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Manganese in PDB 6gsc: Sphingobacterium Sp. T2 Manganese Superoxide Dismutase Catalyses the Oxidative Demethylation of Polymeric Lignin Via Generation of Hydroxyl Radical

Enzymatic activity of Sphingobacterium Sp. T2 Manganese Superoxide Dismutase Catalyses the Oxidative Demethylation of Polymeric Lignin Via Generation of Hydroxyl Radical

All present enzymatic activity of Sphingobacterium Sp. T2 Manganese Superoxide Dismutase Catalyses the Oxidative Demethylation of Polymeric Lignin Via Generation of Hydroxyl Radical:
1.15.1.1;

Protein crystallography data

The structure of Sphingobacterium Sp. T2 Manganese Superoxide Dismutase Catalyses the Oxidative Demethylation of Polymeric Lignin Via Generation of Hydroxyl Radical, PDB code: 6gsc was solved by G.M.M.Rashid, X.Zhang, R.C.Wilkinson, V.Fulop, B.Cottyn, S.Baumberger, T.D.H.Bugg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.66 / 1.32
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.530, 58.610, 75.070, 90.00, 90.37, 90.00
R / Rfree (%) 15 / 16.6

Manganese Binding Sites:

The binding sites of Manganese atom in the Sphingobacterium Sp. T2 Manganese Superoxide Dismutase Catalyses the Oxidative Demethylation of Polymeric Lignin Via Generation of Hydroxyl Radical (pdb code 6gsc). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Sphingobacterium Sp. T2 Manganese Superoxide Dismutase Catalyses the Oxidative Demethylation of Polymeric Lignin Via Generation of Hydroxyl Radical, PDB code: 6gsc:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 6gsc

Go back to Manganese Binding Sites List in 6gsc
Manganese binding site 1 out of 2 in the Sphingobacterium Sp. T2 Manganese Superoxide Dismutase Catalyses the Oxidative Demethylation of Polymeric Lignin Via Generation of Hydroxyl Radical


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Sphingobacterium Sp. T2 Manganese Superoxide Dismutase Catalyses the Oxidative Demethylation of Polymeric Lignin Via Generation of Hydroxyl Radical within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:22.5
occ:1.00
 OD2 A:ASP163 1.9 11.9 1.0
O A:HOH302 2.0 13.1 1.0
NE2 A:HIS26 2.2 11.2 1.0
NE2 A:HIS167 2.2 14.5 1.0
NE2 A:HIS76 2.3 12.5 1.0
CG A:ASP163 3.0 10.7 1.0
CE1 A:HIS26 3.1 11.8 1.0
CE1 A:HIS76 3.1 12.3 1.0
CD2 A:HIS167 3.1 12.0 1.0
CD2 A:HIS26 3.2 10.8 1.0
CE1 A:HIS167 3.3 13.2 1.0
CD2 A:HIS76 3.4 11.1 1.0
OD1 A:ASP163 3.4 11.4 1.0
ND1 A:HIS26 4.2 10.9 1.0
CB A:ASP163 4.2 10.8 1.0
CZ2 A:TRP125 4.3 10.1 1.0
CG A:HIS26 4.3 10.1 1.0
ND1 A:HIS76 4.3 12.2 1.0
CG A:HIS167 4.3 11.6 1.0
ND1 A:HIS167 4.4 13.1 1.0
NE2 A:GLN144 4.5 11.2 1.0
CG A:HIS76 4.5 10.4 1.0
CB A:TRP165 4.6 9.4 1.0
CG A:TRP165 4.7 9.1 1.0
CD1 A:TRP165 4.8 10.3 1.0
CH2 A:TRP125 5.0 10.0 1.0

Manganese binding site 2 out of 2 in 6gsc

Go back to Manganese Binding Sites List in 6gsc
Manganese binding site 2 out of 2 in the Sphingobacterium Sp. T2 Manganese Superoxide Dismutase Catalyses the Oxidative Demethylation of Polymeric Lignin Via Generation of Hydroxyl Radical


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Sphingobacterium Sp. T2 Manganese Superoxide Dismutase Catalyses the Oxidative Demethylation of Polymeric Lignin Via Generation of Hydroxyl Radical within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn301

b:24.8
occ:1.00
 OD2 B:ASP163 1.8 13.0 1.0
O B:HOH302 2.0 13.0 1.0
NE2 B:HIS26 2.2 12.9 1.0
NE2 B:HIS167 2.3 15.4 1.0
NE2 B:HIS76 2.3 13.9 1.0
CG B:ASP163 3.0 11.5 1.0
CE1 B:HIS26 3.1 12.5 1.0
CE1 B:HIS76 3.1 13.6 1.0
CD2 B:HIS26 3.2 12.3 1.0
CD2 B:HIS167 3.2 13.9 1.0
CE1 B:HIS167 3.4 14.4 1.0
CD2 B:HIS76 3.4 13.2 1.0
OD1 B:ASP163 3.4 12.2 1.0
CB B:ASP163 4.2 11.9 1.0
ND1 B:HIS26 4.2 12.0 1.0
CZ2 B:TRP125 4.2 11.4 1.0
CG B:HIS26 4.3 12.0 1.0
ND1 B:HIS76 4.3 12.9 1.0
CG B:HIS167 4.4 12.2 1.0
ND1 B:HIS167 4.4 14.5 1.0
NE2 B:GLN144 4.5 11.6 1.0
CG B:HIS76 4.5 12.2 1.0
CB B:TRP165 4.6 10.3 1.0
CG B:TRP165 4.7 9.8 1.0
CH2 B:TRP125 4.9 12.5 1.0
CD1 B:TRP165 4.9 9.8 1.0
CB B:ALA168 5.0 12.6 1.0

Reference:

G.M.M.Rashid, X.Zhang, R.C.Wilkinson, V.Fulop, B.Cottyn, S.Baumberger, T.D.H.Bugg. Sphingobacterium Sp. T2 Manganese Superoxide Dismutase Catalyzes the Oxidative Demethylation of Polymeric Lignin Via Generation of Hydroxyl Radical. Acs Chem. Biol. V. 13 2920 2018.
ISSN: ESSN 1554-8937
PubMed: 30247873
DOI: 10.1021/ACSCHEMBIO.8B00557
Page generated: Tue Dec 15 04:53:58 2020

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