Iron in PDB 8avk: Superoxide Dismutase SODFM1 From Cpr Parkubacteria Wolfebacteria

All present enzymatic activity of Superoxide Dismutase SODFM1 From Cpr Parkubacteria Wolfebacteria:
1.15.1.1;

The structure of Superoxide Dismutase SODFM1 From Cpr Parkubacteria Wolfebacteria, PDB code: 8avk was solved by A.Basle, A.Barwinska-Sendra, K.M.Sendra, K.Waldron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.86 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.531, 70.586, 57.788, 90, 100.3, 90
R / Rfree (%)	20.9 / 25.6

The binding sites of Iron atom in the Superoxide Dismutase SODFM1 From Cpr Parkubacteria Wolfebacteria (pdb code 8avk). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Superoxide Dismutase SODFM1 From Cpr Parkubacteria Wolfebacteria, PDB code: 8avk:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Superoxide Dismutase SODFM1 From Cpr Parkubacteria Wolfebacteria


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Superoxide Dismutase SODFM1 From Cpr Parkubacteria Wolfebacteria within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:28.8 occ:1.00 O A:HOH405 2.0 19.5 1.0 OD2 A:ASP165 2.0 28.2 1.0 NE2 A:HIS27 2.0 23.6 1.0 NE2 A:HIS169 2.1 30.6 1.0 NE2 A:HIS82 2.2 32.2 1.0 CE1 A:HIS27 2.9 27.5 1.0 CG A:ASP165 3.0 29.3 1.0 CD2 A:HIS169 3.0 30.9 1.0 CD2 A:HIS27 3.0 26.2 1.0 HD2 A:HIS169 3.1 30.7 1.0 HE1 A:HIS27 3.1 26.3 1.0 CD2 A:HIS82 3.1 31.0 1.0 CE1 A:HIS82 3.2 32.0 1.0 CE1 A:HIS169 3.2 31.1 1.0 HD2 A:HIS27 3.2 26.2 1.0 HD2 A:HIS82 3.3 31.4 1.0 HE1 A:HIS82 3.4 32.4 1.0 HE1 A:HIS169 3.4 31.0 1.0 OD1 A:ASP165 3.5 30.3 1.0 HB2 A:TRP167 3.6 31.0 1.0 HH2 A:TRP131 3.9 29.0 1.0 ND1 A:HIS27 4.1 27.6 1.0 HB2 A:ALA170 4.1 28.9 1.0 CG A:HIS27 4.1 27.9 1.0 CG A:HIS169 4.2 30.8 1.0 ND1 A:HIS169 4.3 30.9 1.0 CB A:ASP165 4.3 26.4 1.0 ND1 A:HIS82 4.3 33.6 1.0 CG A:HIS82 4.3 31.9 1.0 HZ2 A:TRP131 4.3 30.1 1.0 CH2 A:TRP131 4.3 28.9 1.0 HB2 A:ASP165 4.4 26.8 1.0 CB A:TRP167 4.5 30.7 1.0 HB3 A:ASP165 4.5 26.8 1.0 OH A:TYR35 4.5 42.4 1.0 HE2 A:TYR35 4.5 41.9 1.0 CZ2 A:TRP131 4.6 30.7 1.0 HB3 A:HIS31 4.6 31.1 1.0 HB3 A:TRP167 4.7 31.2 1.0 CG A:TRP167 4.7 31.7 1.0 HA A:ALA170 4.9 29.5 1.0 CB A:ALA170 5.0 29.2 1.0

Iron binding site 2 out of 2 in the Superoxide Dismutase SODFM1 From Cpr Parkubacteria Wolfebacteria


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Superoxide Dismutase SODFM1 From Cpr Parkubacteria Wolfebacteria within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:26.1 occ:1.00 OD2 B:ASP165 2.0 28.7 1.0 NE2 B:HIS27 2.1 32.2 1.0 NE2 B:HIS169 2.1 25.2 1.0 NE2 B:HIS82 2.1 32.3 1.0 O B:HOH404 2.2 30.3 1.0 CG B:ASP165 3.0 28.1 1.0 CD2 B:HIS169 3.1 24.4 1.0 CE1 B:HIS27 3.1 30.4 1.0 CD2 B:HIS82 3.1 35.1 1.0 CD2 B:HIS27 3.1 25.5 1.0 CE1 B:HIS82 3.1 37.4 1.0 CE1 B:HIS169 3.1 25.0 1.0 HD2 B:HIS169 3.2 24.5 1.0 HD2 B:HIS82 3.2 33.3 1.0 HE1 B:HIS27 3.2 29.7 1.0 HD2 B:HIS27 3.3 27.4 1.0 HE1 B:HIS82 3.3 34.0 1.0 HE1 B:HIS169 3.3 25.1 1.0 OD1 B:ASP165 3.5 27.6 1.0 HB2 B:TRP167 3.6 26.9 1.0 HH2 B:TRP131 3.9 24.3 1.0 HB2 B:ALA170 4.1 24.1 1.0 HZ2 B:TRP131 4.1 25.4 1.0 ND1 B:HIS27 4.2 26.9 1.0 ND1 B:HIS169 4.2 25.2 1.0 CG B:HIS82 4.2 30.5 1.0 ND1 B:HIS82 4.2 29.6 1.0 CG B:HIS169 4.2 23.6 1.0 CG B:HIS27 4.2 27.1 1.0 CH2 B:TRP131 4.2 23.8 1.0 CB B:ASP165 4.3 28.1 1.0 HB2 B:ASP165 4.4 27.4 1.0 CZ2 B:TRP131 4.4 24.8 1.0 CB B:TRP167 4.5 26.8 1.0 HE2 B:TYR35 4.5 35.3 1.0 HB3 B:ASP165 4.5 27.4 1.0 HB3 B:HIS31 4.6 24.9 1.0 OH B:TYR35 4.6 39.2 1.0 CG B:TRP167 4.7 27.8 1.0 HB3 B:TRP167 4.8 27.0 1.0 HB2 B:HIS31 4.9 25.1 1.0 NE2 B:HIS150 4.9 32.4 1.0

K.M.Sendra, A.Barwinska-Sendra, E.S.Mackenzie, A.Basle, T.E.Kehl-Fie, K.J.Waldron. An Ancient Metalloenzyme Evolves Through Metal Preference Modulation. Nat Ecol Evol 2023.
ISSN: ISSN 2397-334X
PubMed: 37037909
DOI: 10.1038/S41559-023-02012-0