Iron in PDB 1uer: Crystal Structure of Porphyromonas Gingivalis Sod

All present enzymatic activity of Crystal Structure of Porphyromonas Gingivalis Sod:
1.15.1.1;

The structure of Crystal Structure of Porphyromonas Gingivalis Sod, PDB code: 1uer was solved by F.Yamakura, S.Sugio, B.Y.Hiraoka, T.Yokota, D.Ohmori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.320, 95.930, 101.390, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 25.6

The binding sites of Iron atom in the Crystal Structure of Porphyromonas Gingivalis Sod (pdb code 1uer). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Porphyromonas Gingivalis Sod, PDB code: 1uer:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Porphyromonas Gingivalis Sod


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Porphyromonas Gingivalis Sod within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe192 b:27.8 occ:1.00 OD2 A:ASP157 2.0 21.5 1.0 O A:HOH193 2.0 21.0 1.0 NE2 A:HIS74 2.2 22.3 1.0 NE2 A:HIS27 2.2 21.3 1.0 NE2 A:HIS161 2.2 21.8 1.0 CE1 A:HIS74 3.0 22.8 1.0 CG A:ASP157 3.1 21.6 1.0 CD2 A:HIS161 3.1 22.1 1.0 CE1 A:HIS27 3.1 21.6 1.0 CD2 A:HIS27 3.2 21.6 1.0 CD2 A:HIS74 3.3 22.7 1.0 CE1 A:HIS161 3.3 22.0 1.0 OD1 A:ASP157 3.5 21.7 1.0 ND1 A:HIS74 4.1 22.3 1.0 CZ2 A:TRP123 4.2 21.1 1.0 ND1 A:HIS27 4.3 21.6 1.0 CG A:HIS161 4.3 21.4 1.0 CB A:ASP157 4.3 21.6 1.0 CG A:HIS74 4.3 22.3 1.0 CG A:HIS27 4.3 22.2 1.0 ND1 A:HIS161 4.4 21.8 1.0 CB A:TRP159 4.5 20.5 1.0 NE2 A:GLN70 4.5 23.7 1.0 CH2 A:TRP123 4.7 21.6 1.0 CG A:TRP159 4.8 20.5 1.0 CB A:ALA162 4.9 21.3 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Porphyromonas Gingivalis Sod


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Porphyromonas Gingivalis Sod within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe392 b:28.5 occ:1.00 OD2 B:ASP357 2.0 22.0 1.0 O B:HOH393 2.1 19.4 1.0 NE2 B:HIS274 2.2 23.9 1.0 NE2 B:HIS361 2.3 22.0 1.0 NE2 B:HIS227 2.3 20.9 1.0 CE1 B:HIS274 3.0 23.6 1.0 CD2 B:HIS361 3.1 22.0 1.0 CG B:ASP357 3.1 22.2 1.0 CE1 B:HIS227 3.2 21.5 1.0 CD2 B:HIS227 3.2 21.9 1.0 CD2 B:HIS274 3.3 23.6 1.0 CE1 B:HIS361 3.3 21.9 1.0 OD1 B:ASP357 3.5 22.6 1.0 CZ2 B:TRP323 4.2 21.2 1.0 ND1 B:HIS274 4.2 23.6 1.0 ND1 B:HIS227 4.3 21.7 1.0 CG B:HIS361 4.3 21.4 1.0 CG B:HIS227 4.3 22.2 1.0 CG B:HIS274 4.3 23.4 1.0 CB B:ASP357 4.3 21.7 1.0 ND1 B:HIS361 4.4 22.1 1.0 CB B:TRP359 4.5 20.4 1.0 NE2 B:GLN270 4.5 22.5 1.0 CG B:TRP359 4.7 20.7 1.0 CH2 B:TRP323 4.8 21.1 1.0 CB B:ALA362 4.8 20.9 1.0 CD1 B:TRP359 5.0 20.6 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Porphyromonas Gingivalis Sod


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Porphyromonas Gingivalis Sod within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe592 b:29.0 occ:1.00 OD2 C:ASP557 2.0 22.8 1.0 O C:HOH593 2.0 23.6 1.0 NE2 C:HIS561 2.2 24.4 1.0 NE2 C:HIS474 2.2 25.6 1.0 NE2 C:HIS427 2.3 23.7 1.0 CG C:ASP557 3.1 22.4 1.0 CE1 C:HIS474 3.1 26.1 1.0 CE1 C:HIS427 3.1 23.9 1.0 CD2 C:HIS561 3.1 24.1 1.0 CE1 C:HIS561 3.2 24.3 1.0 CD2 C:HIS427 3.3 23.8 1.0 CD2 C:HIS474 3.3 26.1 1.0 OD1 C:ASP557 3.5 22.2 1.0 CZ2 C:TRP523 4.2 23.8 1.0 ND1 C:HIS427 4.2 23.6 1.0 ND1 C:HIS474 4.2 26.1 1.0 CG C:HIS561 4.3 23.6 1.0 ND1 C:HIS561 4.3 24.2 1.0 CG C:HIS427 4.3 24.2 1.0 CB C:ASP557 4.4 22.3 1.0 CG C:HIS474 4.4 26.4 1.0 CB C:TRP559 4.4 22.2 1.0 NE2 C:GLN470 4.6 26.7 1.0 CG C:TRP559 4.6 22.4 1.0 CH2 C:TRP523 4.7 23.6 1.0 CD1 C:TRP559 4.9 22.4 1.0 CB C:ALA562 4.9 21.7 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Porphyromonas Gingivalis Sod


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Porphyromonas Gingivalis Sod within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe792 b:35.6 occ:1.00 OD2 D:ASP757 2.1 29.4 1.0 O D:HOH4 2.2 26.9 1.0 NE2 D:HIS761 2.2 26.1 1.0 NE2 D:HIS674 2.2 37.8 1.0 NE2 D:HIS627 2.3 30.5 1.0 CE1 D:HIS674 3.0 38.0 1.0 CD2 D:HIS761 3.1 25.9 1.0 CE1 D:HIS627 3.1 30.8 1.0 CG D:ASP757 3.1 29.2 1.0 CD2 D:HIS627 3.2 30.8 1.0 CE1 D:HIS761 3.2 25.9 1.0 CD2 D:HIS674 3.3 38.0 1.0 OD1 D:ASP757 3.6 29.3 1.0 ND1 D:HIS674 4.2 37.9 1.0 ND1 D:HIS627 4.2 30.8 1.0 CG D:HIS761 4.3 25.7 1.0 CG D:HIS627 4.3 31.1 1.0 ND1 D:HIS761 4.3 25.9 1.0 CZ2 D:TRP723 4.3 32.1 1.0 CB D:ASP757 4.4 29.8 1.0 CG D:HIS674 4.4 38.1 1.0 CB D:TRP759 4.5 26.8 1.0 NE2 D:GLN670 4.6 33.9 1.0 CG D:TRP759 4.8 27.0 1.0 CH2 D:TRP723 4.9 32.1 1.0 CB D:ALA762 4.9 24.8 1.0

F.Yamakura, S.Sugio, B.Y.Hiraoka, D.Ohmori, T.Yokota. Pronounced Conversion of the Metal-Specific Activity of Superoxide Dismutase From Porphyromonas Gingivalis By the Mutation of A Single Amino Acid (GLY155THR) Located Apart From the Active Site Biochemistry V. 42 10790 2003.
ISSN: ISSN 0006-2960
PubMed: 12962504
DOI: 10.1021/BI0349625