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Manganese in PDB 7w6w: Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase L169W

Enzymatic activity of Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase L169W

All present enzymatic activity of Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase L169W:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase L169W, PDB code: 7w6w was solved by D.S.Retnoningrum, H.Yoshida, A.A.Artarini, W.T.Ismaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.59 / 1.94
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.245, 136.527, 55.506, 90, 100.91, 90
R / Rfree (%) 20.2 / 25.6

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase L169W (pdb code 7w6w). 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 L169W, PDB code: 7w6w:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 7w6w

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Manganese binding site 1 out of 4 in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase L169W


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 L169W within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:25.7
occ:1.00
OD2 A:ASP161 1.8 26.1 1.0
NE2 A:HIS27 2.0 25.8 1.0
NE2 A:HIS165 2.1 23.1 1.0
NE2 A:HIS81 2.1 23.5 1.0
O A:HOH417 2.2 22.6 1.0
CG A:ASP161 2.9 30.2 1.0
CE1 A:HIS27 3.0 28.0 1.0
CD2 A:HIS27 3.1 26.7 1.0
CE1 A:HIS81 3.1 24.8 1.0
CE1 A:HIS165 3.1 25.0 1.0
CD2 A:HIS165 3.1 27.6 1.0
CD2 A:HIS81 3.2 29.9 1.0
OD1 A:ASP161 3.4 32.1 1.0
ND1 A:HIS27 4.1 27.6 1.0
CG A:HIS27 4.2 26.3 1.0
ND1 A:HIS165 4.2 26.5 1.0
ND1 A:HIS81 4.2 26.6 1.0
CB A:ASP161 4.2 30.6 1.0
CG A:HIS165 4.3 26.4 1.0
CG A:HIS81 4.3 28.2 1.0
CZ2 A:TRP128 4.5 23.5 1.0
NE2 A:GLN146 4.6 34.7 1.0
CB A:TRP163 4.7 28.0 1.0
CG A:TRP163 4.8 27.3 1.0
CB A:ALA166 5.0 25.7 1.0

Manganese binding site 2 out of 4 in 7w6w

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Manganese binding site 2 out of 4 in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase L169W


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 L169W within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn302

b:24.9
occ:1.00
OD2 B:ASP161 2.0 24.1 1.0
NE2 B:HIS27 2.2 27.2 1.0
NE2 B:HIS81 2.2 23.3 1.0
O B:HOH447 2.3 21.5 1.0
NE2 B:HIS165 2.3 26.6 1.0
CG B:ASP161 3.1 21.4 1.0
CE1 B:HIS27 3.1 25.0 1.0
CE1 B:HIS81 3.1 23.4 1.0
CD2 B:HIS27 3.2 27.6 1.0
CD2 B:HIS165 3.2 24.4 1.0
CD2 B:HIS81 3.3 24.9 1.0
CE1 B:HIS165 3.3 30.2 1.0
OD1 B:ASP161 3.6 23.7 1.0
ND1 B:HIS27 4.2 26.9 1.0
CG B:HIS27 4.3 27.9 1.0
ND1 B:HIS81 4.3 23.3 1.0
CB B:ASP161 4.3 22.2 1.0
CG B:HIS165 4.4 27.2 1.0
CG B:HIS81 4.4 27.0 1.0
ND1 B:HIS165 4.4 22.8 1.0
CZ2 B:TRP128 4.5 24.1 1.0
NE2 B:GLN146 4.6 17.6 1.0
CB B:TRP163 4.8 19.8 1.0
CG B:TRP163 4.8 18.9 1.0

Manganese binding site 3 out of 4 in 7w6w

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Manganese binding site 3 out of 4 in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase L169W


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 L169W within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn301

b:26.4
occ:1.00
OD2 C:ASP161 1.9 32.1 1.0
NE2 C:HIS81 2.1 31.8 1.0
NE2 C:HIS165 2.1 22.9 1.0
NE2 C:HIS27 2.1 32.0 1.0
O C:HOH430 2.3 26.6 1.0
CG C:ASP161 2.9 30.8 1.0
CE1 C:HIS81 3.0 37.5 1.0
CE1 C:HIS165 3.1 24.4 1.0
CE1 C:HIS27 3.1 33.5 1.0
CD2 C:HIS81 3.1 32.0 1.0
CD2 C:HIS27 3.1 29.2 1.0
CD2 C:HIS165 3.1 26.1 1.0
OD1 C:ASP161 3.4 26.8 1.0
ND1 C:HIS81 4.1 31.2 1.0
ND1 C:HIS165 4.2 29.1 1.0
CB C:ASP161 4.2 29.6 1.0
CG C:HIS81 4.2 33.2 1.0
ND1 C:HIS27 4.2 28.0 1.0
CG C:HIS27 4.3 30.3 1.0
CG C:HIS165 4.3 27.4 1.0
CZ2 C:TRP128 4.5 30.6 1.0
NE2 C:GLN146 4.7 27.3 1.0
CB C:TRP163 4.7 24.9 1.0
CG C:TRP163 4.9 22.7 1.0
CB C:ALA166 4.9 21.8 1.0

Manganese binding site 4 out of 4 in 7w6w

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Manganese binding site 4 out of 4 in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase L169W


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 L169W within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn302

b:28.2
occ:1.00
OD2 D:ASP161 1.9 31.0 1.0
NE2 D:HIS27 2.0 35.3 1.0
NE2 D:HIS81 2.1 31.9 1.0
NE2 D:HIS165 2.2 26.1 1.0
CE1 D:HIS27 2.9 31.2 1.0
CG D:ASP161 3.0 28.0 1.0
CE1 D:HIS81 3.1 30.4 1.0
CD2 D:HIS81 3.1 33.9 1.0
CD2 D:HIS27 3.1 34.2 1.0
CE1 D:HIS165 3.1 22.3 1.0
CD2 D:HIS165 3.2 25.5 1.0
OD1 D:ASP161 3.4 26.1 1.0
ND1 D:HIS27 4.1 32.0 1.0
ND1 D:HIS81 4.2 36.8 1.0
CG D:HIS27 4.2 30.8 1.0
CG D:HIS81 4.2 32.9 1.0
CB D:ASP161 4.2 29.5 1.0
ND1 D:HIS165 4.3 25.7 1.0
CG D:HIS165 4.3 25.9 1.0
CZ2 D:TRP128 4.5 29.1 1.0
CB D:TRP163 4.6 25.9 1.0
NE2 D:GLN146 4.7 27.1 1.0
CG D:TRP163 4.8 25.7 1.0
CB D:ALA166 4.9 31.0 1.0

Reference:

D.S.Retnoningrum, H.Yoshida, A.A.Artarini, W.T.Ismaya. Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase L169W To Be Published.
Page generated: Sun Oct 6 10:59:13 2024

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