Sodium in PDB 8ot5: Crystal Structure of the Titin Domain FN3-85

All present enzymatic activity of Crystal Structure of the Titin Domain FN3-85:
2.7.11.1;

The structure of Crystal Structure of the Titin Domain FN3-85, PDB code: 8ot5 was solved by R.Nikoopour, M.Rees, M.Gautel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.19 / 1.56
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.358, 99.829, 62.239, 90, 105.55, 90
R / Rfree (%)	16.3 / 19.1

The structure of Crystal Structure of the Titin Domain FN3-85 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of the Titin Domain FN3-85 (pdb code 8ot5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the Titin Domain FN3-85, PDB code: 8ot5:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the Titin Domain FN3-85


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 Titin Domain FN3-85 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:20.6 occ:1.00 H A:ALA82 2.0 14.5 1.0 HD3 A:PRO9 2.7 16.7 1.0 O A:LYS90 2.7 14.5 1.0 O A:GLY7 2.8 15.6 1.0 HB3 A:ALA82 2.8 17.9 1.0 N A:ALA82 2.9 12.1 1.0 HA3 A:GLY89 3.0 16.8 1.0 HA A:PRO8 3.0 15.8 1.0 H A:GLY89 3.2 15.5 1.0 C A:GLY89 3.2 16.6 1.0 HG2 A:PRO6 3.2 19.8 1.0 HA A:SER81 3.3 12.4 1.0 N A:LYS90 3.4 14.1 1.0 CA A:GLY89 3.4 14.0 1.0 HB3 A:SER81 3.5 17.3 1.0 O A:ALA82 3.5 14.1 1.0 H A:LYS90 3.5 17.0 1.0 CB A:ALA82 3.5 14.9 1.0 C A:GLY7 3.6 14.0 1.0 O A:GLY89 3.6 14.4 1.0 CA A:ALA82 3.6 13.1 1.0 CD A:PRO9 3.6 13.9 1.0 N A:GLY89 3.7 12.9 1.0 C A:LYS90 3.7 14.9 1.0 HB2 A:ALA82 3.8 17.9 1.0 C A:SER81 3.8 11.7 1.0 CA A:PRO8 3.9 13.2 1.0 CA A:SER81 3.9 10.4 1.0 O A:PRO6 3.9 15.6 1.0 C A:ALA82 4.0 13.6 1.0 HB2 A:PRO6 4.1 22.2 1.0 N A:PRO8 4.1 14.2 1.0 HD2 A:PRO9 4.1 16.7 1.0 CB A:SER81 4.1 14.4 1.0 CA A:LYS90 4.1 16.0 1.0 HG3 A:PRO9 4.1 15.8 1.0 CG A:PRO6 4.2 16.5 1.0 C A:PRO6 4.3 13.7 1.0 HA2 A:GLY89 4.4 16.8 1.0 HB1 A:ALA82 4.4 17.9 1.0 CG A:PRO9 4.4 13.2 1.0 N A:PRO9 4.5 14.2 1.0 HA A:ALA82 4.5 15.7 1.0 CB A:PRO6 4.6 18.5 1.0 C A:PRO8 4.6 13.2 1.0 HG2 A:PRO9 4.6 15.8 1.0 HG3 A:PRO6 4.6 19.8 1.0 CA A:GLY7 4.6 17.0 1.0 HA A:PRO91 4.7 17.8 1.0 HG23 A:ILE88 4.7 16.8 1.0 HB2 A:LYS90 4.7 18.3 1.0 N A:GLY7 4.7 15.3 1.0 HG3 A:PRO29 4.8 17.4 1.0 HA2 A:GLY7 4.8 20.4 1.0 N A:PRO91 4.8 13.7 1.0 HA A:LYS90 4.8 19.2 1.0 HB2 A:SER81 4.8 17.3 1.0 HB3 A:PRO8 4.8 19.0 1.0 O A:HOH310 4.9 17.2 1.0 OG A:SER81 4.9 16.6 1.0 HD2 A:PRO6 5.0 19.6 1.0 C A:ILE88 5.0 14.6 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the Titin Domain FN3-85


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 Titin Domain FN3-85 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:23.0 occ:0.77 HD23 C:LEU23 1.9 33.0 0.5 HB3 B:HIS27 2.4 20.7 1.0 HD21 C:LEU23 2.5 33.0 0.5 HD13 C:LEU23 2.5 30.1 0.5 OG1 C:THR15 2.6 16.5 1.0 CD2 C:LEU23 2.6 27.5 0.5 HG2 B:GLU28 2.7 35.7 1.0 O B:GLU28 2.8 17.1 1.0 HB C:THR15 3.1 19.0 1.0 O B:HOH421 3.2 27.5 1.0 H B:GLU28 3.2 20.2 1.0 HD22 C:LEU23 3.2 33.0 0.5 HD22 C:LEU23 3.3 19.1 0.5 HE21 C:GLN25 3.3 28.5 1.0 HB2 C:SER16 3.4 18.5 1.0 CB C:THR15 3.4 15.8 1.0 CB B:HIS27 3.4 17.2 1.0 HB3 C:LEU23 3.4 19.1 0.5 CD1 C:LEU23 3.4 25.1 0.5 N B:GLU28 3.5 16.8 1.0 CG B:GLU28 3.5 29.8 1.0 HG3 B:GLU28 3.5 35.7 1.0 HB3 C:LEU23 3.5 19.1 0.5 HB3 C:SER16 3.6 18.5 1.0 CG C:LEU23 3.7 22.6 0.5 HG C:LEU23 3.7 27.1 0.5 C B:GLU28 3.7 16.1 1.0 HE22 C:GLN25 3.8 28.5 1.0 HB2 B:HIS27 3.8 20.7 1.0 NE2 C:GLN25 3.8 23.8 1.0 HD11 C:LEU23 3.9 30.1 0.5 CB C:SER16 3.9 15.4 1.0 C B:HIS27 3.9 13.9 1.0 HD12 C:LEU23 4.0 30.1 0.5 C C:THR15 4.0 14.6 1.0 CG C:LEU23 4.0 15.1 0.5 CD2 C:LEU23 4.0 15.9 0.5 CA B:GLU28 4.0 18.1 1.0 CB C:LEU23 4.0 15.9 0.5 CB C:LEU23 4.1 15.9 0.5 CA B:HIS27 4.1 16.0 1.0 O C:THR15 4.1 18.0 1.0 HB2 C:LEU23 4.2 19.1 0.5 HA B:HIS27 4.2 19.2 1.0 CG B:HIS27 4.2 21.9 1.0 N C:SER16 4.2 14.5 1.0 CA C:THR15 4.3 14.2 1.0 HB2 C:LEU23 4.3 19.1 0.5 CB B:GLU28 4.3 21.8 1.0 HD21 C:LEU23 4.3 19.1 0.5 H C:SER16 4.5 17.4 1.0 HG21 C:THR15 4.5 21.9 1.0 HD2 B:HIS27 4.5 31.7 1.0 CG2 C:THR15 4.6 18.2 1.0 CD B:GLU28 4.6 53.5 1.0 OE2 B:GLU28 4.6 44.1 1.0 CD2 B:HIS27 4.7 26.4 1.0 H C:THR15 4.7 16.6 1.0 CA C:SER16 4.7 14.2 1.0 HB3 B:GLU28 4.7 26.1 1.0 O B:HIS27 4.7 15.2 1.0 HD23 C:LEU23 4.8 19.1 0.5 HA B:GLU28 4.9 21.7 1.0 HG C:LEU23 4.9 18.2 0.5 N B:PRO29 5.0 15.5 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the Titin Domain FN3-85


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 Titin Domain FN3-85 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na201 b:22.0 occ:0.98 H C:ALA82 2.0 16.3 1.0 HD3 C:PRO9 2.6 19.3 1.0 O C:LYS90 2.6 16.9 1.0 O C:GLY7 2.8 16.8 1.0 N C:ALA82 2.9 13.7 1.0 HA3 C:GLY89 2.9 23.1 1.0 HB3 C:ALA82 3.0 16.5 1.0 HA C:PRO8 3.1 19.9 1.0 C C:GLY89 3.2 17.2 1.0 HA C:SER81 3.3 16.2 1.0 H C:GLY89 3.3 21.9 1.0 CA C:GLY89 3.4 19.2 1.0 HG2 C:PRO6 3.4 35.5 1.0 N C:LYS90 3.4 19.9 1.0 HB3 C:SER81 3.5 18.6 1.0 O C:ALA82 3.5 17.7 1.0 CD C:PRO9 3.6 16.1 1.0 H C:LYS90 3.6 23.9 1.0 C C:GLY7 3.6 17.2 1.0 O C:GLY89 3.6 17.8 1.0 CB C:ALA82 3.6 13.8 1.0 CA C:ALA82 3.6 13.8 1.0 C C:LYS90 3.7 16.6 1.0 HB2 C:PRO6 3.7 22.3 1.0 N C:GLY89 3.8 18.3 1.0 C C:SER81 3.8 14.7 1.0 O C:PRO6 3.8 20.9 1.0 HB2 C:ALA82 3.9 16.5 1.0 CA C:SER81 3.9 13.5 1.0 CA C:PRO8 4.0 16.6 1.0 HD2 C:PRO9 4.0 19.3 1.0 HG3 C:PRO9 4.0 16.7 1.0 C C:ALA82 4.0 15.9 1.0 CB C:SER81 4.1 15.5 1.0 N C:PRO8 4.1 17.3 1.0 CA C:LYS90 4.2 22.0 1.0 C C:PRO6 4.2 18.6 1.0 CG C:PRO9 4.2 13.9 1.0 CG C:PRO6 4.3 29.6 1.0 HA2 C:GLY89 4.3 23.1 1.0 CB C:PRO6 4.4 18.6 1.0 N C:PRO9 4.4 14.2 1.0 HG2 C:PRO9 4.5 16.7 1.0 HB1 C:ALA82 4.5 16.5 1.0 HA C:PRO91 4.5 19.1 1.0 HA C:ALA82 4.5 16.4 1.0 C C:PRO8 4.6 15.2 1.0 CA C:GLY7 4.6 19.4 1.0 N C:GLY7 4.7 19.2 1.0 HB2 C:LYS90 4.7 28.4 1.0 HG3 C:PRO29 4.7 17.5 1.0 N C:PRO91 4.7 17.6 1.0 HA2 C:GLY7 4.8 23.3 1.0 OG C:SER81 4.8 19.8 1.0 HA C:LYS90 4.9 26.4 1.0 HG3 C:PRO6 4.9 35.5 1.0 HB2 C:SER81 4.9 18.6 1.0 O C:HOH322 4.9 25.0 1.0 HG23 C:ILE88 4.9 27.1 1.0 CA C:PRO6 4.9 18.5 1.0 HD2 C:PRO6 5.0 28.6 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the Titin Domain FN3-85


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Titin Domain FN3-85 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na201 b:30.6 occ:0.76 HG21 D:THR11 2.0 23.6 0.0 HG23 D:THR11 2.3 23.6 0.0 CG2 D:THR11 2.5 19.7 0.0 O F:HOH305 2.5 33.7 1.0 O D:HOH399 2.7 49.2 1.0 OG1 D:THR11 2.7 18.8 1.0 HD2 D:LYS93 3.0 33.8 1.0 HG21 D:THR11 3.1 26.3 1.0 HB D:THR11 3.2 23.2 1.0 HG22 D:THR11 3.3 23.6 0.0 OG1 D:THR11 3.4 20.1 0.0 CB D:THR11 3.4 19.3 1.0 HG1 D:THR11 3.4 22.5 1.0 CB D:THR11 3.4 19.2 0.0 HB D:THR11 3.6 23.0 0.0 HB2 D:LYS93 3.7 23.8 1.0 CG2 D:THR11 3.7 21.9 1.0 CD D:LYS93 3.8 28.1 1.0 O F:HOH303 3.8 52.6 1.0 HD3 D:LYS93 3.9 33.8 1.0 O D:HOH409 4.0 44.8 1.0 HG1 D:THR11 4.0 24.2 0.0 O D:HOH383 4.2 29.7 1.0 HZ1 D:LYS93 4.2 41.8 1.0 HG23 D:THR11 4.3 26.3 1.0 OE1 F:GLU96 4.3 33.4 0.5 HB3 D:LYS93 4.3 23.8 1.0 CB D:LYS93 4.4 19.9 1.0 O D:HOH429 4.4 25.9 1.0 O D:HOH337 4.4 21.9 1.0 HG22 D:THR11 4.4 26.3 1.0 H D:THR11 4.6 17.3 1.0 H D:THR11 4.6 17.3 0.0 CG D:LYS93 4.6 22.5 1.0 NZ D:LYS93 4.8 34.8 1.0 CA D:THR11 4.8 15.7 0.0 CA D:THR11 4.8 15.6 1.0 HZ2 D:LYS93 4.8 41.8 1.0 CE D:LYS93 4.8 29.2 1.0 HG3 D:LYS93 4.9 27.0 1.0

M.Rees, R.Nikoopour, A.Alexandrovich, M.Pfuhl, L.R.Lopes, M.M.Akhtar, P.Syrris, P.Elliott, G.Carr-White, M.Gautel. Structure Determination and Analysis of Titin A-Band Fibronectin Type III Domains Provides Insights For Disease-Linked Variants and Protein Oligomerisation. J.Struct.Biol. 08009 2023.
ISSN: ESSN 1095-8657
PubMed: 37549721
DOI: 10.1016/J.JSB.2023.108009