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Manganese in PDB 7ddw: Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase S126C

Enzymatic activity of Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase S126C

All present enzymatic activity of Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase S126C:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase S126C, PDB code: 7ddw 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) 42.44 / 1.88
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.287, 131.732, 80.188, 90, 110.35, 90
R / Rfree (%) 15.7 / 22.2

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase S126C (pdb code 7ddw). 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 S126C, PDB code: 7ddw:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 7ddw

Go back to Manganese Binding Sites List in 7ddw
Manganese binding site 1 out of 6 in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase S126C


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 S126C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:16.3
occ:1.00
 OD2 A:ASP161 2.0 16.1 1.0
NE2 A:HIS27 2.1 16.1 1.0
NE2 A:HIS81 2.1 23.4 1.0
NE2 A:HIS165 2.1 14.5 1.0
O A:HOH489 2.2 17.1 1.0
CE1 A:HIS27 3.0 16.1 1.0
CG A:ASP161 3.0 14.0 1.0
CD2 A:HIS81 3.1 22.6 1.0
CD2 A:HIS27 3.1 16.5 1.0
CE1 A:HIS81 3.1 24.1 1.0
CE1 A:HIS165 3.1 16.0 1.0
CD2 A:HIS165 3.1 15.1 1.0
OD1 A:ASP161 3.5 15.5 1.0
ND1 A:HIS27 4.2 15.8 1.0
CG A:HIS27 4.2 15.7 1.0
ND1 A:HIS81 4.2 24.2 1.0
CG A:HIS81 4.2 21.3 1.0
ND1 A:HIS165 4.2 15.8 1.0
CG A:HIS165 4.3 15.3 1.0
CB A:ASP161 4.3 14.5 1.0
CZ2 A:TRP128 4.6 14.9 1.0
CB A:TRP163 4.6 16.0 1.0
NE2 A:GLN146 4.7 20.9 1.0
CG A:TRP163 4.8 16.3 1.0
CB A:ALA166 4.9 15.8 1.0

Manganese binding site 2 out of 6 in 7ddw

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Manganese binding site 2 out of 6 in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase S126C


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 S126C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn301

b:19.3
occ:1.00
 OD2 B:ASP161 1.9 16.7 1.0
NE2 B:HIS27 2.1 18.6 1.0
O B:HOH473 2.1 42.4 1.0
NE2 B:HIS81 2.2 16.5 1.0
NE2 B:HIS165 2.2 18.6 1.0
CG B:ASP161 2.9 20.2 1.0
CE1 B:HIS27 3.0 18.2 1.0
CD2 B:HIS27 3.1 17.5 1.0
CE1 B:HIS81 3.1 17.5 1.0
CD2 B:HIS165 3.1 17.9 1.0
CD2 B:HIS81 3.2 17.6 1.0
CE1 B:HIS165 3.2 17.2 1.0
OD1 B:ASP161 3.4 22.8 1.0
ND1 B:HIS27 4.1 19.1 1.0
CG B:HIS27 4.2 17.9 1.0
CB B:ASP161 4.2 20.5 1.0
ND1 B:HIS81 4.2 18.5 1.0
CG B:HIS81 4.3 17.9 1.0
CG B:HIS165 4.3 18.0 1.0
ND1 B:HIS165 4.3 18.3 1.0
CZ2 B:TRP128 4.4 20.4 1.0
CB B:TRP163 4.7 18.0 1.0
NE2 B:GLN146 4.7 22.6 1.0
CG B:TRP163 4.8 17.7 1.0
CB B:ALA166 4.9 16.4 1.0

Manganese binding site 3 out of 6 in 7ddw

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Manganese binding site 3 out of 6 in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase S126C


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 S126C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn301

b:20.0
occ:1.00
 OD2 C:ASP161 1.9 12.9 1.0
O C:HOH458 2.0 40.4 1.0
NE2 C:HIS27 2.1 19.0 1.0
NE2 C:HIS81 2.2 13.0 1.0
NE2 C:HIS165 2.2 21.5 1.0
CG C:ASP161 3.0 13.3 1.0
CE1 C:HIS27 3.0 17.4 1.0
CD2 C:HIS27 3.1 15.7 1.0
CD2 C:HIS81 3.1 14.6 1.0
CD2 C:HIS165 3.1 18.0 1.0
CE1 C:HIS81 3.2 14.1 1.0
CE1 C:HIS165 3.2 18.6 1.0
OD1 C:ASP161 3.4 13.8 1.0
ND1 C:HIS27 4.1 17.8 1.0
CG C:HIS27 4.2 15.5 1.0
CB C:ASP161 4.2 13.6 1.0
ND1 C:HIS81 4.3 14.4 1.0
CG C:HIS81 4.3 14.3 1.0
ND1 C:HIS165 4.3 18.8 1.0
CG C:HIS165 4.3 18.3 1.0
CZ2 C:TRP128 4.6 16.5 1.0
CB C:TRP163 4.7 17.1 1.0
NE2 C:GLN146 4.7 17.4 1.0
CG C:TRP163 4.8 17.6 1.0
CB C:ALA166 5.0 15.7 1.0

Manganese binding site 4 out of 6 in 7ddw

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Manganese binding site 4 out of 6 in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase S126C


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 S126C within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn301

b:13.8
occ:1.00
 OD2 D:ASP161 1.9 13.3 1.0
NE2 D:HIS81 2.1 17.1 1.0
NE2 D:HIS165 2.1 9.9 1.0
NE2 D:HIS27 2.1 13.0 1.0
O D:HOH479 2.2 19.0 1.0
CG D:ASP161 3.0 13.0 1.0
CE1 D:HIS165 3.1 10.4 1.0
CE1 D:HIS81 3.1 16.9 1.0
CD2 D:HIS27 3.1 12.3 1.0
CD2 D:HIS81 3.1 16.3 1.0
CE1 D:HIS27 3.1 13.2 1.0
CD2 D:HIS165 3.1 10.0 1.0
OD1 D:ASP161 3.5 14.9 1.0
ND1 D:HIS165 4.2 10.7 1.0
ND1 D:HIS81 4.2 17.3 1.0
ND1 D:HIS27 4.2 12.9 1.0
CG D:HIS27 4.2 13.1 1.0
CG D:HIS81 4.2 15.8 1.0
CG D:HIS165 4.3 11.8 1.0
CB D:ASP161 4.3 13.9 1.0
CZ2 D:TRP128 4.5 13.2 1.0
CB D:TRP163 4.7 15.1 1.0
NE2 D:GLN146 4.7 18.3 1.0
CG D:TRP163 4.8 15.8 1.0
CB D:ALA166 5.0 13.6 1.0
OH D:TYR35 5.0 33.1 1.0

Manganese binding site 5 out of 6 in 7ddw

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Manganese binding site 5 out of 6 in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase S126C


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 S126C within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn301

b:22.0
occ:1.00
 OD2 E:ASP161 1.9 21.7 1.0
O E:HOH425 2.1 28.8 1.0
NE2 E:HIS81 2.1 23.1 1.0
NE2 E:HIS27 2.1 29.5 1.0
NE2 E:HIS165 2.2 18.8 1.0
CG E:ASP161 3.0 20.9 1.0
CD2 E:HIS81 3.0 24.5 1.0
CD2 E:HIS27 3.1 27.6 1.0
CE1 E:HIS165 3.1 19.8 1.0
CE1 E:HIS81 3.1 22.4 1.0
CE1 E:HIS27 3.1 28.6 1.0
CD2 E:HIS165 3.2 18.8 1.0
OD1 E:ASP161 3.6 20.0 1.0
ND1 E:HIS81 4.2 23.3 1.0
CG E:HIS81 4.2 24.6 1.0
ND1 E:HIS27 4.2 27.7 1.0
CB E:ASP161 4.2 20.6 1.0
CG E:HIS27 4.2 26.7 1.0
ND1 E:HIS165 4.2 18.6 1.0
CG E:HIS165 4.3 18.2 1.0
CZ2 E:TRP128 4.5 17.2 1.0
CB E:TRP163 4.6 19.5 1.0
NE2 E:GLN146 4.7 23.7 1.0
CG E:TRP163 4.8 19.1 1.0
CE2 E:TYR35 5.0 32.9 1.0

Manganese binding site 6 out of 6 in 7ddw

Go back to Manganese Binding Sites List in 7ddw
Manganese binding site 6 out of 6 in the Crystal Structure of A Mutant Staphylococcus Equorum Manganese Superoxide Dismutase S126C


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 S126C within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn301

b:24.9
occ:1.00
 OD2 F:ASP161 1.9 26.4 1.0
O F:HOH436 2.0 30.9 1.0
NE2 F:HIS27 2.1 37.6 1.0
NE2 F:HIS165 2.2 24.9 1.0
NE2 F:HIS81 2.2 26.5 1.0
CG F:ASP161 3.0 24.0 1.0
CD2 F:HIS27 3.1 35.5 1.0
CE1 F:HIS165 3.1 22.7 1.0
CE1 F:HIS27 3.1 35.1 1.0
CD2 F:HIS81 3.1 25.5 1.0
CD2 F:HIS165 3.2 23.1 1.0
CE1 F:HIS81 3.3 25.0 1.0
OD1 F:ASP161 3.6 23.7 1.0
ND1 F:HIS27 4.2 34.7 1.0
CG F:HIS27 4.2 34.2 1.0
ND1 F:HIS165 4.2 22.8 1.0
CB F:ASP161 4.2 23.2 1.0
CG F:HIS81 4.3 26.8 1.0
CG F:HIS165 4.3 22.8 1.0
ND1 F:HIS81 4.4 26.3 1.0
CZ2 F:TRP128 4.5 23.4 1.0
CB F:TRP163 4.6 19.9 1.0
NE2 F:GLN146 4.7 26.4 1.0
CG F:TRP163 4.8 19.8 1.0
CB F:ALA166 5.0 22.4 1.0

Reference:

D.S.Retnoningrum, H.Yoshida, M.D.Razani, R.Muliadi, V.F.Meidianto, A.Artarini, W.T.Ismaya. The Role of S126 in the Staphylococcus Equorum Mnsod Activity and Stability To Be Published.
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