Manganese in PDB 7dbt: Crystal Structure of Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (MN2+- Bound Form)

The structure of Crystal Structure of Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (MN2+- Bound Form), PDB code: 7dbt was solved by Y.Yoshida, T.Satoh, C.Ota, S.Tanaka, D.D.Horikawa, M.Tomita, K.Kato, K.Arakawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.93 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.4, 41.16, 79.768, 90, 92, 90
R / Rfree (%)	26.2 / 32.5

The binding sites of Manganese atom in the Crystal Structure of Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (MN2+- Bound Form) (pdb code 7dbt). 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 Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (MN2+- Bound Form), PDB code: 7dbt:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (MN2+- Bound Form)


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 Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (MN2+- Bound Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1001 b:44.0 occ:1.00 O A:HOH1109 2.2 31.6 1.0 O A:ALA96 2.3 31.6 1.0 OD1 A:ASP131 2.4 36.4 1.0 OD1 A:ASP98 2.4 33.6 1.0 O A:HOH1120 2.9 33.5 1.0 OD2 A:ASP92 2.9 40.7 1.0 CG A:ASP98 3.0 30.2 1.0 OD2 A:ASP98 3.2 35.1 1.0 C A:ALA96 3.5 33.9 1.0 CG A:ASP131 3.6 40.6 1.0 CB A:ASP92 3.7 42.2 1.0 CG A:ASP92 3.8 42.5 1.0 N A:ALA96 4.0 34.9 1.0 C A:CYS97 4.1 33.7 1.0 N A:ASP98 4.2 30.8 1.0 O A:CYS97 4.2 30.1 1.0 OD2 A:ASP131 4.3 42.1 1.0 CB A:ASP98 4.3 29.7 1.0 N A:ASP131 4.3 32.9 1.0 CA A:ALA96 4.3 36.3 1.0 CA A:ASP131 4.4 28.7 1.0 N A:CYS97 4.5 35.0 1.0 CA A:CYS97 4.5 34.5 1.0 CB A:ASP131 4.6 34.1 1.0 CA A:ASP98 4.7 26.3 1.0 C A:GLY95 4.8 44.6 1.0 OD1 A:ASP161 4.9 32.4 1.0 CA A:GLY95 5.0 46.5 1.0 OD1 A:ASP92 5.0 43.1 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (MN2+- Bound Form)


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 Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (MN2+- Bound Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1002 b:22.4 occ:1.00 O A:HOH1133 2.3 29.1 1.0 OE2 A:GLU72 2.3 40.0 1.0 OE1 A:GLU72 2.6 37.0 1.0 CD A:GLU72 2.8 34.5 1.0 CG A:GLU72 4.2 28.2 1.0 CD1 A:ILE142 4.4 27.4 1.0 CZ A:PHE218 4.5 24.7 1.0 NH2 A:ARG216 4.5 31.9 1.0 CD A:ARG70 4.7 28.2 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (MN2+- Bound Form)


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 Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (MN2+- Bound Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:49.4 occ:1.00 O B:HOH409 2.2 37.5 1.0 OD1 B:ASP131 2.2 35.6 1.0 O B:ALA96 2.5 35.3 1.0 OD1 B:ASP98 2.5 36.8 1.0 OD2 B:ASP92 2.9 44.9 1.0 CG B:ASP98 3.0 30.4 1.0 OD2 B:ASP98 3.1 28.3 1.0 CG B:ASP131 3.3 41.7 1.0 C B:ALA96 3.6 32.9 1.0 CG B:ASP92 3.8 51.4 1.0 CB B:ASP92 3.8 48.9 1.0 N B:ALA96 3.9 34.1 1.0 OD2 B:ASP131 4.0 41.9 1.0 N B:ASP131 4.2 34.2 1.0 C B:CYS97 4.2 33.8 1.0 CA B:ASP131 4.3 32.1 1.0 N B:ASP98 4.3 31.0 1.0 CB B:ASP98 4.3 32.7 1.0 CA B:ALA96 4.3 32.4 1.0 O B:CYS97 4.4 30.4 1.0 CB B:ASP131 4.4 39.5 1.0 N B:CYS97 4.6 29.9 1.0 CA B:CYS97 4.7 32.0 1.0 CA B:ASP98 4.8 30.8 1.0 C B:GLY95 4.8 48.4 1.0 CA B:GLY95 4.9 51.1 1.0 OD1 B:ASP92 5.0 52.3 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (MN2+- Bound Form)


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 Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (MN2+- Bound Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:21.4 occ:1.00 OE1 B:GLU72 2.3 31.5 1.0 O B:HOH437 2.5 33.0 1.0 OE2 B:GLU72 2.5 36.1 1.0 O B:HOH445 2.5 23.8 1.0 CD B:GLU72 2.7 34.0 1.0 CD1 B:ILE142 4.2 23.1 1.0 CG B:GLU72 4.2 27.8 1.0 CZ B:PHE218 4.4 27.9 1.0 CD B:ARG70 4.7 23.3 1.0 NH2 B:ARG216 4.8 28.1 1.0

Y.Yoshida, T.Satoh, C.Ota, S.Tanaka, D.D.Horikawa, M.Tomita, K.Kato, K.Arakawa. A Novel Mn-Dependent Peroxidase Contributes to Tardigrade Anhydrobiosis To Be Published.