphorylated Aminopeptidase N (Apn, CD13) Binding Motif

The structure of 14-3-3 Sigma Bound to Canonical Mono-Phosphorylated Aminopeptidase N (Apn, CD13) Binding Motif, PDB code: 6xwd was solved by S.Kiehstaller, S.Hennig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.37 / 1.60
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.000, 111.600, 62.400, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 19.6

The structure of 14-3-3 Sigma Bound to Canonical Mono-Phosphorylated Aminopeptidase N (Apn, CD13) Binding Motif also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Calcium	(Ca)	1 atom

The binding sites of Sodium atom in the 14-3-3 Sigma Bound to Canonical Mono-Phosphorylated Aminopeptidase N (Apn, CD13) Binding Motif (pdb code 6xwd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the 14-3-3 Sigma Bound to Canonical Mono-Phosphorylated Aminopeptidase N (Apn, CD13) Binding Motif, PDB code: 6xwd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the 14-3-3 Sigma Bound to Canonical Mono-Phosphorylated Aminopeptidase N (Apn, CD13) Binding Motif


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 14-3-3 Sigma Bound to Canonical Mono-Phosphorylated Aminopeptidase N (Apn, CD13) Binding Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:32.5 occ:1.00 O A:LYS77 2.4 35.8 1.0 OE1 A:GLU80 2.4 19.5 1.0 O A:HOH635 2.5 38.4 1.0 OE2 A:GLU80 2.8 24.5 1.0 CD A:GLU80 2.8 23.8 1.0 O A:HOH514 2.9 28.8 1.0 C A:LYS77 3.5 34.1 1.0 CA A:GLY78 4.1 24.4 1.0 CG A:GLU80 4.2 18.9 1.0 N A:GLY78 4.3 28.3 1.0 CA A:LYS77 4.5 31.9 1.0 CB A:GLU80 4.7 16.4 1.0 C A:GLY78 4.8 20.3 1.0 CB A:LYS77 4.9 36.1 1.0 O A:HOH684 4.9 45.5 1.0 CD A:PRO79 4.9 20.1 1.0

Sodium binding site 2 out of 2 in the 14-3-3 Sigma Bound to Canonical Mono-Phosphorylated Aminopeptidase N (Apn, CD13) Binding Motif


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 14-3-3 Sigma Bound to Canonical Mono-Phosphorylated Aminopeptidase N (Apn, CD13) Binding Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:20.9 occ:1.00 O A:GLU161 2.3 21.6 1.0 O A:HOH542 2.4 35.7 1.0 O A:HOH617 2.5 35.4 1.0 C A:GLU161 3.5 18.6 1.0 N A:MET162 4.3 18.3 1.0 CA A:MET162 4.4 18.9 0.6 CA A:GLU161 4.4 17.9 1.0 OE2 A:GLU115 4.4 43.2 1.0 CA A:MET162 4.5 19.3 0.4 CB A:GLU161 4.8 21.1 1.0 OE1 A:GLU161 4.8 36.2 1.0 CD A:PRO163 4.9 22.2 1.0

S.Kiehstaller, C.Ottmann, S.Hennig. Mmp Activation Associated Aminopeptidase N Reveals A Bivalent 14-3-3 Binding Motif. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 33109610
DOI: 10.1074/JBC.RA120.014708