Magnesium in PDB 8qwt: Ligninolytic Manganese Peroxidase Cst-MNP1 From Agaricales Mushrooms in Complex with A Manganese Ion

Enzymatic activity of Ligninolytic Manganese Peroxidase Cst-MNP1 From Agaricales Mushrooms in Complex with A Manganese Ion

All present enzymatic activity of Ligninolytic Manganese Peroxidase Cst-MNP1 From Agaricales Mushrooms in Complex with A Manganese Ion:
1.11.1.13;

Protein crystallography data

The structure of Ligninolytic Manganese Peroxidase Cst-MNP1 From Agaricales Mushrooms in Complex with A Manganese Ion, PDB code: 8qwt was solved by E.Santillana, A.Romero, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.76 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.79, 56.64, 109.51, 90, 90, 90
R / Rfree (%) 16.3 / 18.9

Other elements in 8qwt:

The structure of Ligninolytic Manganese Peroxidase Cst-MNP1 From Agaricales Mushrooms in Complex with A Manganese Ion also contains other interesting chemical elements:

Iron (Fe) 1 atom
Calcium (Ca) 2 atoms
Manganese (Mn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ligninolytic Manganese Peroxidase Cst-MNP1 From Agaricales Mushrooms in Complex with A Manganese Ion (pdb code 8qwt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Ligninolytic Manganese Peroxidase Cst-MNP1 From Agaricales Mushrooms in Complex with A Manganese Ion, PDB code: 8qwt:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 8qwt

Go back to Magnesium Binding Sites List in 8qwt
Magnesium binding site 1 out of 3 in the Ligninolytic Manganese Peroxidase Cst-MNP1 From Agaricales Mushrooms in Complex with A Manganese Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ligninolytic Manganese Peroxidase Cst-MNP1 From Agaricales Mushrooms in Complex with A Manganese Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:25.5
occ:1.00
 O A:HOH633 2.9 30.4 1.0
NE2 A:GLN246 3.3 17.6 1.0
CG A:GLN246 3.7 15.4 1.0
CA A:ALA247 3.8 12.5 1.0
O A:GLN246 3.9 12.1 1.0
C A:GLN246 3.9 12.1 1.0
N A:ALA247 4.0 13.1 1.0
CD A:GLN246 4.0 16.9 1.0
O A:THR311 4.0 18.1 1.0
CB A:SER310 4.2 22.7 1.0
CB A:GLN246 4.3 13.7 1.0
CD A:PRO313 4.4 18.0 1.0
CB A:ALA247 4.5 12.3 1.0
O A:HOH511 4.7 20.8 1.0
CA A:GLN246 4.8 12.1 1.0
C A:ALA247 4.9 12.4 1.0
OG A:SER310 5.0 26.3 1.0

Magnesium binding site 2 out of 3 in 8qwt

Go back to Magnesium Binding Sites List in 8qwt
Magnesium binding site 2 out of 3 in the Ligninolytic Manganese Peroxidase Cst-MNP1 From Agaricales Mushrooms in Complex with A Manganese Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ligninolytic Manganese Peroxidase Cst-MNP1 From Agaricales Mushrooms in Complex with A Manganese Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:28.3
occ:1.00
 O A:HOH639 2.6 22.2 1.0
O A:SER239 2.7 20.2 1.0
N A:CYS243 2.9 16.0 1.0
CB A:CYS243 3.3 20.9 1.0
SG A:CYS243 3.4 31.3 1.0
N A:ALA242 3.5 14.6 1.0
C A:SER239 3.6 19.9 1.0
CA A:CYS243 3.7 16.3 1.0
C A:ALA242 3.9 14.3 1.0
C A:ARG240 4.0 17.5 1.0
N A:THR241 4.0 16.0 1.0
CA A:ALA242 4.0 14.1 1.0
C A:THR241 4.1 14.9 1.0
O A:ARG240 4.2 19.4 1.0
CB A:ALA242 4.2 15.0 1.0
N A:ARG240 4.5 18.5 1.0
CA A:SER239 4.5 21.4 0.5
CA A:SER239 4.5 20.1 0.5
CA A:THR241 4.5 15.9 1.0
CA A:ARG240 4.5 18.4 1.0
O A:ASP238 4.5 16.6 1.0
N A:LEU244 4.6 14.2 1.0
C A:CYS243 4.7 15.3 1.0
O A:THR241 4.8 14.5 1.0

Magnesium binding site 3 out of 3 in 8qwt

Go back to Magnesium Binding Sites List in 8qwt
Magnesium binding site 3 out of 3 in the Ligninolytic Manganese Peroxidase Cst-MNP1 From Agaricales Mushrooms in Complex with A Manganese Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ligninolytic Manganese Peroxidase Cst-MNP1 From Agaricales Mushrooms in Complex with A Manganese Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg407

b:25.2
occ:1.00
 OG A:SER331 1.9 44.9 1.0
OD2 A:ASP30 2.1 27.8 1.0
OE2 A:GLU37 2.1 25.1 1.0
C A:SER331 2.6 41.1 1.0
OE1 A:GLU37 2.7 21.9 1.0
CD A:GLU37 2.7 20.8 1.0
CB A:SER331 2.8 46.9 1.0
CA A:SER331 2.9 45.2 1.0
CG A:ASP30 3.0 24.1 1.0
OD1 A:ASP30 3.3 29.2 1.0
O A:SER331 3.8 39.2 1.0
O A:HOH615 3.8 25.9 1.0
CG A:GLU37 4.2 15.9 1.0
N A:SER331 4.4 45.0 1.0
CB A:ASP30 4.4 20.9 1.0
NH2 A:ARG88 4.4 21.9 1.0
NE A:ARG88 4.8 18.8 1.0
O A:LEU28 4.9 13.6 1.0

Reference:

M.I.Sanchez-Ruiz, E.Santillana, D.Linde, A.Romero, A.T.Martinez, F.J.Ruiz-Duenas. Structure-Function Characterization of Two Enzymes From Novel Subfamilies of Manganese Peroxidases Secreted By the Lignocellulose-Degrading Agaricales Fungi Agrocybe Pediades and Cyathus Striatus. Biotechnol Biofuels Bioprod V. 17 74 2024.
ISSN: ISSN 2731-3654
PubMed: 38824538
DOI: 10.1186/S13068-024-02517-1
Page generated: Fri Oct 4 17:00:20 2024

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