Manganese in PDB 1d5n: Crystal Structure of E. Coli Mnsod at 100K

All present enzymatic activity of Crystal Structure of E. Coli Mnsod at 100K:
1.15.1.1;

The structure of Crystal Structure of E. Coli Mnsod at 100K, PDB code: 1d5n was solved by G.E.O.Borgstahl, M.Pokross, R.Chehab, A.Sekher, E.H.Snell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.55
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	99.110, 107.300, 179.110, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 23.3

The binding sites of Manganese atom in the Crystal Structure of E. Coli Mnsod at 100K (pdb code 1d5n). 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 E. Coli Mnsod at 100K, PDB code: 1d5n:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of E. Coli Mnsod at 100K


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 E. Coli Mnsod at 100K within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2206 b:6.6 occ:1.00 OD2 A:ASP167 2.0 9.5 1.0 NE2 A:HIS26 2.2 8.3 1.0 NE2 A:HIS81 2.2 9.4 1.0 NE2 A:HIS171 2.2 7.9 1.0 O A:HOH2478 2.2 8.1 1.0 O A:HOH2479 2.4 27.1 1.0 CE1 A:HIS81 3.1 9.5 1.0 CE1 A:HIS171 3.1 6.7 1.0 CG A:ASP167 3.1 10.0 1.0 CE1 A:HIS26 3.1 7.9 1.0 CD2 A:HIS26 3.2 8.9 1.0 CD2 A:HIS81 3.2 9.2 1.0 CD2 A:HIS171 3.2 8.7 1.0 OD1 A:ASP167 3.5 7.4 1.0 ND1 A:HIS81 4.2 8.9 1.0 ND1 A:HIS26 4.2 9.4 1.0 ND1 A:HIS171 4.2 10.2 1.0 CG A:HIS26 4.3 9.8 1.0 CG A:HIS81 4.3 8.5 1.0 CB A:ASP167 4.3 6.6 1.0 CG A:HIS171 4.3 7.9 1.0 CZ2 A:TRP128 4.6 7.2 1.0 CB A:TRP169 4.6 4.7 1.0 NE2 A:GLN146 4.6 5.5 1.0 CG A:TRP169 4.7 5.1 1.0 OH A:TYR34 4.9 17.6 1.0 CB A:ALA172 4.9 6.8 1.0 CD1 A:TRP169 5.0 5.2 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of E. Coli Mnsod at 100K


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 E. Coli Mnsod at 100K within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2207 b:7.5 occ:1.00 OD2 B:ASP167 2.0 10.1 1.0 NE2 B:HIS26 2.2 10.6 1.0 O B:HOH2471 2.2 9.5 1.0 NE2 B:HIS81 2.2 9.5 1.0 NE2 B:HIS171 2.2 11.0 1.0 O B:HOH2472 2.4 28.6 1.0 CG B:ASP167 3.1 8.9 1.0 CE1 B:HIS26 3.1 10.8 1.0 CE1 B:HIS81 3.1 10.8 1.0 CE1 B:HIS171 3.1 11.3 1.0 CD2 B:HIS26 3.2 10.1 1.0 CD2 B:HIS81 3.2 9.2 1.0 CD2 B:HIS171 3.3 7.3 1.0 OD1 B:ASP167 3.5 8.4 1.0 ND1 B:HIS26 4.2 10.2 1.0 ND1 B:HIS81 4.2 10.4 1.0 ND1 B:HIS171 4.3 8.6 1.0 CG B:HIS26 4.3 9.6 1.0 CG B:HIS81 4.3 9.3 1.0 CB B:ASP167 4.3 7.0 1.0 CG B:HIS171 4.4 7.1 1.0 CZ2 B:TRP128 4.6 9.2 1.0 CB B:TRP169 4.6 6.6 1.0 NE2 B:GLN146 4.6 7.5 1.0 CG B:TRP169 4.8 5.2 1.0 CB B:ALA172 4.9 6.9 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of E. Coli Mnsod at 100K


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 E. Coli Mnsod at 100K within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn2208 b:6.8 occ:1.00 OD2 C:ASP167 2.1 8.3 1.0 O C:HOH2475 2.2 7.3 1.0 NE2 C:HIS171 2.2 5.6 1.0 NE2 C:HIS81 2.2 8.7 1.0 NE2 C:HIS26 2.2 7.9 1.0 O C:HOH2476 2.4 22.9 1.0 CE1 C:HIS171 3.1 4.3 1.0 CG C:ASP167 3.1 9.2 1.0 CE1 C:HIS81 3.1 8.6 1.0 CE1 C:HIS26 3.2 7.1 1.0 CD2 C:HIS26 3.2 9.3 1.0 CD2 C:HIS81 3.2 8.1 1.0 CD2 C:HIS171 3.2 4.7 1.0 OD1 C:ASP167 3.5 8.1 1.0 ND1 C:HIS171 4.3 3.9 1.0 ND1 C:HIS26 4.3 6.5 1.0 ND1 C:HIS81 4.3 7.5 1.0 CG C:HIS26 4.3 7.8 1.0 CG C:HIS81 4.4 8.0 1.0 CG C:HIS171 4.4 5.1 1.0 CB C:ASP167 4.4 6.8 1.0 NE2 C:GLN146 4.6 6.5 1.0 CZ2 C:TRP128 4.6 8.2 1.0 CB C:TRP169 4.6 6.3 1.0 CG C:TRP169 4.7 4.5 1.0 OH C:TYR34 4.9 17.7 1.0 CB C:ALA172 4.9 6.9 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of E. Coli Mnsod at 100K


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 E. Coli Mnsod at 100K within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn2209 b:7.4 occ:1.00 OD2 D:ASP167 2.1 7.6 1.0 O D:HOH2487 2.2 6.5 1.0 NE2 D:HIS171 2.2 5.9 1.0 NE2 D:HIS81 2.2 8.2 1.0 NE2 D:HIS26 2.2 8.2 1.0 O D:HOH2488 2.5 31.3 1.0 CE1 D:HIS171 3.1 5.4 1.0 CE1 D:HIS26 3.2 8.3 1.0 CG D:ASP167 3.2 6.4 1.0 CD2 D:HIS81 3.2 7.9 1.0 CE1 D:HIS81 3.2 8.6 1.0 CD2 D:HIS171 3.2 5.7 1.0 CD2 D:HIS26 3.2 6.3 1.0 OD1 D:ASP167 3.6 6.7 1.0 ND1 D:HIS171 4.2 7.8 1.0 ND1 D:HIS81 4.3 8.6 1.0 ND1 D:HIS26 4.3 9.2 1.0 CG D:HIS81 4.3 6.9 1.0 CG D:HIS171 4.3 7.8 1.0 CG D:HIS26 4.4 8.3 1.0 CB D:ASP167 4.4 7.1 1.0 CZ2 D:TRP128 4.5 9.0 1.0 NE2 D:GLN146 4.6 5.7 1.0 CB D:TRP169 4.7 5.9 1.0 CG D:TRP169 4.8 6.3 1.0 CB D:ALA172 4.9 8.4 1.0 CH2 D:TRP128 5.0 9.3 1.0

G.E.Borgstahl, M.Pokross, R.Chehab, A.Sekher, E.H.Snell. Cryo-Trapping the Six-Coordinate, Distorted-Octahedral Active Site of Manganese Superoxide Dismutase. J.Mol.Biol. V. 296 951 2000.
ISSN: ISSN 0022-2836
PubMed: 10686094
DOI: 10.1006/JMBI.1999.3506