Sodium in PDB 7pf8: Synftn Variant E141A

All present enzymatic activity of Synftn Variant E141A:
1.16.3.2;

The structure of Synftn Variant E141A, PDB code: 7pf8 was solved by A.M.Hemmings, J.M.Bradley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.57 / 1.85
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	176.85, 176.85, 176.85, 90, 90, 90
R / Rfree (%)	19.3 / 21.6

The structure of Synftn Variant E141A also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Synftn Variant E141A (pdb code 7pf8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Synftn Variant E141A, PDB code: 7pf8:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Synftn Variant E141A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Synftn Variant E141A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:58.0 occ:1.00 OD2 A:ASP90 3.5 59.5 1.0 N A:ASP90 3.6 38.3 1.0 CG A:ASP90 3.6 52.4 1.0 O A:HOH301 3.8 49.0 1.0 OD1 A:ASP90 4.0 54.9 1.0 O A:THR88 4.0 41.8 1.0 CB A:ASP90 4.0 38.9 1.0 CD1 A:LEU89 4.1 40.5 1.0 CD1 A:TYR35 4.1 30.4 1.0 CB A:TYR35 4.2 32.9 1.0 CA A:LEU89 4.2 40.5 1.0 CG A:TYR35 4.3 32.8 1.0 C A:LEU89 4.4 39.1 1.0 CA A:ASP90 4.4 37.8 1.0 O A:SER31 4.6 31.3 1.0 CB A:SER31 4.8 29.3 1.0 CE1 A:TYR35 4.8 34.1 1.0 CG A:LEU89 4.9 38.2 1.0 C A:THR88 5.0 33.9 1.0

Sodium binding site 2 out of 4 in the Synftn Variant E141A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Synftn Variant E141A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:34.4 occ:0.25 O A:HOH400 3.4 32.3 1.0 O A:HOH475 4.0 40.0 0.2 CG2 A:VAL169 4.5 32.2 1.0 O A:HOH366 4.8 35.0 1.0 O A:HOH466 4.9 53.1 1.0

Sodium binding site 3 out of 4 in the Synftn Variant E141A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Synftn Variant E141A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:48.9 occ:0.33 OD2 A:ASP137 2.9 33.4 1.0 O A:HOH391 3.3 51.2 1.0 CG A:ASP137 3.6 31.5 1.0 OD1 A:ASP137 3.8 32.6 1.0 OH A:TYR121 4.0 37.7 1.0 CB A:ASP137 4.9 28.0 1.0

Sodium binding site 4 out of 4 in the Synftn Variant E141A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Synftn Variant E141A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:51.5 occ:1.00 OE1 A:GLU49 2.8 33.4 1.0 O A:GLN94 3.0 46.5 1.0 O A:HOH382 3.1 40.2 1.0 O A:HOH314 3.3 38.5 1.0 CD A:GLU49 3.5 30.6 1.0 OE2 A:GLU49 3.6 35.5 1.0 CD1 A:TRP46 3.7 34.1 1.0 O A:HOH385 3.7 47.3 1.0 O A:HOH357 4.1 36.0 1.0 O A:HOH444 4.1 51.1 1.0 CA A:TRP46 4.2 29.4 1.0 C A:GLN94 4.2 35.3 1.0 CB A:TRP46 4.3 32.9 1.0 CG A:TRP46 4.4 31.4 1.0 NH1 A:ARG50 4.4 32.2 1.0 OD1 A:ASN95 4.5 51.6 1.0 O A:HOH420 4.5 39.4 1.0 N A:TRP46 4.6 29.9 1.0 NE1 A:TRP46 4.8 32.8 1.0 CB A:GLN94 4.8 36.2 1.0 CG A:GLU49 4.9 32.4 1.0 CG2 A:ILE45 4.9 31.1 1.0 CA A:GLN94 5.0 37.9 1.0

J.M.Bradley, J.Fair, A.M.Hemmings, N.E.Le Brun. Key Carboxylate Residues For Iron Transit Through the Prokaryotic Ferritin Syn Ftn. Microbiology (Reading, V. 167 2021ENGL.).
ISSN: ESSN 1465-2080
PubMed: 34825885
DOI: 10.1099/MIC.0.001105