Manganese in PDB 1ues: 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: 1ues 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 (°)	71.680, 95.120, 98.750, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 25

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

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Porphyromonas Gingivalis Sod within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn192 b:18.4 occ:1.00 OD2 A:ASP157 2.1 19.7 1.0 NE2 A:HIS27 2.2 19.6 1.0 NE2 A:HIS74 2.2 18.9 1.0 NE2 A:HIS161 2.2 18.5 1.0 O A:HOH193 2.2 20.2 1.0 CD2 A:HIS161 3.1 18.5 1.0 CE1 A:HIS27 3.1 19.4 1.0 CG A:ASP157 3.1 19.9 1.0 CD2 A:HIS74 3.2 19.5 1.0 CE1 A:HIS74 3.2 19.3 1.0 CD2 A:HIS27 3.2 19.9 1.0 CE1 A:HIS161 3.3 19.0 1.0 OD1 A:ASP157 3.6 19.6 1.0 CH2 A:TRP123 4.1 21.4 1.0 ND1 A:HIS27 4.2 19.6 1.0 ND1 A:HIS74 4.3 18.9 1.0 CZ2 A:TRP123 4.3 21.0 1.0 CG A:HIS74 4.3 19.3 1.0 CG A:HIS27 4.3 20.0 1.0 CG A:HIS161 4.3 18.5 1.0 ND1 A:HIS161 4.3 18.9 1.0 CB A:ASP157 4.4 19.3 1.0 CB A:TRP159 4.4 19.3 1.0 CG A:TRP159 4.7 19.2 1.0 NE2 A:GLN70 4.8 22.9 1.0 CB A:ALA162 4.8 19.4 1.0 CZ3 A:TRP123 5.0 21.3 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Porphyromonas Gingivalis Sod within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn392 b:22.2 occ:1.00 O B:HOH393 2.1 22.3 1.0 OD2 B:ASP357 2.1 22.7 1.0 NE2 B:HIS361 2.2 21.6 1.0 NE2 B:HIS227 2.2 22.4 1.0 NE2 B:HIS274 2.2 24.2 1.0 CD2 B:HIS361 3.1 21.9 1.0 CE1 B:HIS227 3.1 22.1 1.0 CG B:ASP357 3.1 23.7 1.0 CD2 B:HIS274 3.2 24.6 1.0 CE1 B:HIS274 3.2 24.0 1.0 CD2 B:HIS227 3.2 22.6 1.0 CE1 B:HIS361 3.3 22.4 1.0 OD1 B:ASP357 3.5 23.4 1.0 CH2 B:TRP323 4.1 25.1 1.0 CZ2 B:TRP323 4.2 25.2 1.0 ND1 B:HIS227 4.2 22.7 1.0 ND1 B:HIS274 4.3 24.7 1.0 CG B:HIS361 4.3 22.3 1.0 CG B:HIS227 4.3 23.2 1.0 CG B:HIS274 4.3 25.0 1.0 ND1 B:HIS361 4.3 21.9 1.0 CB B:TRP359 4.4 20.9 1.0 CB B:ASP357 4.4 23.2 1.0 CG B:TRP359 4.7 21.2 1.0 CB B:ALA362 4.7 21.2 1.0 NE2 B:GLN270 4.9 28.7 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Porphyromonas Gingivalis Sod within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn592 b:21.6 occ:1.00 OD2 C:ASP557 2.1 24.3 1.0 O C:HOH3 2.1 24.7 1.0 NE2 C:HIS474 2.2 24.2 1.0 NE2 C:HIS561 2.2 21.9 1.0 NE2 C:HIS427 2.2 21.5 1.0 CE1 C:HIS474 3.0 24.3 1.0 CD2 C:HIS561 3.1 22.1 1.0 CE1 C:HIS427 3.1 21.2 1.0 CG C:ASP557 3.1 25.1 1.0 CD2 C:HIS427 3.2 21.5 1.0 CE1 C:HIS561 3.2 22.4 1.0 CD2 C:HIS474 3.2 25.2 1.0 OD1 C:ASP557 3.5 25.0 1.0 ND1 C:HIS474 4.2 24.9 1.0 CH2 C:TRP523 4.2 26.3 1.0 ND1 C:HIS427 4.2 21.5 1.0 CG C:HIS561 4.2 22.3 1.0 ND1 C:HIS561 4.3 22.1 1.0 CG C:HIS474 4.3 24.9 1.0 CG C:HIS427 4.3 21.4 1.0 CZ2 C:TRP523 4.4 26.0 1.0 CB C:ASP557 4.4 25.3 1.0 CB C:TRP559 4.4 22.2 1.0 CG C:TRP559 4.7 22.4 1.0 CB C:ALA562 4.9 22.8 1.0 NE2 C:GLN470 4.9 26.6 1.0 CD1 C:TRP559 5.0 21.9 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Porphyromonas Gingivalis Sod within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn792 b:22.0 occ:1.00 OD2 D:ASP757 2.0 22.2 1.0 NE2 D:HIS674 2.2 21.4 1.0 NE2 D:HIS627 2.3 23.3 1.0 O D:HOH4 2.3 23.1 1.0 NE2 D:HIS761 2.3 24.6 1.0 CG D:ASP757 3.1 22.7 1.0 CD2 D:HIS761 3.2 23.3 1.0 CE1 D:HIS674 3.2 22.2 1.0 CE1 D:HIS627 3.2 23.5 1.0 CD2 D:HIS627 3.2 24.1 1.0 CD2 D:HIS674 3.2 22.0 1.0 CE1 D:HIS761 3.4 23.9 1.0 OD1 D:ASP757 3.5 22.9 1.0 CH2 D:TRP723 4.0 23.5 1.0 CZ2 D:TRP723 4.1 23.5 1.0 ND1 D:HIS627 4.3 23.9 1.0 ND1 D:HIS674 4.3 21.9 1.0 CB D:ASP757 4.3 22.4 1.0 CG D:HIS627 4.3 24.4 1.0 CG D:HIS674 4.3 21.9 1.0 CG D:HIS761 4.3 23.9 1.0 ND1 D:HIS761 4.4 24.1 1.0 CB D:TRP759 4.4 21.2 1.0 NE2 D:GLN670 4.7 25.2 1.0 CG D:TRP759 4.7 21.3 1.0 CB D:ALA762 4.9 21.8 1.0 CZ3 D:TRP723 5.0 23.7 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