Iron in PDB 6gka: 20 Minute FE2+ Soak Structure of Synftn

All present enzymatic activity of 20 Minute FE2+ Soak Structure of Synftn:
1.16.3.2;

The structure of 20 Minute FE2+ Soak Structure of Synftn, PDB code: 6gka 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)	40.67 / 1.76
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	177.260, 177.260, 177.260, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 18.7

The structure of 20 Minute FE2+ Soak Structure of Synftn also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Iron atom in the 20 Minute FE2+ Soak Structure of Synftn (pdb code 6gka). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the 20 Minute FE2+ Soak Structure of Synftn, PDB code: 6gka:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the 20 Minute FE2+ Soak Structure of Synftn


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 20 Minute FE2+ Soak Structure of Synftn within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:27.4 occ:0.90 O A:HOH326 2.1 33.3 1.0 OE1 A:GLU33 2.1 30.2 1.0 OE1 A:GLU66 2.1 27.2 1.0 O A:HOH307 2.1 28.9 1.0 ND1 A:HIS69 2.3 28.6 1.0 CD A:GLU33 3.0 30.8 1.0 CD A:GLU66 3.0 28.5 1.0 CE1 A:HIS69 3.2 32.8 1.0 OE2 A:GLU33 3.3 28.7 1.0 CG A:HIS69 3.3 27.9 1.0 OE2 A:GLU66 3.3 28.6 1.0 FE A:FE202 3.5 31.8 0.6 CB A:HIS69 3.6 21.6 1.0 CG2 A:THR113 4.0 27.2 1.0 O A:HOH394 4.1 50.1 1.0 OE1 A:GLN143 4.1 29.9 1.0 O A:HOH469 4.2 58.6 1.0 NE2 A:HIS69 4.4 31.3 1.0 CG A:GLU66 4.4 21.0 1.0 O A:HOH365 4.4 30.1 1.0 CG A:GLU33 4.4 22.8 1.0 CD2 A:HIS69 4.4 33.2 1.0 CA A:GLU66 4.4 20.3 1.0 O A:HOH432 4.5 30.1 1.0 CB A:GLU66 4.6 20.1 1.0 CB A:GLU33 4.8 22.8 1.0 OE2 A:GLU110 4.8 37.9 1.0 O A:GLU66 4.9 20.6 1.0

Iron binding site 2 out of 3 in the 20 Minute FE2+ Soak Structure of Synftn


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 20 Minute FE2+ Soak Structure of Synftn within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:31.8 occ:0.55 OE2 A:GLU66 1.9 28.6 1.0 O A:HOH326 2.0 33.3 1.0 OE2 A:GLU110 2.1 37.9 1.0 O A:HOH394 2.3 50.1 1.0 O A:HOH365 2.3 30.1 1.0 OE1 A:GLU110 2.6 44.8 1.0 CD A:GLU110 2.6 40.1 1.0 CD A:GLU66 2.8 28.5 1.0 O A:HOH316 2.9 48.0 1.0 OE1 A:GLU66 3.2 27.2 1.0 FE A:FE201 3.5 27.4 0.9 OE1 A:GLN143 4.0 29.9 1.0 CG A:GLU110 4.1 40.5 1.0 CG A:GLU66 4.1 21.0 1.0 OH A:TYR40 4.2 35.2 1.0 NE2 A:GLN143 4.2 23.6 1.0 CE2 A:TYR40 4.3 26.2 1.0 OG A:SER146 4.3 26.5 0.5 OG1 A:THR113 4.5 29.3 1.0 CG2 A:THR113 4.5 27.2 1.0 O A:HOH478 4.6 51.1 1.0 CD A:GLN143 4.6 28.8 1.0 CB A:THR113 4.7 25.6 1.0 O A:HOH307 4.7 28.9 1.0 CA A:GLU110 4.7 25.5 1.0 CE1 A:HIS69 4.8 32.8 1.0 CZ A:TYR40 4.8 30.8 1.0 ND1 A:HIS69 4.8 28.6 1.0 CB A:GLU110 4.8 29.0 1.0 O A:HOH363 4.9 45.3 1.0

Iron binding site 3 out of 3 in the 20 Minute FE2+ Soak Structure of Synftn


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of 20 Minute FE2+ Soak Structure of Synftn within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:27.9 occ:0.28 O A:HOH308 2.2 28.9 1.0 O A:HOH498 2.3 29.2 1.0 O A:HOH386 3.7 32.7 1.0 OD2 A:ASP137 4.0 27.3 1.0 CB A:ASP137 4.1 22.6 1.0 O A:HOH505 4.2 46.3 1.0 CG A:ASP137 4.4 26.3 1.0

J.M.Bradley, D.A.Svistunenko, J.Pullin, N.Hill, R.K.Stuart, B.Palenik, M.T.Wilson, A.M.Hemmings, G.R.Moore, N.E.Le Brun. Reaction of O2WITH A Diiron Protein Generates A Mixed-Valent FE2+/FE3+Center and Peroxide. Proc. Natl. Acad. Sci. V. 116 2058 2019U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30659147
DOI: 10.1073/PNAS.1809913116