Atomistry » Manganese » PDB 7d7z-7eww » 7ddw
Atomistry »
  Manganese »
    PDB 7d7z-7eww »
      7ddw »

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

Go back to Manganese Binding Sites List in 7ddw
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

Go back to Manganese Binding Sites List in 7ddw
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

Go back to Manganese Binding Sites List in 7ddw
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

Go back to Manganese Binding Sites List in 7ddw
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.
Page generated: Sun Oct 6 08:26:02 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy