Manganese in PDB 3k9s: Crystal Structure of the Peroxide-Bound Manganese Superoxide Dismutase.

All present enzymatic activity of Crystal Structure of the Peroxide-Bound Manganese Superoxide Dismutase.:
1.15.1.1;

The structure of Crystal Structure of the Peroxide-Bound Manganese Superoxide Dismutase., PDB code: 3k9s was solved by J.C.Porta, A.Vahedi-Faridi, G.E.O.Borgstahl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.30 / 1.55
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	100.849, 107.418, 180.044, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 27

The binding sites of Manganese atom in the Crystal Structure of the Peroxide-Bound Manganese Superoxide Dismutase. (pdb code 3k9s). 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 the Peroxide-Bound Manganese Superoxide Dismutase., PDB code: 3k9s:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of the Peroxide-Bound Manganese Superoxide Dismutase.


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 the Peroxide-Bound Manganese Superoxide Dismutase. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn206 b:0.8 occ:1.00 OD2 A:ASP167 2.0 1.9 1.0 NE2 A:HIS26 2.1 2.3 1.0 NE2 A:HIS81 2.1 1.9 1.0 NE2 A:HIS171 2.1 1.7 1.0 O A:HOH207 2.2 3.0 0.7 O A:HOH208 2.4 2.9 1.0 CE1 A:HIS26 2.9 2.2 1.0 CE1 A:HIS171 3.0 2.8 1.0 CE1 A:HIS81 3.0 2.9 1.0 CG A:ASP167 3.1 1.6 1.0 CD2 A:HIS81 3.1 2.0 1.0 CD2 A:HIS26 3.1 2.2 1.0 CD2 A:HIS171 3.2 2.7 1.0 OD1 A:ASP167 3.5 2.5 1.0 ND1 A:HIS26 4.1 3.9 1.0 ND1 A:HIS81 4.1 1.7 1.0 ND1 A:HIS171 4.2 2.9 1.0 CG A:HIS26 4.2 3.4 1.0 CG A:HIS81 4.2 2.2 1.0 OH A:TYR34 4.3 3.8 1.0 CG A:HIS171 4.3 2.0 1.0 CB A:ASP167 4.3 1.9 1.0 NE2 A:GLN146 4.6 2.3 1.0 CZ2 A:TRP128 4.6 1.3 1.0 CB A:TRP169 4.7 2.3 1.0 CG A:TRP169 4.8 2.1 1.0 CE2 A:TYR34 4.9 3.7 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of the Peroxide-Bound Manganese Superoxide Dismutase.


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 the Peroxide-Bound Manganese Superoxide Dismutase. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn206 b:1.6 occ:1.00 OD2 B:ASP167 2.0 1.9 1.0 NE2 B:HIS171 2.1 2.4 1.0 NE2 B:HIS81 2.1 1.9 1.0 O1 B:PEO207 2.1 2.8 0.5 NE2 B:HIS26 2.1 1.8 1.0 O B:HOH208 2.1 9.2 0.5 O2 B:PEO207 2.6 6.4 0.5 CE1 B:HIS171 3.0 2.0 1.0 CE1 B:HIS26 3.0 2.7 1.0 CE1 B:HIS81 3.0 1.7 1.0 CG B:ASP167 3.0 1.4 1.0 CD2 B:HIS81 3.1 2.2 1.0 CD2 B:HIS171 3.1 1.7 1.0 CD2 B:HIS26 3.2 2.8 1.0 OD1 B:ASP167 3.4 1.1 1.0 ND1 B:HIS26 4.1 2.9 1.0 ND1 B:HIS171 4.1 1.4 1.0 ND1 B:HIS81 4.2 2.9 1.0 CG B:HIS81 4.2 3.4 1.0 CG B:HIS26 4.2 2.7 1.0 CG B:HIS171 4.2 1.8 1.0 CB B:ASP167 4.3 1.7 1.0 NE2 B:GLN146 4.5 2.0 1.0 CZ2 B:TRP128 4.6 3.2 1.0 CB B:TRP169 4.7 1.7 1.0 CG B:TRP169 4.8 1.6 1.0 CB B:ALA172 4.9 4.0 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of the Peroxide-Bound Manganese Superoxide Dismutase.


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 the Peroxide-Bound Manganese Superoxide Dismutase. within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn206 b:2.4 occ:1.00 OD2 C:ASP167 1.9 2.2 1.0 NE2 C:HIS171 2.1 2.9 1.0 O1 C:PEO207 2.1 0.9 0.5 NE2 C:HIS81 2.1 2.7 1.0 NE2 C:HIS26 2.1 1.8 1.0 O2 C:PEO207 2.1 3.0 0.5 O C:HOH209 2.2 0.5 0.5 O C:HOH208 2.3 1.5 0.5 CE1 C:HIS26 3.0 2.9 1.0 CE1 C:HIS81 3.0 3.6 1.0 CE1 C:HIS171 3.0 2.5 1.0 CG C:ASP167 3.0 3.0 1.0 CD2 C:HIS26 3.1 2.5 1.0 CD2 C:HIS171 3.1 2.3 1.0 CD2 C:HIS81 3.1 3.3 1.0 OD1 C:ASP167 3.5 1.3 1.0 ND1 C:HIS26 4.1 3.5 1.0 ND1 C:HIS81 4.2 2.5 1.0 ND1 C:HIS171 4.2 3.2 1.0 OH C:TYR34 4.2 6.8 1.0 CG C:HIS26 4.2 2.5 1.0 CG C:HIS81 4.3 2.3 1.0 CG C:HIS171 4.3 2.2 1.0 CB C:ASP167 4.3 1.4 1.0 NE2 C:GLN146 4.5 3.3 1.0 CB C:TRP169 4.6 2.2 1.0 CZ2 C:TRP128 4.7 2.2 1.0 CG C:TRP169 4.8 2.0 1.0 CB C:ALA172 5.0 3.1 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of the Peroxide-Bound Manganese Superoxide Dismutase.


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 the Peroxide-Bound Manganese Superoxide Dismutase. within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn206 b:2.5 occ:1.00 OD2 D:ASP167 1.9 2.2 1.0 NE2 D:HIS26 2.1 3.0 1.0 NE2 D:HIS171 2.1 3.4 1.0 NE2 D:HIS81 2.1 4.6 1.0 O1 D:PEO208 2.1 2.0 0.5 O D:HOH209 2.2 0.5 0.5 O2 D:PEO208 2.5 5.0 0.5 CE1 D:HIS26 2.9 3.6 1.0 CG D:ASP167 3.0 4.0 1.0 CE1 D:HIS171 3.0 2.9 1.0 CE1 D:HIS81 3.0 4.5 1.0 CD2 D:HIS81 3.1 3.8 1.0 CD2 D:HIS171 3.1 3.0 1.0 CD2 D:HIS26 3.2 3.6 1.0 OD1 D:ASP167 3.4 2.8 1.0 ND1 D:HIS26 4.1 4.7 1.0 ND1 D:HIS171 4.2 3.1 1.0 ND1 D:HIS81 4.2 4.2 1.0 CG D:HIS81 4.2 4.0 1.0 CG D:HIS171 4.2 3.0 1.0 CG D:HIS26 4.2 3.7 1.0 CB D:ASP167 4.3 3.6 1.0 CZ2 D:TRP128 4.5 2.8 1.0 NE2 D:GLN146 4.5 4.3 1.0 CB D:TRP169 4.6 2.4 1.0 CG D:TRP169 4.7 2.1 1.0 OH D:TYR34 4.8 9.0 1.0 CH2 D:TRP128 5.0 3.6 1.0

J.Porta, A.Vahedi-Faridi, G.E.Borgstahl. Structural Analysis of Peroxide-Soaked Mnsod Crystals Reveals Side-on Binding of Peroxide to Active-Site Manganese. J.Mol.Biol. V. 399 377 2010.
ISSN: ISSN 0022-2836
PubMed: 20417642
DOI: 10.1016/J.JMB.2010.04.031