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Manganese in PDB 6m30: Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase N73F

Enzymatic activity of Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase N73F

All present enzymatic activity of Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase N73F:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase N73F, PDB code: 6m30 was solved by D.S.Retnoningrum, H.Yoshida, M.D.Razani, V.F.Meidianto, A.Hartanto, A.Artarini, W.T.Ismaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.84 / 1.74
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.123, 132.504, 80.507, 90, 110.67, 90
R / Rfree (%) 16.2 / 21.3

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase N73F (pdb code 6m30). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase N73F, PDB code: 6m30:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 6m30

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Manganese binding site 1 out of 6 in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase N73F


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 N73F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn201

b:13.3
occ:1.00
 OD2 A:ASP161 1.9 15.3 1.0
O A:HOH341 2.1 14.8 1.0
NE2 A:HIS27 2.1 13.7 1.0
NE2 A:HIS81 2.1 14.4 1.0
NE2 A:HIS165 2.2 13.6 1.0
O A:HOH308 2.2 28.9 1.0
CG A:ASP161 3.0 13.6 1.0
CE1 A:HIS27 3.0 15.3 1.0
CE1 A:HIS81 3.1 15.8 1.0
CE1 A:HIS165 3.1 15.1 1.0
CD2 A:HIS27 3.1 13.3 1.0
CD2 A:HIS165 3.2 14.2 1.0
CD2 A:HIS81 3.2 15.1 1.0
OD1 A:ASP161 3.5 15.1 1.0
ND1 A:HIS27 4.2 14.5 1.0
ND1 A:HIS81 4.2 15.5 1.0
CG A:HIS27 4.2 14.8 1.0
ND1 A:HIS165 4.2 13.8 1.0
CB A:ASP161 4.3 13.3 1.0
CG A:HIS81 4.3 15.6 1.0
CG A:HIS165 4.3 13.0 1.0
CZ2 A:TRP128 4.5 15.2 1.0
CB A:TRP163 4.6 12.0 1.0
NE2 A:GLN146 4.6 14.3 1.0
O A:HOH304 4.7 28.5 1.0
CG A:TRP163 4.7 12.9 1.0
CD1 A:TRP163 5.0 12.1 1.0
CB A:ALA166 5.0 13.1 1.0

Manganese binding site 2 out of 6 in 6m30

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Manganese binding site 2 out of 6 in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase N73F


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 N73F within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn201

b:14.6
occ:1.00
 O B:HOH301 1.9 31.9 1.0
OD2 B:ASP161 1.9 14.2 1.0
NE2 B:HIS27 2.1 13.1 1.0
NE2 B:HIS81 2.1 17.5 1.0
O B:HOH359 2.2 15.8 1.0
NE2 B:HIS165 2.2 14.8 1.0
CG B:ASP161 3.0 15.2 1.0
CE1 B:HIS81 3.1 18.0 1.0
CE1 B:HIS27 3.1 14.0 1.0
CD2 B:HIS27 3.1 14.2 1.0
CD2 B:HIS81 3.2 17.7 1.0
CD2 B:HIS165 3.2 14.9 1.0
CE1 B:HIS165 3.2 16.0 1.0
OD1 B:ASP161 3.5 16.4 1.0
ND1 B:HIS27 4.2 13.4 1.0
ND1 B:HIS81 4.2 16.5 1.0
CB B:ASP161 4.3 15.4 1.0
CG B:HIS27 4.3 14.6 1.0
CG B:HIS81 4.3 17.0 1.0
ND1 B:HIS165 4.3 14.1 1.0
CG B:HIS165 4.3 14.6 1.0
CZ2 B:TRP128 4.4 17.9 1.0
CB B:TRP163 4.6 13.4 1.0
NE2 B:GLN146 4.7 16.1 1.0
CG B:TRP163 4.7 14.0 1.0
CB B:ALA166 4.9 16.6 1.0
CD1 B:TRP163 5.0 13.3 1.0
CH2 B:TRP128 5.0 19.0 1.0

Manganese binding site 3 out of 6 in 6m30

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Manganese binding site 3 out of 6 in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase N73F


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 N73F within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn201

b:14.9
occ:1.00
 O C:HOH301 1.9 35.6 1.0
OD2 C:ASP161 1.9 13.2 1.0
NE2 C:HIS81 2.1 16.1 1.0
NE2 C:HIS27 2.2 13.6 1.0
NE2 C:HIS165 2.2 13.2 1.0
O C:HOH364 2.2 13.7 1.0
CG C:ASP161 3.0 14.6 1.0
CE1 C:HIS81 3.1 16.9 1.0
CE1 C:HIS27 3.1 14.7 1.0
CD2 C:HIS81 3.1 16.0 1.0
CE1 C:HIS165 3.1 17.2 1.0
CD2 C:HIS27 3.2 15.5 1.0
CD2 C:HIS165 3.2 14.6 1.0
OD1 C:ASP161 3.5 16.5 1.0
ND1 C:HIS81 4.2 17.1 1.0
ND1 C:HIS27 4.2 14.8 1.0
CB C:ASP161 4.3 13.9 1.0
ND1 C:HIS165 4.3 15.4 1.0
CG C:HIS81 4.3 15.8 1.0
CG C:HIS27 4.3 15.7 1.0
CG C:HIS165 4.3 14.1 1.0
CZ2 C:TRP128 4.4 15.8 1.0
CB C:TRP163 4.6 14.3 1.0
NE2 C:GLN146 4.7 15.9 1.0
CG C:TRP163 4.7 15.4 1.0
O C:HOH306 4.8 31.8 1.0
CB C:ALA166 4.9 12.2 1.0

Manganese binding site 4 out of 6 in 6m30

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Manganese binding site 4 out of 6 in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase N73F


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 N73F within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn201

b:12.8
occ:1.00
 OD2 D:ASP161 1.9 12.7 1.0
NE2 D:HIS165 2.1 11.5 1.0
NE2 D:HIS27 2.1 13.4 1.0
NE2 D:HIS81 2.2 15.4 1.0
O D:HOH358 2.2 14.5 1.0
O D:HOH311 2.3 30.1 1.0
CG D:ASP161 3.0 11.4 1.0
CE1 D:HIS27 3.1 13.2 1.0
CE1 D:HIS165 3.1 13.2 1.0
CD2 D:HIS81 3.1 16.0 1.0
CD2 D:HIS165 3.1 12.2 1.0
CD2 D:HIS27 3.2 12.1 1.0
CE1 D:HIS81 3.2 16.0 1.0
OD1 D:ASP161 3.5 11.8 1.0
ND1 D:HIS27 4.2 12.6 1.0
ND1 D:HIS165 4.2 11.8 1.0
CB D:ASP161 4.2 12.4 1.0
CG D:HIS165 4.3 11.2 1.0
CG D:HIS27 4.3 12.9 1.0
CG D:HIS81 4.3 15.6 1.0
ND1 D:HIS81 4.3 14.4 1.0
CZ2 D:TRP128 4.4 16.3 1.0
CB D:TRP163 4.6 12.8 1.0
NE2 D:GLN146 4.6 12.6 1.0
O D:HOH303 4.7 29.6 1.0
CG D:TRP163 4.7 14.4 1.0
CD1 D:TRP163 5.0 14.5 1.0
CB D:ALA166 5.0 12.8 1.0

Manganese binding site 5 out of 6 in 6m30

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Manganese binding site 5 out of 6 in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase N73F


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase N73F within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn201

b:17.5
occ:1.00
 OD2 E:ASP161 1.9 19.1 1.0
NE2 E:HIS27 2.1 18.7 1.0
NE2 E:HIS165 2.1 17.3 1.0
NE2 E:HIS81 2.1 20.8 1.0
O E:HOH301 2.2 33.7 1.0
O E:HOH342 2.2 23.6 1.0
CG E:ASP161 3.0 17.9 1.0
CE1 E:HIS27 3.1 18.2 1.0
CE1 E:HIS165 3.1 20.8 1.0
CE1 E:HIS81 3.1 20.3 1.0
CD2 E:HIS27 3.1 18.6 1.0
CD2 E:HIS165 3.2 18.0 1.0
CD2 E:HIS81 3.2 22.2 1.0
OD1 E:ASP161 3.5 19.3 1.0
ND1 E:HIS27 4.2 19.2 1.0
ND1 E:HIS165 4.2 20.4 1.0
ND1 E:HIS81 4.2 20.8 1.0
CG E:HIS27 4.2 18.5 1.0
CG E:HIS165 4.3 18.6 1.0
CB E:ASP161 4.3 16.9 1.0
CG E:HIS81 4.3 21.3 1.0
CZ2 E:TRP128 4.4 21.0 1.0
CB E:TRP163 4.5 17.6 1.0
NE2 E:GLN146 4.6 20.6 1.0
CG E:TRP163 4.7 17.6 1.0
O E:HOH308 4.7 33.8 1.0
CD1 E:TRP163 5.0 17.0 1.0

Manganese binding site 6 out of 6 in 6m30

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Manganese binding site 6 out of 6 in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase N73F


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase N73F within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn201

b:17.1
occ:1.00
 OD2 F:ASP161 1.9 16.6 1.0
NE2 F:HIS81 2.1 18.8 1.0
NE2 F:HIS27 2.1 18.3 1.0
O F:HOH356 2.1 19.9 1.0
NE2 F:HIS165 2.2 17.9 1.0
O F:HOH301 2.2 30.6 1.0
CG F:ASP161 3.0 16.9 1.0
CE1 F:HIS81 3.1 19.0 1.0
CE1 F:HIS165 3.1 18.5 1.0
CE1 F:HIS27 3.1 17.9 1.0
CD2 F:HIS81 3.1 19.7 1.0
CD2 F:HIS27 3.1 17.4 1.0
CD2 F:HIS165 3.2 18.7 1.0
OD1 F:ASP161 3.5 16.3 1.0
ND1 F:HIS81 4.2 18.5 1.0
ND1 F:HIS27 4.2 17.2 1.0
ND1 F:HIS165 4.2 16.4 1.0
CG F:HIS81 4.3 20.5 1.0
CB F:ASP161 4.3 17.1 1.0
CG F:HIS27 4.3 18.4 1.0
CG F:HIS165 4.3 17.8 1.0
CZ2 F:TRP128 4.4 19.1 1.0
CB F:TRP163 4.6 16.9 1.0
NE2 F:GLN146 4.6 19.6 1.0
CG F:TRP163 4.8 17.1 1.0
O F:HOH304 4.9 35.9 1.0

Reference:

D.S.Retnoningrum, H.Yoshida, M.D.Razani, V.F.Meidianto, A.Hartanto, A.Artarini, W.T.Ismaya. Unprecedented Role of the N73-F124 Pair in the Staphylococcus Equorum Mnsod Activity. Curr Enzym Inhib 2021.
ISSN: ISSN 1875-6662
DOI: 10.2174/1573408016999201027212952
Page generated: Sun Oct 6 05:29:59 2024

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