Iron in PDB 3ak3: Superoxide Dismutase From Aeropyrum Pernix K1, Fe-Bound Form

All present enzymatic activity of Superoxide Dismutase From Aeropyrum Pernix K1, Fe-Bound Form:
1.15.1.1;

The structure of Superoxide Dismutase From Aeropyrum Pernix K1, Fe-Bound Form, PDB code: 3ak3 was solved by T.Nakamura, K.Uegaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.75 / 1.48
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.057, 71.755, 76.404, 90.00, 91.72, 90.00
R / Rfree (%)	22.5 / 25.6

The binding sites of Iron atom in the Superoxide Dismutase From Aeropyrum Pernix K1, Fe-Bound Form (pdb code 3ak3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Superoxide Dismutase From Aeropyrum Pernix K1, Fe-Bound Form, PDB code: 3ak3:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Superoxide Dismutase From Aeropyrum Pernix K1, Fe-Bound Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Superoxide Dismutase From Aeropyrum Pernix K1, Fe-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe215 b:14.9 occ:1.00 OD2 A:ASP165 1.9 15.6 1.0 O A:HOH217 2.1 17.8 1.0 NE2 A:HIS79 2.1 14.3 1.0 NE2 A:HIS169 2.2 15.1 1.0 NE2 A:HIS31 2.2 13.8 1.0 O A:HOH288 2.2 25.7 1.0 CE1 A:HIS79 3.0 13.7 1.0 CG A:ASP165 3.0 11.9 1.0 CE1 A:HIS169 3.1 15.9 1.0 CD2 A:HIS31 3.1 13.5 1.0 CE1 A:HIS31 3.2 15.3 1.0 CD2 A:HIS169 3.2 15.9 1.0 CD2 A:HIS79 3.2 13.9 1.0 OD1 A:ASP165 3.5 13.9 1.0 ND1 A:HIS79 4.2 14.7 1.0 ND1 A:HIS169 4.2 16.0 1.0 ND1 A:HIS31 4.3 12.9 1.0 CG A:HIS31 4.3 15.2 1.0 CB A:ASP165 4.3 13.1 1.0 CG A:HIS79 4.3 14.5 1.0 CG A:HIS169 4.3 15.6 1.0 OH A:TYR39 4.4 21.9 1.0 CB A:TRP167 4.5 13.9 1.0 CZ2 A:TRP130 4.5 11.2 1.0 CG A:TRP167 4.6 12.4 1.0 CH2 A:TRP130 4.6 12.3 1.0 NE2 A:HIS150 4.8 15.7 1.0 CD1 A:TRP167 4.9 14.2 1.0 CE2 A:TYR39 4.9 17.7 1.0

Iron binding site 2 out of 4 in the Superoxide Dismutase From Aeropyrum Pernix K1, Fe-Bound Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Superoxide Dismutase From Aeropyrum Pernix K1, Fe-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe215 b:13.8 occ:1.00 OD2 B:ASP165 2.0 14.6 1.0 O B:HOH221 2.1 15.2 1.0 NE2 B:HIS31 2.1 13.1 1.0 NE2 B:HIS79 2.2 15.3 1.0 NE2 B:HIS169 2.2 16.2 1.0 O B:HOH250 2.3 16.3 1.0 CG B:ASP165 3.1 13.1 1.0 CE1 B:HIS79 3.1 14.5 1.0 CD2 B:HIS31 3.1 13.7 1.0 CE1 B:HIS169 3.1 13.8 1.0 CE1 B:HIS31 3.1 14.9 1.0 CD2 B:HIS169 3.2 14.7 1.0 CD2 B:HIS79 3.2 13.9 1.0 OD1 B:ASP165 3.5 13.8 1.0 ND1 B:HIS31 4.2 14.7 1.0 ND1 B:HIS79 4.2 11.9 1.0 CG B:HIS31 4.2 15.8 1.0 OH B:TYR39 4.3 21.9 1.0 ND1 B:HIS169 4.3 14.4 1.0 CB B:ASP165 4.3 12.4 1.0 CG B:HIS79 4.3 12.5 1.0 CG B:HIS169 4.4 14.1 1.0 CB B:TRP167 4.6 12.8 1.0 CZ2 B:TRP130 4.6 12.9 1.0 CH2 B:TRP130 4.6 11.6 1.0 CG B:TRP167 4.7 12.6 1.0 NE2 B:HIS150 4.8 14.8 1.0 CD1 B:TRP167 4.9 13.7 1.0

Iron binding site 3 out of 4 in the Superoxide Dismutase From Aeropyrum Pernix K1, Fe-Bound Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Superoxide Dismutase From Aeropyrum Pernix K1, Fe-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe215 b:17.8 occ:1.00 OD2 C:ASP165 1.9 18.3 1.0 O C:HOH253 1.9 24.9 1.0 O C:HOH219 2.0 13.4 1.0 NE2 C:HIS31 2.2 15.8 1.0 NE2 C:HIS79 2.2 21.1 1.0 NE2 C:HIS169 2.3 18.8 1.0 CG C:ASP165 3.0 16.9 1.0 CE1 C:HIS79 3.1 19.9 1.0 CE1 C:HIS31 3.1 18.8 1.0 CD2 C:HIS31 3.1 20.0 1.0 CD2 C:HIS169 3.3 16.8 1.0 CD2 C:HIS79 3.3 20.1 1.0 CE1 C:HIS169 3.3 17.5 1.0 OD1 C:ASP165 3.5 15.6 1.0 ND1 C:HIS31 4.2 18.3 1.0 OH C:TYR39 4.2 22.5 1.0 CB C:ASP165 4.2 16.6 1.0 CG C:HIS31 4.3 18.9 1.0 ND1 C:HIS79 4.3 19.8 1.0 CG C:HIS79 4.4 19.7 1.0 ND1 C:HIS169 4.4 17.7 1.0 CG C:HIS169 4.4 18.1 1.0 CB C:TRP167 4.6 15.2 1.0 CG C:TRP167 4.7 14.8 1.0 CZ2 C:TRP130 4.7 17.5 1.0 CH2 C:TRP130 4.7 17.6 1.0 NE2 C:HIS150 4.8 14.9 1.0 CD1 C:TRP167 4.9 14.9 1.0 CE2 C:TYR39 5.0 22.3 1.0

Iron binding site 4 out of 4 in the Superoxide Dismutase From Aeropyrum Pernix K1, Fe-Bound Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Superoxide Dismutase From Aeropyrum Pernix K1, Fe-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe215 b:17.6 occ:1.00 OD2 D:ASP165 2.0 18.4 1.0 O D:HOH219 2.0 16.6 1.0 NE2 D:HIS31 2.1 16.2 1.0 NE2 D:HIS169 2.2 17.4 1.0 NE2 D:HIS79 2.2 17.5 1.0 O D:HOH267 2.2 27.4 1.0 CG D:ASP165 3.1 16.7 1.0 CE1 D:HIS79 3.1 19.8 1.0 CE1 D:HIS31 3.1 17.3 1.0 CE1 D:HIS169 3.1 16.7 1.0 CD2 D:HIS31 3.1 18.8 1.0 CD2 D:HIS169 3.2 18.7 1.0 CD2 D:HIS79 3.3 18.8 1.0 OD1 D:ASP165 3.5 16.6 1.0 OH D:TYR39 4.2 22.6 1.0 ND1 D:HIS31 4.2 17.3 1.0 ND1 D:HIS169 4.3 17.9 1.0 ND1 D:HIS79 4.3 17.7 1.0 CG D:HIS31 4.3 17.9 1.0 CG D:HIS169 4.3 16.4 1.0 CB D:ASP165 4.4 15.7 1.0 CG D:HIS79 4.4 19.1 1.0 CB D:TRP167 4.5 15.0 1.0 CG D:TRP167 4.7 15.1 1.0 CZ2 D:TRP130 4.7 16.4 1.0 CH2 D:TRP130 4.7 17.1 1.0 NE2 D:HIS150 4.9 17.1 1.0 CE2 D:TYR39 4.9 21.2 1.0 CD1 D:TRP167 4.9 14.7 1.0

T.Nakamura, K.Torikai, K.Uegaki, J.Morita, K.Machida, A.Suzuki, Y.Kawata. Crystal Structure of the Cambialistic Superoxide Dismutase From Aeropyrum Pernix K1 - Insights Into the Enzyme Mechanism and Stability Febs J. V. 278 598 2011.
ISSN: ISSN 1742-464X
PubMed: 21182595
DOI: 10.1111/J.1742-4658.2010.07977.X