Iron in PDB 7pfb: 2 Minute FE2+ Soaked Structure of Synftn Variant D65A

All present enzymatic activity of 2 Minute FE2+ Soaked Structure of Synftn Variant D65A:
1.16.3.2;

The structure of 2 Minute FE2+ Soaked Structure of Synftn Variant D65A, PDB code: 7pfb 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)	40.66 / 1.70
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	177.24, 177.24, 177.24, 90, 90, 90
R / Rfree (%)	17.4 / 19.9

The structure of 2 Minute FE2+ Soaked Structure of Synftn Variant D65A also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Iron atom in the 2 Minute FE2+ Soaked Structure of Synftn Variant D65A (pdb code 7pfb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the 2 Minute FE2+ Soaked Structure of Synftn Variant D65A, PDB code: 7pfb:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the 2 Minute FE2+ Soaked Structure of Synftn Variant D65A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 2 Minute FE2+ Soaked Structure of Synftn Variant D65A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:31.8 occ:0.65 O A:HOH312 2.0 35.7 1.0 OE1 A:GLU33 2.1 35.0 1.0 OE1 A:GLU66 2.1 34.9 1.0 O A:HOH309 2.3 38.3 1.0 ND1 A:HIS69 2.4 32.8 1.0 CD A:GLU66 2.9 29.5 1.0 CD A:GLU33 3.0 35.5 1.0 OE2 A:GLU66 3.2 36.7 1.0 OE2 A:GLU33 3.3 31.2 1.0 CG A:HIS69 3.3 28.0 1.0 CE1 A:HIS69 3.3 36.5 1.0 CB A:HIS69 3.5 26.8 1.0 FE A:FE202 3.7 37.6 0.2 CG2 A:THR113 3.9 31.7 1.0 O A:HOH389 4.0 39.1 1.0 OE1 A:GLN143 4.1 33.0 1.0 CG A:GLU66 4.3 28.3 1.0 CG A:GLU33 4.4 27.9 1.0 CA A:GLU66 4.4 26.7 1.0 NE2 A:HIS69 4.5 30.4 1.0 CD2 A:HIS69 4.5 29.1 1.0 O A:HOH424 4.5 31.8 1.0 CB A:GLU66 4.6 26.1 1.0 O A:HOH393 4.6 32.3 1.0 CB A:GLU33 4.7 27.3 1.0 O A:HOH303 4.7 44.3 1.0 O A:GLU66 4.8 25.1 1.0 CD A:GLN143 4.9 29.4 1.0 OE1 A:GLU110 5.0 33.8 1.0

Iron binding site 2 out of 3 in the 2 Minute FE2+ Soaked Structure of Synftn Variant D65A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 2 Minute FE2+ Soaked Structure of Synftn Variant D65A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:37.6 occ:0.25 OE2 A:GLU66 1.9 36.7 1.0 OE1 A:GLU110 2.0 33.8 1.0 O A:HOH309 2.1 38.3 1.0 O A:HOH303 2.2 44.3 1.0 O A:HOH393 2.2 32.3 1.0 CD A:GLU110 2.6 32.3 1.0 OE2 A:GLU110 2.6 36.4 1.0 CD A:GLU66 2.9 29.5 1.0 OE1 A:GLU66 3.4 34.9 1.0 FE A:FE201 3.7 31.8 0.7 CG A:GLU110 4.0 37.5 1.0 OE1 A:GLN143 4.0 33.0 1.0 OH A:TYR40 4.0 34.1 1.0 CG A:GLU66 4.1 28.3 1.0 NE2 A:GLN143 4.2 29.5 1.0 CE2 A:TYR40 4.2 28.6 1.0 OG1 A:THR113 4.4 30.2 1.0 O A:HOH317 4.5 41.9 1.0 CG2 A:THR113 4.5 31.7 1.0 CA A:GLU110 4.5 27.4 1.0 CD A:GLN143 4.5 29.4 1.0 CB A:THR113 4.6 29.1 1.0 CZ A:TYR40 4.6 30.4 1.0 CB A:GLU110 4.6 31.4 1.0 O A:HOH479 4.6 44.7 1.0 O A:HOH312 4.8 35.7 1.0 ND1 A:HIS69 5.0 32.8 1.0

Iron binding site 3 out of 3 in the 2 Minute FE2+ Soaked Structure of Synftn Variant D65A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of 2 Minute FE2+ Soaked Structure of Synftn Variant D65A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:34.9 occ:0.20 O A:HOH313 2.1 36.5 1.0 O A:HOH495 2.2 40.7 1.0 O A:HOH409 3.7 38.6 1.0 OD2 A:ASP137 4.1 30.6 1.0 CB A:ASP137 4.1 25.9 1.0 CG A:ASP137 4.4 26.5 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