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Manganese in PDB 7wnl: Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase K38R and A121Y

Enzymatic activity of Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase K38R and A121Y

All present enzymatic activity of Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase K38R and A121Y:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase K38R and A121Y, PDB code: 7wnl 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) 44.79 / 1.51
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 100.926, 102.624, 179.017, 90, 90, 90
R / Rfree (%) 17.1 / 24.1

Other elements in 7wnl:

The structure of Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase K38R and A121Y also contains other interesting chemical elements:

Bromine (Br) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase K38R and A121Y (pdb code 7wnl). 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 K38R and A121Y, PDB code: 7wnl:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 7wnl

Go back to Manganese Binding Sites List in 7wnl
Manganese binding site 1 out of 4 in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase K38R and A121Y


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 K38R and A121Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn302

b:11.7
occ:1.00
 OD2 A:ASP161 1.9 15.0 1.0
NE2 A:HIS165 2.1 11.4 1.0
NE2 A:HIS27 2.1 9.4 1.0
NE2 A:HIS81 2.1 12.6 1.0
O A:HOH478 2.2 13.3 1.0
CG A:ASP161 3.0 15.4 1.0
CE1 A:HIS81 3.1 12.9 1.0
CE1 A:HIS27 3.1 14.0 1.0
CD2 A:HIS165 3.1 11.1 1.0
CE1 A:HIS165 3.1 11.5 1.0
CD2 A:HIS27 3.1 10.8 1.0
CD2 A:HIS81 3.2 13.9 1.0
OD1 A:ASP161 3.5 15.8 1.0
ND1 A:HIS27 4.2 13.3 1.0
ND1 A:HIS81 4.2 13.0 1.0
ND1 A:HIS165 4.2 12.1 1.0
CG A:HIS165 4.2 11.6 1.0
CB A:ASP161 4.3 12.9 1.0
CG A:HIS27 4.3 12.5 1.0
CG A:HIS81 4.3 11.7 1.0
CZ2 A:TRP128 4.5 16.1 1.0
CB A:TRP163 4.6 11.3 1.0
NE2 A:GLN146 4.7 14.2 1.0
CG A:TRP163 4.7 11.7 1.0
CB A:ALA166 4.9 14.2 1.0
CD1 A:TRP163 5.0 10.9 1.0

Manganese binding site 2 out of 4 in 7wnl

Go back to Manganese Binding Sites List in 7wnl
Manganese binding site 2 out of 4 in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase K38R and A121Y


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 K38R and A121Y within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:12.7
occ:1.00
 OD2 B:ASP161 1.9 15.6 1.0
O B:HOH624 2.1 20.3 1.0
NE2 B:HIS81 2.1 14.9 1.0
NE2 B:HIS165 2.2 11.1 1.0
NE2 B:HIS27 2.2 16.7 1.0
CG B:ASP161 3.0 15.7 1.0
CE1 B:HIS81 3.1 16.2 1.0
CD2 B:HIS165 3.1 14.8 1.0
CE1 B:HIS27 3.1 11.2 1.0
CD2 B:HIS27 3.2 16.3 1.0
CD2 B:HIS81 3.2 14.8 1.0
CE1 B:HIS165 3.2 11.9 1.0
OD1 B:ASP161 3.5 12.2 1.0
ND1 B:HIS81 4.2 16.0 1.0
ND1 B:HIS27 4.2 14.5 1.0
CG B:HIS165 4.3 13.8 1.0
CB B:ASP161 4.3 14.3 1.0
ND1 B:HIS165 4.3 13.2 1.0
CG B:HIS27 4.3 14.9 1.0
CG B:HIS81 4.3 15.0 1.0
CZ2 B:TRP128 4.4 14.8 1.0
NE2 B:GLN146 4.5 16.5 1.0
CB B:TRP163 4.5 10.6 1.0
CG B:TRP163 4.6 11.3 1.0
CD1 B:TRP163 4.9 12.1 1.0
CB B:ALA166 5.0 12.2 1.0

Manganese binding site 3 out of 4 in 7wnl

Go back to Manganese Binding Sites List in 7wnl
Manganese binding site 3 out of 4 in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase K38R and A121Y


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 K38R and A121Y within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn301

b:12.3
occ:1.00
 OD2 C:ASP161 2.0 13.4 1.0
O C:HOH525 2.0 14.5 1.0
NE2 C:HIS27 2.1 12.0 1.0
NE2 C:HIS165 2.1 8.1 1.0
NE2 C:HIS81 2.1 16.2 1.0
CG C:ASP161 3.0 13.6 1.0
CE1 C:HIS27 3.1 11.1 1.0
CE1 C:HIS165 3.1 12.3 1.0
CE1 C:HIS81 3.1 16.4 1.0
CD2 C:HIS81 3.1 14.7 1.0
CD2 C:HIS165 3.1 10.3 1.0
CD2 C:HIS27 3.2 13.2 1.0
OD1 C:ASP161 3.5 13.2 1.0
ND1 C:HIS27 4.2 11.8 1.0
ND1 C:HIS81 4.2 13.6 1.0
ND1 C:HIS165 4.2 12.2 1.0
CG C:HIS81 4.3 13.7 1.0
CG C:HIS165 4.3 12.2 1.0
CG C:HIS27 4.3 10.8 1.0
CB C:ASP161 4.3 11.7 1.0
CZ2 C:TRP128 4.4 15.4 1.0
CB C:TRP163 4.5 11.7 1.0
CG C:TRP163 4.6 13.0 1.0
NE2 C:GLN146 4.6 15.0 1.0
CD1 C:TRP163 4.9 12.7 1.0
CB C:ALA166 5.0 12.2 1.0
CH2 C:TRP128 5.0 15.0 1.0

Manganese binding site 4 out of 4 in 7wnl

Go back to Manganese Binding Sites List in 7wnl
Manganese binding site 4 out of 4 in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase K38R and A121Y


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 K38R and A121Y within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn301

b:12.5
occ:1.00
 OD2 D:ASP161 1.9 15.7 1.0
O D:HOH497 2.1 13.1 1.0
NE2 D:HIS81 2.1 15.6 1.0
NE2 D:HIS165 2.1 16.4 1.0
NE2 D:HIS27 2.2 11.8 1.0
O D:HOH401 2.2 32.3 1.0
CG D:ASP161 3.0 14.9 1.0
CE1 D:HIS81 3.0 14.8 1.0
CD2 D:HIS165 3.1 13.1 1.0
CD2 D:HIS81 3.1 19.0 1.0
CE1 D:HIS165 3.2 17.4 1.0
CE1 D:HIS27 3.2 15.6 1.0
CD2 D:HIS27 3.2 12.1 1.0
OD1 D:ASP161 3.5 13.3 1.0
ND1 D:HIS81 4.2 16.8 1.0
CB D:ASP161 4.2 12.4 1.0
CG D:HIS81 4.2 17.2 1.0
ND1 D:HIS165 4.3 14.4 1.0
CG D:HIS165 4.3 12.5 1.0
ND1 D:HIS27 4.3 14.7 1.0
CG D:HIS27 4.4 12.1 1.0
CZ2 D:TRP128 4.5 18.3 1.0
CB D:TRP163 4.6 11.8 1.0
NE2 D:GLN146 4.6 14.4 1.0
CG D:TRP163 4.7 11.2 1.0
CD1 D:TRP163 5.0 12.7 1.0
CB D:ALA166 5.0 16.4 1.0

Reference:

D.S.Retnoningrum, H.Yoshida, A.A.Artarini, W.T.Ismaya. Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase K38R and A121Y To Be Published.
Page generated: Sun Oct 6 11:01:55 2024

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