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Manganese in PDB 7wnk: Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase K38R and A121E

Enzymatic activity of Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase K38R and A121E

All present enzymatic activity of Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase K38R and A121E:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase K38R and A121E, PDB code: 7wnk 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) 44.94 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.765, 113.174, 119.908, 90, 90, 90
R / Rfree (%) 17.8 / 19.4

Other elements in 7wnk:

The structure of Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase K38R and A121E also contains other interesting chemical elements:

Bromine (Br) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase K38R and A121E (pdb code 7wnk). 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 A121E, PDB code: 7wnk:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 7wnk

Go back to Manganese Binding Sites List in 7wnk
Manganese binding site 1 out of 4 in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase K38R and A121E


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 A121E within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:10.5
occ:1.00
 OD2 A:ASP161 2.0 10.5 1.0
O A:HOH520 2.0 11.2 1.0
NE2 A:HIS81 2.1 11.9 1.0
NE2 A:HIS165 2.2 9.8 1.0
NE2 A:HIS27 2.2 9.7 1.0
CG A:ASP161 3.0 11.7 1.0
CE1 A:HIS81 3.1 11.7 1.0
CE1 A:HIS165 3.1 9.7 1.0
CD2 A:HIS81 3.2 10.9 1.0
CE1 A:HIS27 3.2 10.6 1.0
CD2 A:HIS165 3.2 9.5 1.0
CD2 A:HIS27 3.2 10.6 1.0
OD1 A:ASP161 3.5 10.5 1.0
ND1 A:HIS81 4.2 12.1 1.0
ND1 A:HIS165 4.3 9.9 1.0
CG A:HIS81 4.3 10.3 1.0
ND1 A:HIS27 4.3 10.3 1.0
CG A:HIS165 4.3 9.6 1.0
CB A:ASP161 4.3 9.6 1.0
CG A:HIS27 4.3 10.0 1.0
CZ2 A:TRP128 4.4 11.6 1.0
CB A:TRP163 4.6 9.6 1.0
NE2 A:GLN146 4.6 11.5 1.0
CG A:TRP163 4.7 9.9 1.0
CD1 A:TRP163 4.9 10.0 1.0
CB A:ALA166 5.0 9.7 1.0

Manganese binding site 2 out of 4 in 7wnk

Go back to Manganese Binding Sites List in 7wnk
Manganese binding site 2 out of 4 in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase K38R and A121E


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 A121E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:10.5
occ:1.00
 OD2 B:ASP161 2.0 11.6 1.0
O B:HOH627 2.1 13.4 1.0
NE2 B:HIS165 2.1 11.4 1.0
NE2 B:HIS81 2.1 12.8 1.0
NE2 B:HIS27 2.2 11.1 1.0
CG B:ASP161 3.0 10.4 1.0
CE1 B:HIS81 3.1 13.7 1.0
CE1 B:HIS165 3.1 10.8 1.0
CD2 B:HIS165 3.1 10.7 1.0
CE1 B:HIS27 3.1 10.3 1.0
CD2 B:HIS81 3.1 11.9 1.0
CD2 B:HIS27 3.1 11.5 1.0
OD1 B:ASP161 3.5 11.6 1.0
ND1 B:HIS81 4.2 13.1 1.0
ND1 B:HIS165 4.2 10.8 1.0
ND1 B:HIS27 4.2 10.8 1.0
CG B:HIS81 4.3 11.9 1.0
CG B:HIS165 4.3 10.0 1.0
CG B:HIS27 4.3 11.4 1.0
CB B:ASP161 4.3 10.3 1.0
CZ2 B:TRP128 4.4 12.0 1.0
CB B:TRP163 4.6 10.1 1.0
NE2 B:GLN146 4.7 12.9 1.0
CG B:TRP163 4.7 9.4 1.0
CB B:ALA166 4.9 10.0 1.0

Manganese binding site 3 out of 4 in 7wnk

Go back to Manganese Binding Sites List in 7wnk
Manganese binding site 3 out of 4 in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase K38R and A121E


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 A121E within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn301

b:10.3
occ:1.00
 OD2 C:ASP161 2.0 11.0 1.0
NE2 C:HIS81 2.1 11.3 1.0
NE2 C:HIS165 2.2 11.2 1.0
O C:HOH509 2.2 12.9 1.0
NE2 C:HIS27 2.2 10.9 1.0
CG C:ASP161 3.0 11.1 1.0
CE1 C:HIS81 3.1 13.2 1.0
CE1 C:HIS27 3.1 11.2 1.0
CD2 C:HIS165 3.1 11.4 1.0
CE1 C:HIS165 3.2 11.8 1.0
CD2 C:HIS81 3.2 11.3 1.0
CD2 C:HIS27 3.2 11.1 1.0
OD1 C:ASP161 3.5 10.8 1.0
O C:HOH401 3.8 20.4 1.0
ND1 C:HIS81 4.2 12.9 1.0
ND1 C:HIS27 4.2 11.9 1.0
ND1 C:HIS165 4.3 11.4 1.0
CG C:HIS81 4.3 12.2 1.0
CG C:HIS165 4.3 11.1 1.0
CB C:ASP161 4.3 10.1 1.0
CG C:HIS27 4.3 10.9 1.0
CZ2 C:TRP128 4.4 11.8 1.0
CB C:TRP163 4.6 10.2 1.0
NE2 C:GLN146 4.7 11.7 1.0
CG C:TRP163 4.7 9.3 1.0
CB C:ALA166 5.0 10.0 1.0
CD1 C:TRP163 5.0 10.6 1.0

Manganese binding site 4 out of 4 in 7wnk

Go back to Manganese Binding Sites List in 7wnk
Manganese binding site 4 out of 4 in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase K38R and A121E


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 A121E within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn301

b:9.6
occ:1.00
 OD2 D:ASP161 1.9 10.3 1.0
NE2 D:HIS81 2.1 10.8 1.0
NE2 D:HIS165 2.1 10.6 1.0
NE2 D:HIS27 2.2 10.1 1.0
O D:HOH497 2.2 12.2 1.0
CG D:ASP161 3.0 9.8 1.0
CE1 D:HIS81 3.1 11.5 1.0
CD2 D:HIS165 3.1 10.4 1.0
CE1 D:HIS27 3.1 10.5 1.0
CD2 D:HIS81 3.1 9.9 1.0
CE1 D:HIS165 3.2 11.6 1.0
CD2 D:HIS27 3.2 10.1 1.0
OD1 D:ASP161 3.5 10.3 1.0
O D:HOH401 3.7 23.2 1.0
ND1 D:HIS81 4.2 11.5 1.0
ND1 D:HIS27 4.2 11.5 1.0
CG D:HIS81 4.3 10.8 1.0
ND1 D:HIS165 4.3 10.8 1.0
CB D:ASP161 4.3 9.4 1.0
CG D:HIS165 4.3 10.3 1.0
CG D:HIS27 4.3 11.2 1.0
CZ2 D:TRP128 4.4 11.4 1.0
CB D:TRP163 4.6 9.7 1.0
NE2 D:GLN146 4.7 10.9 1.0
CG D:TRP163 4.7 8.9 1.0
CB D:ALA166 4.9 10.7 1.0
CH2 D:TRP128 5.0 11.8 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 A121E To Be Published.
Page generated: Sun Oct 6 11:01:43 2024

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