Sodium in PDB 6f9m: The Lipy/F-Motif in An Intracellular Subtilisin Protease Is Involved in Inhibition

The structure of The Lipy/F-Motif in An Intracellular Subtilisin Protease Is Involved in Inhibition, PDB code: 6f9m was solved by G.E.K.Bjerga, O.Larsen, H.Arsin, A.K.Williamson, A.Garcia-Moyano, I.Leiros, P.Puntervoll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.56 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.170, 85.180, 104.580, 90.00, 90.00, 90.00
R / Rfree (%)	13 / 15

The binding sites of Sodium atom in the The Lipy/F-Motif in An Intracellular Subtilisin Protease Is Involved in Inhibition (pdb code 6f9m). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The Lipy/F-Motif in An Intracellular Subtilisin Protease Is Involved in Inhibition, PDB code: 6f9m:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the The Lipy/F-Motif in An Intracellular Subtilisin Protease Is Involved in Inhibition


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Lipy/F-Motif in An Intracellular Subtilisin Protease Is Involved in Inhibition within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:47.4 occ:1.00 O A:SER97 2.4 21.7 1.0 HE A:ARG99 2.5 33.4 1.0 O A:VAL104 2.5 21.0 1.0 O A:HOH656 2.6 28.5 1.0 HG3 A:ARG99 3.0 35.4 1.0 OD2 A:ASP58 3.2 28.1 1.0 HA3 A:GLY103 3.2 37.1 1.0 NE A:ARG99 3.3 27.8 1.0 CG A:ASP58 3.3 26.1 1.0 HB2 A:ARG99 3.4 36.6 1.0 HA A:ASP58 3.4 20.9 1.0 HB3 A:ASP58 3.5 24.2 1.0 HH21 A:ARG99 3.5 31.7 1.0 C A:SER97 3.5 19.5 1.0 H A:ARG99 3.6 34.9 1.0 C A:VAL104 3.7 18.7 1.0 CG A:ARG99 3.7 29.5 1.0 HB2 A:SER97 3.8 21.6 1.0 OD1 A:ASP58 3.8 30.5 1.0 CB A:ASP58 3.8 20.2 1.0 H A:VAL104 3.8 25.8 1.0 N A:VAL104 3.8 21.5 1.0 C A:GLY103 3.9 26.0 1.0 HB1 A:ALA96 3.9 20.0 1.0 H A:SER97 3.9 21.0 1.0 CA A:GLY103 4.0 30.9 1.0 CB A:ARG99 4.0 30.5 1.0 O A:GLU102 4.0 47.9 1.0 CD A:ARG99 4.0 29.5 1.0 CA A:ASP58 4.1 17.4 1.0 N A:SER97 4.1 17.5 1.0 NH2 A:ARG99 4.1 26.4 1.0 HG22 A:VAL105 4.1 24.9 0.5 CZ A:ARG99 4.1 27.4 1.0 N A:ARG99 4.1 29.1 1.0 CA A:SER97 4.2 17.9 1.0 HA A:VAL105 4.3 21.9 0.5 HA A:VAL105 4.3 22.5 0.5 HD3 A:ARG99 4.3 35.4 1.0 HA A:LEU98 4.3 28.5 1.0 CA A:VAL104 4.4 19.9 1.0 O A:GLY103 4.5 28.0 1.0 CB A:SER97 4.5 18.0 1.0 HA2 A:GLY103 4.5 37.1 1.0 HG2 A:ARG99 4.6 35.4 1.0 N A:LEU98 4.6 20.0 1.0 C A:ALA96 4.6 16.9 1.0 CA A:ARG99 4.7 33.0 1.0 N A:VAL105 4.7 18.7 0.5 HB2 A:ASP58 4.7 24.2 1.0 N A:VAL105 4.7 19.0 0.5 O A:ASP58 4.7 18.0 1.0 HB3 A:ARG99 4.8 36.6 1.0 CA A:LEU98 4.8 23.8 1.0 CB A:ALA96 4.8 16.6 1.0 C A:LEU98 4.8 26.6 1.0 HD2 A:ARG99 4.9 35.4 1.0 HG23 A:VAL104 4.9 26.0 1.0 HH22 A:ARG99 4.9 31.7 1.0 HB A:VAL105 4.9 23.4 0.5 HG23 A:VAL105 4.9 24.9 0.5 CA A:VAL105 4.9 18.3 0.5 C A:GLU102 4.9 48.0 1.0 HG22 A:VAL104 4.9 26.0 1.0 HB3 A:SER97 4.9 21.6 1.0 CG2 A:VAL105 4.9 20.8 0.5 C A:ASP58 5.0 17.1 1.0 CA A:VAL105 5.0 18.8 0.5 N A:GLY103 5.0 39.1 1.0 HB3 A:ALA96 5.0 20.0 1.0

Sodium binding site 2 out of 2 in the The Lipy/F-Motif in An Intracellular Subtilisin Protease Is Involved in Inhibition


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Lipy/F-Motif in An Intracellular Subtilisin Protease Is Involved in Inhibition within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:37.9 occ:1.00 HE B:ARG99 2.1 28.0 1.0 OD1 B:ASP58 2.3 18.4 0.6 O B:SER97 2.6 17.6 1.0 O B:VAL104 2.8 17.6 0.5 HA B:ASP58 2.8 20.8 0.5 O B:VAL104 2.9 17.0 0.5 HG3 B:ARG99 2.9 27.5 1.0 HB3 B:ASP58 2.9 20.6 0.6 HA B:ASP58 2.9 19.7 0.6 NE B:ARG99 3.0 23.4 1.0 O B:HOH720 3.1 33.1 1.0 OD2 B:ASP58 3.1 20.5 0.5 CG B:ASP58 3.2 18.1 0.6 HH21 B:ARG99 3.2 28.6 1.0 CG B:ASP58 3.3 19.5 0.5 HB2 B:SER97 3.3 18.9 1.0 CB B:ASP58 3.3 17.1 0.6 H B:VAL104 3.4 23.8 0.5 HB3 B:ASP58 3.4 22.1 0.5 H B:VAL104 3.6 23.8 0.5 CA B:ASP58 3.6 16.4 0.6 C B:SER97 3.6 16.1 1.0 CA B:ASP58 3.6 17.3 0.5 CG B:ARG99 3.6 22.9 1.0 CB B:ASP58 3.6 18.4 0.5 HB2 B:ARG99 3.6 29.0 1.0 HA3 B:GLY103 3.7 32.7 1.0 H B:SER97 3.7 17.9 1.0 CD B:ARG99 3.7 23.7 1.0 HB1 B:ALA96 3.8 17.2 1.0 OD1 B:ASP58 3.8 20.1 0.5 NH2 B:ARG99 3.8 23.8 1.0 CZ B:ARG99 3.9 23.2 1.0 N B:SER97 3.9 14.9 1.0 HD3 B:ARG99 3.9 28.4 1.0 C B:VAL104 4.0 17.8 0.5 C B:VAL104 4.0 18.0 0.5 H B:ARG99 4.0 29.0 1.0 N B:VAL104 4.0 19.9 0.5 N B:VAL104 4.1 19.8 0.5 CA B:SER97 4.1 15.3 1.0 CB B:SER97 4.1 15.7 1.0 CB B:ARG99 4.1 24.2 1.0 O B:ASP58 4.2 16.8 0.6 O B:ASP58 4.2 17.4 0.5 HB2 B:ASP58 4.2 20.6 0.6 HG22 B:VAL105 4.3 21.5 0.5 OD2 B:ASP58 4.3 19.2 0.6 HA B:VAL105 4.4 20.6 0.5 C B:ASP58 4.4 16.2 0.6 C B:ASP58 4.4 16.8 0.5 HG2 B:ARG99 4.4 27.5 1.0 N B:ARG99 4.4 24.1 1.0 HA B:VAL105 4.4 19.9 0.5 CA B:GLY103 4.5 27.2 1.0 HB3 B:SER97 4.5 18.9 1.0 C B:ALA96 4.6 14.4 1.0 HB2 B:ASP58 4.6 22.1 0.5 H B:GLY103 4.6 38.8 1.0 HD2 B:ARG99 4.6 28.4 1.0 HA B:LEU98 4.6 23.8 1.0 N B:ASP58 4.7 15.9 0.6 N B:LEU98 4.7 16.8 1.0 HH22 B:ARG99 4.7 28.6 1.0 N B:ASP58 4.7 16.6 0.5 CA B:VAL104 4.7 18.5 0.5 CA B:VAL104 4.7 18.5 0.5 C B:GLY103 4.7 23.8 1.0 CB B:ALA96 4.7 14.3 1.0 HG23 B:VAL104 4.8 24.4 0.5 HG12 B:VAL104 4.8 24.1 0.5 HB3 B:ARG99 4.9 29.0 1.0 N B:VAL105 4.9 17.0 0.5 N B:GLY103 4.9 32.3 1.0 CA B:ARG99 5.0 25.1 1.0 N B:VAL105 5.0 16.6 0.5 HB3 B:ALA96 5.0 17.2 1.0

G.E.K.Bjerga, O.Larsen, A.Williamson, A.Garcia-Moyano, I.Leiros, P.Puntervoll. Mutational Analysis of the Pro-Peptide of A Marine Intracellular Subtilisin Protease Supports Its Role in Inhibition. Proteins V. 86 965 2018.
ISSN: ESSN 1097-0134
PubMed: 29907987
DOI: 10.1002/PROT.25528