Iron in PDB 2bkb: Q69E-Fesod

All present enzymatic activity of Q69E-Fesod:
1.15.1.1;

The structure of Q69E-Fesod, PDB code: 2bkb was solved by E.Yikilmaz, D.W.Rodgers, A.-F.Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.97 / 1.7
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.500, 107.700, 84.200, 90.00, 95.02, 90.00
R / Rfree (%)	20.7 / 23.1

The binding sites of Iron atom in the Q69E-Fesod (pdb code 2bkb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Q69E-Fesod, PDB code: 2bkb:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Q69E-Fesod


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Q69E-Fesod within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1193 b:8.6 occ:1.00 OD1 A:ASP156 1.9 7.8 1.0 NE2 A:HIS73 2.1 6.1 1.0 O A:HOH2081 2.1 9.2 1.0 NE2 A:HIS26 2.2 5.0 1.0 NE2 A:HIS160 2.2 6.2 1.0 CE1 A:HIS26 3.0 7.7 1.0 CE1 A:HIS73 3.0 6.4 1.0 CG A:ASP156 3.1 10.1 1.0 CD2 A:HIS73 3.1 4.7 1.0 CE1 A:HIS160 3.1 8.4 1.0 CD2 A:HIS26 3.2 7.3 1.0 CD2 A:HIS160 3.2 8.6 1.0 OD2 A:ASP156 3.6 8.5 1.0 ND1 A:HIS73 4.1 5.7 1.0 ND1 A:HIS26 4.2 7.5 1.0 CG A:HIS73 4.2 4.2 1.0 CZ2 A:TRP122 4.2 8.2 1.0 ND1 A:HIS160 4.2 8.1 1.0 CG A:HIS26 4.3 5.9 1.0 CB A:ASP156 4.3 9.0 1.0 CG A:HIS160 4.3 7.4 1.0 CH2 A:TRP122 4.3 9.0 1.0 CB A:TRP158 4.5 6.2 1.0 OE2 A:GLU69 4.6 9.5 1.0 CG A:TRP158 4.6 7.7 1.0 CD1 A:TRP158 4.9 7.5 1.0 CB A:ALA161 4.9 6.6 1.0

Iron binding site 2 out of 4 in the Q69E-Fesod


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Q69E-Fesod within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1393 b:8.7 occ:1.00 OD2 B:ASP356 2.0 8.0 1.0 NE2 B:HIS360 2.1 5.3 1.0 O B:HOH2078 2.2 7.9 1.0 NE2 B:HIS273 2.2 5.0 1.0 NE2 B:HIS226 2.2 6.9 1.0 CE1 B:HIS360 3.0 9.3 1.0 CD2 B:HIS360 3.1 8.4 1.0 CG B:ASP356 3.1 5.7 1.0 CE1 B:HIS273 3.1 9.5 1.0 CD2 B:HIS273 3.1 7.3 1.0 CE1 B:HIS226 3.2 6.2 1.0 CD2 B:HIS226 3.2 7.4 1.0 OD1 B:ASP356 3.5 5.9 1.0 ND1 B:HIS360 4.1 7.8 1.0 CG B:HIS360 4.2 6.6 1.0 ND1 B:HIS273 4.2 9.1 1.0 CZ2 B:TRP322 4.2 7.4 1.0 CG B:HIS273 4.3 7.3 1.0 ND1 B:HIS226 4.3 8.5 1.0 CG B:HIS226 4.3 6.8 1.0 CB B:ASP356 4.3 5.9 1.0 CH2 B:TRP322 4.4 7.7 1.0 CB B:TRP358 4.4 6.4 1.0 CG B:TRP358 4.6 8.5 1.0 OE1 B:GLU269 4.6 8.8 1.0 CD1 B:TRP358 4.8 7.8 1.0 CB B:ALA361 4.9 8.0 1.0

Iron binding site 3 out of 4 in the Q69E-Fesod


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Q69E-Fesod within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1193 b:10.4 occ:1.00 OD1 C:ASP156 2.0 8.8 1.0 NE2 C:HIS73 2.1 8.7 1.0 O C:HOH2052 2.2 12.6 1.0 NE2 C:HIS160 2.2 7.9 1.0 NE2 C:HIS26 2.3 8.5 1.0 CE1 C:HIS73 3.0 9.2 1.0 CD2 C:HIS73 3.1 10.0 1.0 CG C:ASP156 3.1 7.8 1.0 CE1 C:HIS160 3.1 10.6 1.0 CD2 C:HIS160 3.2 10.0 1.0 CE1 C:HIS26 3.2 8.6 1.0 CD2 C:HIS26 3.2 9.2 1.0 OD2 C:ASP156 3.6 10.6 1.0 ND1 C:HIS73 4.1 9.0 1.0 CZ2 C:TRP122 4.2 8.0 1.0 CG C:HIS73 4.2 9.7 1.0 ND1 C:HIS160 4.3 8.9 1.0 CH2 C:TRP122 4.3 8.6 1.0 CG C:HIS160 4.3 9.0 1.0 ND1 C:HIS26 4.3 8.4 1.0 CB C:ASP156 4.3 8.7 1.0 CG C:HIS26 4.4 8.3 1.0 CB C:TRP158 4.4 9.6 1.0 OE1 C:GLU69 4.5 13.8 1.0 CG C:TRP158 4.6 10.2 1.0 CD1 C:TRP158 4.8 9.2 1.0 CB C:ALA161 5.0 10.6 1.0

Iron binding site 4 out of 4 in the Q69E-Fesod


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Q69E-Fesod within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe1393 b:11.0 occ:1.00 OD1 D:ASP356 1.9 8.1 1.0 O D:HOH2058 2.1 7.6 1.0 NE2 D:HIS360 2.1 7.8 1.0 NE2 D:HIS273 2.2 10.2 1.0 NE2 D:HIS226 2.3 7.3 1.0 CG D:ASP356 3.0 9.9 1.0 CE1 D:HIS360 3.1 10.2 1.0 CE1 D:HIS273 3.1 9.0 1.0 CD2 D:HIS360 3.1 8.9 1.0 CD2 D:HIS273 3.2 10.9 1.0 CE1 D:HIS226 3.2 6.9 1.0 CD2 D:HIS226 3.2 9.7 1.0 OD2 D:ASP356 3.5 10.2 1.0 ND1 D:HIS273 4.2 9.8 1.0 ND1 D:HIS360 4.2 8.4 1.0 CZ2 D:TRP322 4.3 11.2 1.0 CG D:HIS360 4.3 8.5 1.0 CG D:HIS273 4.3 8.7 1.0 CB D:ASP356 4.3 9.6 1.0 ND1 D:HIS226 4.3 9.9 1.0 CH2 D:TRP322 4.4 10.3 1.0 CG D:HIS226 4.4 7.5 1.0 CB D:TRP358 4.4 8.6 1.0 OE1 D:GLU269 4.5 10.0 1.0 CG D:TRP358 4.6 9.5 1.0 CD1 D:TRP358 4.8 7.8 1.0 CB D:ALA361 4.8 11.4 1.0

E.Yikilmaz, D.W.Rodgers, A.-F.Miller. The Crucial Importance of Chemistry in the Structure-Function Link: Manipulating Hydrogen Bonding in Iron-Containing Superoxide Dismutase. Biochemistry V. 45 1151 2006.
ISSN: ISSN 0006-2960
PubMed: 16430211
DOI: 10.1021/BI051495D