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Manganese in PDB 4mig: Pyranose 2-Oxidase From Phanerochaete Chrysosporium, Recombinant Wild Type

Enzymatic activity of Pyranose 2-Oxidase From Phanerochaete Chrysosporium, Recombinant Wild Type

All present enzymatic activity of Pyranose 2-Oxidase From Phanerochaete Chrysosporium, Recombinant Wild Type:
1.1.3.10;

Protein crystallography data

The structure of Pyranose 2-Oxidase From Phanerochaete Chrysosporium, Recombinant Wild Type, PDB code: 4mig was solved by N.Hassan, T.C.Tan, O.Spadiut, I.Pisanelli, L.Fusco, D.Haltrich, C.Peterbauer, C.Divne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.05 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.544, 166.448, 91.844, 90.00, 106.41, 90.00
R / Rfree (%) 17.3 / 21.4

Other elements in 4mig:

The structure of Pyranose 2-Oxidase From Phanerochaete Chrysosporium, Recombinant Wild Type also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Pyranose 2-Oxidase From Phanerochaete Chrysosporium, Recombinant Wild Type (pdb code 4mig). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Pyranose 2-Oxidase From Phanerochaete Chrysosporium, Recombinant Wild Type, PDB code: 4mig:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4mig

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Manganese binding site 1 out of 8 in the Pyranose 2-Oxidase From Phanerochaete Chrysosporium, Recombinant Wild Type


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Pyranose 2-Oxidase From Phanerochaete Chrysosporium, Recombinant Wild Type within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn803

b:33.3
occ:1.00
 O A:HOH1001 2.2 30.8 1.0
NE2 A:HIS572 2.3 20.6 1.0
O A:HOH1002 2.3 15.1 1.0
CD2 A:HIS572 3.0 18.1 1.0
CE1 A:HIS572 3.4 20.9 1.0
O A:HOH1201 3.5 24.4 1.0
CG A:HIS572 4.3 16.8 1.0
MN A:MN804 4.4 30.1 1.0
ND1 A:HIS572 4.5 19.4 1.0
NH1 A:ARG607 4.6 14.1 1.0
O A:ARG607 4.7 10.4 1.0
O A:HOH1003 4.7 24.4 1.0
CZ A:ARG607 4.8 13.6 1.0
NH2 A:ARG607 4.8 14.7 1.0

Manganese binding site 2 out of 8 in 4mig

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Manganese binding site 2 out of 8 in the Pyranose 2-Oxidase From Phanerochaete Chrysosporium, Recombinant Wild Type


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Pyranose 2-Oxidase From Phanerochaete Chrysosporium, Recombinant Wild Type within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn804

b:30.1
occ:1.00
 O A:HOH1001 2.3 30.8 1.0
O A:HOH1003 2.3 24.4 1.0
NH1 A:ARG607 3.4 14.1 1.0
CG A:ARG607 3.9 12.5 1.0
CG2 A:ILE192 4.0 10.9 1.0
CD2 A:LEU196 4.2 10.6 1.0
CD1 A:LEU196 4.4 10.5 1.0
MN A:MN803 4.4 33.3 1.0
CZ A:ARG607 4.5 13.6 1.0
CG A:LEU196 4.6 10.5 1.0
CD A:ARG607 4.6 12.2 1.0
CA A:ARG607 4.8 11.1 1.0
CB A:ARG607 4.9 11.5 1.0
NE A:ARG607 4.9 12.7 1.0

Manganese binding site 3 out of 8 in 4mig

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Manganese binding site 3 out of 8 in the Pyranose 2-Oxidase From Phanerochaete Chrysosporium, Recombinant Wild Type


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Pyranose 2-Oxidase From Phanerochaete Chrysosporium, Recombinant Wild Type within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn805

b:34.1
occ:1.00
 O D:HOH901 2.3 22.3 1.0
O A:HOH1056 3.3 15.4 1.0
CE1 A:PHE510 3.9 14.7 1.0
CB A:PRO548 3.9 10.6 1.0
CG A:PRO387 4.1 13.1 1.0
N A:PRO387 4.1 12.0 1.0
CE A:MET512 4.2 12.3 1.0
CA A:PRO387 4.3 12.6 1.0
CA A:PRO548 4.3 10.3 1.0
CD2 A:LEU143 4.3 12.3 1.0
CD A:PRO387 4.4 12.7 1.0
CD1 A:PHE510 4.4 14.3 1.0
C A:GLN386 4.4 12.3 1.0
O A:GLU385 4.5 14.8 1.0
CB A:GLU385 4.5 16.0 1.0
CB A:PRO387 4.6 12.8 1.0
C A:GLU385 4.6 14.1 1.0
CG A:PRO548 4.6 11.5 1.0
CG A:GLU385 4.6 17.4 1.0
O A:GLN386 4.7 11.9 1.0
CZ A:PHE510 4.8 14.5 1.0
N A:GLN386 4.8 12.5 1.0
O D:HOH1118 4.8 22.6 1.0
N A:GLY549 4.9 10.4 1.0
CG2 A:THR483 4.9 10.3 1.0
O D:HOH1014 5.0 19.7 1.0

Manganese binding site 4 out of 8 in 4mig

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Manganese binding site 4 out of 8 in the Pyranose 2-Oxidase From Phanerochaete Chrysosporium, Recombinant Wild Type


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Pyranose 2-Oxidase From Phanerochaete Chrysosporium, Recombinant Wild Type within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn803

b:38.6
occ:1.00
 O C:HOH1001 2.3 28.7 1.0
O B:HOH1185 3.1 18.2 1.0
CE1 B:PHE510 3.8 17.3 1.0
CB B:PRO548 4.0 15.0 1.0
CE B:MET512 4.0 16.2 1.0
CG B:PRO387 4.1 14.7 1.0
CD2 B:LEU143 4.2 14.4 1.0
CD B:PRO387 4.3 14.9 1.0
N B:PRO387 4.3 13.9 1.0
CD1 B:PHE510 4.4 17.5 1.0
CB B:GLU385 4.4 19.7 1.0
CA B:PRO387 4.4 13.8 1.0
CA B:PRO548 4.4 14.7 1.0
C B:GLN386 4.4 14.0 1.0
CZ B:PHE510 4.5 18.7 1.0
C B:GLU385 4.5 17.2 1.0
CG B:PRO548 4.5 15.2 1.0
O B:GLN386 4.6 13.7 1.0
O B:GLU385 4.6 19.0 1.0
CG B:GLU385 4.7 20.5 1.0
N B:GLN386 4.7 14.8 1.0
CG2 B:THR483 4.7 15.5 1.0
CB B:PRO387 4.8 15.0 1.0
O B:HOH1186 4.9 22.8 1.0
O C:HOH1167 4.9 21.8 1.0
N B:GLY549 4.9 13.2 1.0

Manganese binding site 5 out of 8 in 4mig

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Manganese binding site 5 out of 8 in the Pyranose 2-Oxidase From Phanerochaete Chrysosporium, Recombinant Wild Type


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Pyranose 2-Oxidase From Phanerochaete Chrysosporium, Recombinant Wild Type within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn803

b:35.9
occ:1.00
 O B:HOH1001 2.3 19.2 1.0
O C:HOH1079 3.3 16.3 1.0
CE1 C:PHE510 3.7 18.4 1.0
CE C:MET512 4.0 16.6 1.0
CB C:PRO548 4.1 14.2 1.0
CD2 C:LEU143 4.2 14.2 1.0
CB C:GLU385 4.3 17.9 1.0
CG C:PRO387 4.3 15.5 1.0
N C:PRO387 4.3 14.1 1.0
CD1 C:PHE510 4.3 17.0 1.0
CG C:GLU385 4.4 18.8 1.0
O C:GLU385 4.4 18.5 1.0
CA C:PRO387 4.4 14.0 1.0
CZ C:PHE510 4.4 18.8 1.0
CA C:PRO548 4.4 14.1 1.0
C C:GLU385 4.5 15.6 1.0
C C:GLN386 4.5 14.1 1.0
CD C:PRO387 4.5 14.4 1.0
CG C:PRO548 4.6 15.2 1.0
CG2 C:THR483 4.7 17.2 1.0
N C:GLN386 4.7 14.2 1.0
CB C:PRO387 4.8 13.9 1.0
O C:GLN386 4.8 15.3 1.0
O B:HOH1359 4.9 24.1 1.0
N C:GLY549 4.9 12.9 1.0
CA C:GLU385 5.0 16.2 1.0

Manganese binding site 6 out of 8 in 4mig

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Manganese binding site 6 out of 8 in the Pyranose 2-Oxidase From Phanerochaete Chrysosporium, Recombinant Wild Type


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Pyranose 2-Oxidase From Phanerochaete Chrysosporium, Recombinant Wild Type within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn803

b:13.0
occ:0.50
 O D:HOH902 2.2 22.8 1.0
NE2 D:HIS572 2.3 16.1 1.0
O D:HOH903 2.3 14.4 1.0
CD2 D:HIS572 3.2 15.8 1.0
O D:HOH1304 3.2 23.7 1.0
CE1 D:HIS572 3.3 16.5 1.0
CG D:HIS572 4.3 14.8 1.0
ND1 D:HIS572 4.4 16.0 1.0
MN D:MN804 4.4 32.4 1.0
NH1 D:ARG607 4.5 14.6 1.0
O D:ARG607 4.7 12.2 1.0
O D:HOH904 4.8 27.6 1.0
CZ D:ARG607 4.8 13.7 1.0
NH2 D:ARG607 4.9 14.0 1.0

Manganese binding site 7 out of 8 in 4mig

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Manganese binding site 7 out of 8 in the Pyranose 2-Oxidase From Phanerochaete Chrysosporium, Recombinant Wild Type


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Pyranose 2-Oxidase From Phanerochaete Chrysosporium, Recombinant Wild Type within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn804

b:32.4
occ:1.00
 O D:HOH902 2.3 22.8 1.0
O D:HOH904 2.3 27.6 1.0
NH1 D:ARG607 3.4 14.6 1.0
CG D:ARG607 3.9 13.5 1.0
CG2 D:ILE192 4.0 10.8 1.0
CD2 D:LEU196 4.1 12.1 1.0
MN D:MN803 4.4 13.0 0.5
CD D:ARG607 4.4 13.2 1.0
CZ D:ARG607 4.5 13.7 1.0
CD1 D:LEU196 4.5 13.5 1.0
CG D:LEU196 4.6 11.4 1.0
CA D:ARG607 4.7 12.3 1.0
NE D:ARG607 4.8 14.0 1.0
CB D:ARG607 4.8 12.6 1.0

Manganese binding site 8 out of 8 in 4mig

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Manganese binding site 8 out of 8 in the Pyranose 2-Oxidase From Phanerochaete Chrysosporium, Recombinant Wild Type


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Pyranose 2-Oxidase From Phanerochaete Chrysosporium, Recombinant Wild Type within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn805

b:33.0
occ:1.00
 O A:HOH1004 2.3 20.6 1.0
O D:HOH950 3.3 14.2 1.0
CE1 D:PHE510 3.8 13.2 1.0
CB D:PRO548 4.0 11.0 1.0
CE D:MET512 4.0 12.3 1.0
CG D:PRO387 4.2 12.3 1.0
N D:PRO387 4.2 11.6 1.0
CD2 D:LEU143 4.3 9.3 1.0
CB D:GLU385 4.3 14.0 1.0
CD1 D:PHE510 4.3 12.5 1.0
CD D:PRO387 4.3 11.8 1.0
CA D:PRO548 4.4 10.5 1.0
C D:GLN386 4.4 11.3 1.0
CA D:PRO387 4.5 11.7 1.0
CZ D:PHE510 4.5 12.9 1.0
O D:GLU385 4.6 12.9 1.0
CG D:GLU385 4.6 15.6 1.0
O D:GLN386 4.6 11.5 1.0
C D:GLU385 4.6 12.4 1.0
CG D:PRO548 4.6 11.1 1.0
CG2 D:THR483 4.8 10.1 1.0
CB D:PRO387 4.8 12.1 1.0
N D:GLN386 4.8 11.8 1.0
N D:GLY549 4.9 10.7 1.0
O A:HOH1256 5.0 23.7 1.0

Reference:

N.Hassan, T.C.Tan, O.Spadiut, I.Pisanelli, L.Fusco, D.Haltrich, C.K.Peterbauer, C.Divne. Crystal Structures of Phanerochaete Chrysosporium Pyranose 2-Oxidase Suggest That the N-Terminus Acts As A Propeptide That Assists in Homotetramer Assembly. Febs Open Bio V. 3 496 2013.
ISSN: ESSN 2211-5463
PubMed: 24282677
DOI: 10.1016/J.FOB.2013.10.010
Page generated: Sat Oct 5 20:21:08 2024

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