Sodium in PDB 7pf7: Apo Structure of Synftn Variant D65A

All present enzymatic activity of Apo Structure of Synftn Variant D65A:
1.16.3.2;

The structure of Apo Structure of Synftn Variant D65A, PDB code: 7pf7 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)	40.64 / 1.70
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	177.14, 177.14, 177.14, 90, 90, 90
R / Rfree (%)	18.2 / 20.8

The structure of Apo Structure of Synftn Variant D65A also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Apo Structure of Synftn Variant D65A (pdb code 7pf7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Apo Structure of Synftn Variant D65A, PDB code: 7pf7:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Apo Structure of Synftn Variant D65A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Apo Structure of Synftn Variant D65A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:32.6 occ:0.25 O A:HOH429 3.4 30.6 1.0 O A:HOH512 4.1 44.0 0.2 CG2 A:VAL169 4.4 29.0 1.0 O A:HOH405 4.8 32.4 1.0 O A:HOH501 5.0 48.7 1.0

Sodium binding site 2 out of 3 in the Apo Structure of Synftn Variant D65A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Apo Structure of Synftn Variant D65A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:51.9 occ:1.00 O A:SER24 2.8 31.6 0.4 O A:SER24 2.8 31.6 0.6 NE2 A:GLN87 3.1 46.4 1.0 OG A:SER24 3.2 33.9 0.6 N A:GLN28 3.5 29.6 1.0 CB A:GLN28 3.6 32.6 1.0 C A:SER24 3.7 31.1 0.4 C A:SER24 3.7 31.1 0.6 CA A:GLN28 3.9 32.0 1.0 CA A:SER24 3.9 32.9 0.4 CA A:SER24 4.0 32.9 0.6 CB A:GLN27 4.0 26.4 1.0 CB A:SER24 4.1 31.1 0.4 CB A:SER24 4.1 31.0 0.6 OE1 A:GLN28 4.2 59.0 1.0 C A:GLN27 4.2 31.2 1.0 OE1 A:GLN27 4.2 34.6 1.0 CD A:GLN87 4.3 40.0 1.0 OE1 A:GLN87 4.6 38.8 1.0 CA A:GLN27 4.7 31.0 1.0 CG A:GLN28 4.7 39.5 1.0 N A:ALA25 4.9 30.3 1.0 OG A:SER24 4.9 36.4 0.4 CD A:GLN28 4.9 57.6 1.0 O A:GLN27 5.0 28.2 1.0

Sodium binding site 3 out of 3 in the Apo Structure of Synftn Variant D65A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Apo Structure of Synftn Variant D65A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:47.6 occ:0.33 O A:HOH401 3.4 42.4 0.3 OH A:TYR121 4.0 29.8 1.0 OE1 A:GLU125 4.9 56.0 1.0 CZ A:TYR121 5.0 32.7 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