Manganese in PDB 3ak2: Superoxide Dismutase From Aeropyrum Pernix K1, Mn-Bound Form

All present enzymatic activity of Superoxide Dismutase From Aeropyrum Pernix K1, Mn-Bound Form:
1.15.1.1;

The structure of Superoxide Dismutase From Aeropyrum Pernix K1, Mn-Bound Form, PDB code: 3ak2 was solved by T.Nakamura, K.Uegaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.86 / 1.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.064, 71.782, 76.853, 90.00, 91.81, 90.00
R / Rfree (%)	18.7 / 20.3

The binding sites of Manganese atom in the Superoxide Dismutase From Aeropyrum Pernix K1, Mn-Bound Form (pdb code 3ak2). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Superoxide Dismutase From Aeropyrum Pernix K1, Mn-Bound Form, PDB code: 3ak2:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Superoxide Dismutase From Aeropyrum Pernix K1, Mn-Bound Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Superoxide Dismutase From Aeropyrum Pernix K1, Mn-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn215 b:9.4 occ:1.00 OD2 A:ASP165 2.0 11.6 1.0 O A:HOH223 2.1 14.6 1.0 NE2 A:HIS31 2.2 8.8 1.0 NE2 A:HIS79 2.2 9.7 1.0 NE2 A:HIS169 2.2 9.8 1.0 CE1 A:HIS79 3.1 9.0 1.0 CG A:ASP165 3.1 10.6 1.0 CE1 A:HIS31 3.2 10.0 1.0 CD2 A:HIS31 3.2 9.1 1.0 CE1 A:HIS169 3.2 10.1 1.0 CD2 A:HIS169 3.2 9.5 1.0 CD2 A:HIS79 3.3 9.4 1.0 OD1 A:ASP165 3.5 11.6 1.0 ND1 A:HIS79 4.2 9.2 1.0 ND1 A:HIS31 4.3 9.8 1.0 ND1 A:HIS169 4.3 10.1 1.0 CG A:HIS31 4.3 9.6 1.0 CG A:HIS169 4.3 9.8 1.0 CG A:HIS79 4.3 9.4 1.0 CB A:ASP165 4.4 10.1 1.0 CB A:TRP167 4.5 9.4 1.0 CZ2 A:TRP130 4.5 9.0 1.0 CH2 A:TRP130 4.5 9.2 1.0 CG A:TRP167 4.6 9.2 1.0 OH A:TYR39 4.7 15.8 1.0 CD1 A:TRP167 4.8 9.7 1.0 CE2 A:TYR39 4.8 12.4 1.0 CB A:HIS35 5.0 11.0 1.0

Manganese binding site 2 out of 4 in the Superoxide Dismutase From Aeropyrum Pernix K1, Mn-Bound Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Superoxide Dismutase From Aeropyrum Pernix K1, Mn-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn215 b:9.6 occ:1.00 OD2 B:ASP165 2.0 11.2 1.0 O B:HOH221 2.0 14.2 1.0 NE2 B:HIS31 2.2 10.2 1.0 NE2 B:HIS79 2.2 10.2 1.0 NE2 B:HIS169 2.3 10.0 1.0 CE1 B:HIS79 3.1 10.7 1.0 CG B:ASP165 3.1 9.9 1.0 CD2 B:HIS31 3.1 9.6 1.0 CE1 B:HIS31 3.2 10.1 1.0 CE1 B:HIS169 3.2 10.8 1.0 CD2 B:HIS169 3.2 11.1 1.0 CD2 B:HIS79 3.2 9.4 1.0 OD1 B:ASP165 3.5 11.7 1.0 ND1 B:HIS79 4.2 9.3 1.0 ND1 B:HIS31 4.3 10.1 1.0 CG B:HIS31 4.3 10.4 1.0 ND1 B:HIS169 4.3 10.7 1.0 CG B:HIS79 4.3 9.1 1.0 CB B:ASP165 4.4 9.6 1.0 CG B:HIS169 4.4 10.6 1.0 CB B:TRP167 4.5 9.2 1.0 CZ2 B:TRP130 4.5 9.4 1.0 CH2 B:TRP130 4.6 9.0 1.0 CG B:TRP167 4.6 9.2 1.0 OH B:TYR39 4.7 16.4 1.0 CD1 B:TRP167 4.8 9.8 1.0 CE2 B:TYR39 4.9 13.2 1.0 NE2 B:HIS150 5.0 11.1 1.0

Manganese binding site 3 out of 4 in the Superoxide Dismutase From Aeropyrum Pernix K1, Mn-Bound Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Superoxide Dismutase From Aeropyrum Pernix K1, Mn-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn215 b:11.0 occ:1.00 O C:HOH220 2.0 14.6 1.0 OD2 C:ASP165 2.0 12.5 1.0 NE2 C:HIS31 2.2 10.9 1.0 NE2 C:HIS79 2.2 11.8 1.0 NE2 C:HIS169 2.3 10.5 1.0 CE1 C:HIS79 3.1 11.8 1.0 CG C:ASP165 3.1 12.3 1.0 CD2 C:HIS31 3.1 10.9 1.0 CE1 C:HIS31 3.2 11.2 1.0 CD2 C:HIS169 3.2 10.7 1.0 CE1 C:HIS169 3.3 11.2 1.0 CD2 C:HIS79 3.3 12.1 1.0 OD1 C:ASP165 3.6 12.3 1.0 ND1 C:HIS79 4.2 11.7 1.0 ND1 C:HIS31 4.3 11.7 1.0 CG C:HIS31 4.3 11.4 1.0 CG C:HIS79 4.4 11.4 1.0 CB C:ASP165 4.4 11.3 1.0 ND1 C:HIS169 4.4 11.3 1.0 CG C:HIS169 4.4 11.4 1.0 CB C:TRP167 4.5 10.2 1.0 CZ2 C:TRP130 4.6 10.5 1.0 CG C:TRP167 4.6 10.1 1.0 OH C:TYR39 4.6 17.5 1.0 CH2 C:TRP130 4.6 10.4 1.0 CD1 C:TRP167 4.8 10.5 1.0 CE2 C:TYR39 4.8 15.2 1.0 NE2 C:HIS150 5.0 12.2 1.0

Manganese binding site 4 out of 4 in the Superoxide Dismutase From Aeropyrum Pernix K1, Mn-Bound Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Superoxide Dismutase From Aeropyrum Pernix K1, Mn-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn215 b:10.6 occ:1.00 OD2 D:ASP165 2.1 11.8 1.0 O D:HOH221 2.1 14.5 1.0 NE2 D:HIS31 2.2 10.7 1.0 NE2 D:HIS79 2.2 10.4 1.0 NE2 D:HIS169 2.2 11.4 1.0 CE1 D:HIS79 3.0 11.3 1.0 CG D:ASP165 3.1 11.5 1.0 CE1 D:HIS31 3.2 11.2 1.0 CD2 D:HIS31 3.2 10.8 1.0 CE1 D:HIS169 3.2 11.4 1.0 CD2 D:HIS169 3.2 11.4 1.0 CD2 D:HIS79 3.3 11.7 1.0 OD1 D:ASP165 3.5 12.7 1.0 ND1 D:HIS79 4.2 11.4 1.0 ND1 D:HIS31 4.3 11.1 1.0 CG D:HIS31 4.3 11.3 1.0 ND1 D:HIS169 4.3 11.3 1.0 CG D:HIS79 4.3 11.8 1.0 CG D:HIS169 4.3 11.0 1.0 CB D:ASP165 4.4 11.1 1.0 CB D:TRP167 4.5 10.1 1.0 CZ2 D:TRP130 4.5 10.3 1.0 CH2 D:TRP130 4.6 10.9 1.0 CG D:TRP167 4.6 10.3 1.0 OH D:TYR39 4.7 17.2 1.0 CE2 D:TYR39 4.8 14.3 1.0 CD1 D:TRP167 4.9 10.2 1.0 CB D:HIS35 5.0 13.7 1.0

T.Nakamura, K.Torikai, K.Uegaki, J.Morita, K.Machida, A.Suzuki, Y.Kawata. Crystal Structure of the Cambialistic Superoxide Dismutase From Aeropyrum Pernix K1 - Insights Into the Enzyme Mechanism and Stability Febs J. V. 278 598 2011.
ISSN: ISSN 1742-464X
PubMed: 21182595
DOI: 10.1111/J.1742-4658.2010.07977.X