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Manganese in PDB 8y17: Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase T89C and N187C

Enzymatic activity of Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase T89C and N187C

All present enzymatic activity of Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase T89C and N187C:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase T89C and N187C, PDB code: 8y17 was solved by N.A.Putri, M.D.Fadillah, H.Yoshida, D.S.Retnoningrum, A.A.Artarini, R.A.Utami, W.T.Ismaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.81 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 156.92, 135.82, 76.38, 90, 102.74, 90
R / Rfree (%) 23.4 / 27.6

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase T89C and N187C (pdb code 8y17). 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 A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase T89C and N187C, PDB code: 8y17:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 8y17

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Manganese binding site 1 out of 4 in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase T89C and N187C


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 A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase T89C and N187C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:49.0
occ:1.00
 OD2 A:ASP161 1.9 49.9 1.0
NE2 A:HIS81 2.0 51.6 1.0
NE2 A:HIS165 2.1 50.7 1.0
NE2 A:HIS27 2.3 53.5 1.0
CE1 A:HIS165 2.8 50.1 1.0
CE1 A:HIS81 2.8 52.1 1.0
CG A:ASP161 3.1 48.9 1.0
CD2 A:HIS81 3.1 52.4 1.0
CD2 A:HIS165 3.3 51.1 1.0
CE1 A:HIS27 3.3 54.5 1.0
CD2 A:HIS27 3.3 53.9 1.0
OD1 A:ASP161 3.6 49.7 1.0
ND1 A:HIS81 4.0 51.6 1.0
ND1 A:HIS165 4.0 49.6 1.0
CG A:HIS81 4.2 52.0 1.0
CG A:HIS165 4.3 50.4 1.0
CB A:ASP161 4.3 48.5 1.0
CZ2 A:TRP128 4.4 49.5 1.0
ND1 A:HIS27 4.4 54.3 1.0
NE2 A:GLN146 4.4 46.7 1.0
CG A:HIS27 4.5 54.8 1.0
CB A:TRP163 4.6 48.3 1.0
CG A:TRP163 4.6 47.9 1.0
OH A:TYR35 4.8 59.1 1.0
CD1 A:TRP163 4.9 48.3 1.0
CB A:ALA166 4.9 51.6 1.0
CE2 A:TYR35 5.0 59.2 1.0

Manganese binding site 2 out of 4 in 8y17

Go back to Manganese Binding Sites List in 8y17
Manganese binding site 2 out of 4 in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase T89C and N187C


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 A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase T89C and N187C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn301

b:43.6
occ:1.00
 OD2 B:ASP161 1.7 47.8 1.0
NE2 B:HIS81 1.9 46.5 1.0
NE2 B:HIS165 2.1 49.8 1.0
NE2 B:HIS27 2.2 50.6 1.0
CE1 B:HIS81 2.7 47.0 1.0
CE1 B:HIS165 2.9 50.9 1.0
CG B:ASP161 2.9 46.8 1.0
CD2 B:HIS81 3.1 47.9 1.0
CD2 B:HIS27 3.2 50.5 1.0
CE1 B:HIS27 3.2 50.5 1.0
CD2 B:HIS165 3.3 49.8 1.0
OD1 B:ASP161 3.5 46.5 1.0
ND1 B:HIS81 3.9 47.3 1.0
ND1 B:HIS165 4.1 49.8 1.0
CB B:ASP161 4.1 46.8 1.0
CG B:HIS81 4.1 48.3 1.0
ND1 B:HIS27 4.3 49.9 1.0
CG B:HIS165 4.3 49.5 1.0
CG B:HIS27 4.3 49.5 1.0
NE2 B:GLN146 4.3 43.1 1.0
CZ2 B:TRP128 4.3 53.9 1.0
CB B:TRP163 4.6 43.6 1.0
CG B:TRP163 4.7 42.7 1.0
CE2 B:TYR35 4.9 44.9 1.0
CB B:ALA166 4.9 48.5 1.0
CE2 B:TRP128 5.0 53.4 1.0
CD1 B:TRP163 5.0 42.4 1.0

Manganese binding site 3 out of 4 in 8y17

Go back to Manganese Binding Sites List in 8y17
Manganese binding site 3 out of 4 in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase T89C and N187C


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 A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase T89C and N187C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn301

b:42.4
occ:1.00
 OD2 C:ASP161 1.9 56.0 1.0
NE2 C:HIS81 2.0 48.9 1.0
NE2 C:HIS165 2.1 43.3 1.0
NE2 C:HIS27 2.3 46.5 1.0
CE1 C:HIS81 2.7 49.7 1.0
CE1 C:HIS165 2.7 43.6 1.0
CG C:ASP161 3.0 55.8 1.0
CE1 C:HIS27 3.1 46.8 1.0
CD2 C:HIS81 3.2 49.9 1.0
CD2 C:HIS165 3.3 43.9 1.0
CD2 C:HIS27 3.4 46.9 1.0
OD1 C:ASP161 3.6 59.2 1.0
ND1 C:HIS81 3.9 50.2 1.0
ND1 C:HIS165 3.9 43.5 1.0
CB C:ASP161 4.1 53.1 1.0
CG C:HIS81 4.1 50.9 1.0
CG C:HIS165 4.2 43.8 1.0
ND1 C:HIS27 4.3 46.7 1.0
CB C:TRP163 4.4 49.7 1.0
NE2 C:GLN146 4.4 46.4 1.0
CZ2 C:TRP128 4.4 48.7 1.0
CG C:HIS27 4.4 47.0 1.0
CG C:TRP163 4.5 49.6 1.0
CD1 C:TRP163 4.8 50.0 1.0
OH C:TYR35 4.9 65.8 1.0
CB C:ALA166 4.9 44.4 1.0
CE2 C:TYR35 5.0 62.3 1.0
CD2 C:TRP163 5.0 50.1 1.0

Manganese binding site 4 out of 4 in 8y17

Go back to Manganese Binding Sites List in 8y17
Manganese binding site 4 out of 4 in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase T89C and N187C


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 A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase T89C and N187C within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn301

b:47.2
occ:1.00
 OD2 D:ASP161 1.9 42.5 1.0
NE2 D:HIS81 2.0 51.3 1.0
NE2 D:HIS165 2.1 42.2 1.0
NE2 D:HIS27 2.2 47.6 1.0
CE1 D:HIS81 2.7 51.7 1.0
CE1 D:HIS165 2.8 42.5 1.0
CG D:ASP161 3.1 42.2 1.0
CD2 D:HIS27 3.1 48.1 1.0
CD2 D:HIS81 3.2 51.9 1.0
CE1 D:HIS27 3.2 48.5 1.0
CD2 D:HIS165 3.3 41.6 1.0
OD1 D:ASP161 3.7 41.2 1.0
ND1 D:HIS81 3.9 51.1 1.0
ND1 D:HIS165 4.0 42.5 1.0
CG D:HIS81 4.1 51.9 1.0
CB D:ASP161 4.2 42.4 1.0
ND1 D:HIS27 4.3 47.6 1.0
CG D:HIS27 4.3 48.5 1.0
CG D:HIS165 4.3 42.0 1.0
NE2 D:GLN146 4.3 51.3 1.0
CZ2 D:TRP128 4.4 49.0 1.0
CB D:TRP163 4.6 41.9 1.0
CG D:TRP163 4.7 42.7 1.0
CE2 D:TYR35 4.8 61.1 1.0
CB D:ALA166 4.9 45.6 1.0

Reference:

N.A.Putri, M.D.Fadillah, H.Yoshida, D.S.Retnoningrum, A.A.Artarini, R.A.Utami, W.T.Ismaya. Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase T89C and N187C To Be Published.
Page generated: Sun Feb 9 08:27:43 2025

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