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Calcium in PDB 8bap: Eugenol Oxidase (Eugo) From Rhodococcus Jostii RHA1, Eightfold Mutant Active on Propanol Syringol

Enzymatic activity of Eugenol Oxidase (Eugo) From Rhodococcus Jostii RHA1, Eightfold Mutant Active on Propanol Syringol

All present enzymatic activity of Eugenol Oxidase (Eugo) From Rhodococcus Jostii RHA1, Eightfold Mutant Active on Propanol Syringol:
1.1.3.38;

Protein crystallography data

The structure of Eugenol Oxidase (Eugo) From Rhodococcus Jostii RHA1, Eightfold Mutant Active on Propanol Syringol, PDB code: 8bap was solved by L.Alvigini, A.Mattevi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.04 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 113.556, 142.995, 154.6, 114.87, 97, 93.28
R / Rfree (%) 19.3 / 24.9

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Eugenol Oxidase (Eugo) From Rhodococcus Jostii RHA1, Eightfold Mutant Active on Propanol Syringol (pdb code 8bap). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Eugenol Oxidase (Eugo) From Rhodococcus Jostii RHA1, Eightfold Mutant Active on Propanol Syringol, PDB code: 8bap:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in 8bap

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Calcium binding site 1 out of 12 in the Eugenol Oxidase (Eugo) From Rhodococcus Jostii RHA1, Eightfold Mutant Active on Propanol Syringol


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Eugenol Oxidase (Eugo) From Rhodococcus Jostii RHA1, Eightfold Mutant Active on Propanol Syringol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:42.3
occ:1.00
 OE2 A:GLU64 1.9 43.7 1.0
O P:HOH701 2.3 32.5 1.0
OD1 P:ASP400 2.4 35.4 1.0
O A:HOH765 2.8 25.2 1.0
CD A:GLU64 3.1 40.4 1.0
CG P:ASP400 3.4 33.3 1.0
OD2 P:ASP400 3.6 31.4 1.0
CG A:GLU64 3.7 36.0 1.0
OE1 A:GLU64 4.1 40.0 1.0
OD2 P:ASP259 4.1 38.7 1.0
OD1 P:ASP259 4.4 41.4 1.0
NZ G:LYS119 4.5 26.9 1.0
CG P:ASP259 4.6 39.8 1.0
N P:ARG402 4.6 33.9 1.0
N P:GLY401 4.7 31.3 1.0
OD2 A:ASP68 4.7 33.4 1.0
CB P:ASP400 4.7 34.5 1.0
CB P:ARG402 4.8 42.5 1.0
CD P:ARG402 4.9 59.6 1.0
CG P:ARG402 4.9 48.0 1.0
OD1 A:ASP68 4.9 39.7 1.0

Calcium binding site 2 out of 12 in 8bap

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Calcium binding site 2 out of 12 in the Eugenol Oxidase (Eugo) From Rhodococcus Jostii RHA1, Eightfold Mutant Active on Propanol Syringol


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Eugenol Oxidase (Eugo) From Rhodococcus Jostii RHA1, Eightfold Mutant Active on Propanol Syringol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca604

b:32.1
occ:1.00
 OD1 A:ASP400 2.4 25.8 1.0
O A:HOH729 2.4 29.5 1.0
O B:HOH775 2.7 31.9 1.0
NH2 A:ARG402 2.8 41.0 1.0
OE1 B:GLU64 2.9 31.7 1.0
CZ A:ARG402 3.3 49.8 1.0
CG A:ASP400 3.4 23.1 1.0
NE A:ARG402 3.4 57.1 1.0
CD B:GLU64 3.6 36.6 1.0
OD2 A:ASP400 3.7 23.4 1.0
NZ D:LYS119 4.0 19.2 1.0
CG B:GLU64 4.0 33.0 1.0
OD1 A:ASP259 4.1 18.5 1.0
OD2 A:ASP259 4.2 21.7 1.0
NH1 A:ARG402 4.3 48.3 1.0
CG A:ASP259 4.5 21.5 1.0
OE2 B:GLU64 4.5 37.4 1.0
CD A:ARG402 4.6 45.9 1.0
CB A:ASP400 4.8 17.6 1.0
N A:GLY401 4.8 16.2 1.0
N A:ARG402 4.8 22.7 1.0
CB B:GLU64 4.9 21.1 1.0
OD2 B:ASP68 4.9 30.8 1.0
OD1 B:ASP68 4.9 31.8 1.0
CG A:ARG402 4.9 31.9 1.0
CB A:ARG402 5.0 24.6 1.0
CE D:LYS119 5.0 17.3 1.0

Calcium binding site 3 out of 12 in 8bap

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Calcium binding site 3 out of 12 in the Eugenol Oxidase (Eugo) From Rhodococcus Jostii RHA1, Eightfold Mutant Active on Propanol Syringol


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Eugenol Oxidase (Eugo) From Rhodococcus Jostii RHA1, Eightfold Mutant Active on Propanol Syringol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca603

b:32.2
occ:1.00
 O B:HOH714 2.4 20.6 1.0
OD1 B:ASP400 2.5 23.4 1.0
O B:HOH734 2.8 20.9 1.0
NH1 B:ARG402 2.9 65.9 1.0
CG B:ASP400 3.5 23.4 1.0
OD2 B:ASP400 3.7 26.2 1.0
O J:HOH702 3.7 51.5 1.0
CZ B:ARG402 4.0 64.4 1.0
NZ J:LYS119 4.3 29.7 1.0
OD2 B:ASP259 4.3 22.3 1.0
OD1 B:ASP259 4.3 21.1 1.0
CD B:ARG402 4.7 51.9 1.0
NE B:ARG402 4.7 59.8 1.0
CG B:ASP259 4.7 19.6 1.0
NH2 B:ARG402 4.7 63.0 1.0
N B:ARG402 4.8 24.3 1.0
CB B:ASP400 4.9 25.8 1.0
CB B:ARG402 4.9 26.9 1.0
N B:GLY401 4.9 21.7 1.0

Calcium binding site 4 out of 12 in 8bap

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Calcium binding site 4 out of 12 in the Eugenol Oxidase (Eugo) From Rhodococcus Jostii RHA1, Eightfold Mutant Active on Propanol Syringol


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Eugenol Oxidase (Eugo) From Rhodococcus Jostii RHA1, Eightfold Mutant Active on Propanol Syringol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca603

b:32.3
occ:1.00
 O C:HOH734 2.4 23.4 1.0
OD1 C:ASP400 2.5 27.3 1.0
O C:HOH762 2.5 28.7 1.0
OE2 I:GLU64 2.7 48.9 1.0
O I:HOH701 3.0 51.9 1.0
CD I:GLU64 3.2 45.2 1.0
CG C:ASP400 3.4 23.0 1.0
OE1 I:GLU64 3.6 49.4 1.0
OD2 C:ASP400 3.7 25.3 1.0
CG I:GLU64 4.1 44.9 1.0
NZ H:LYS119 4.3 24.5 1.0
OD2 C:ASP259 4.4 24.4 1.0
OD1 C:ASP259 4.5 22.2 1.0
OD2 I:ASP68 4.7 35.6 1.0
CG C:ARG402 4.8 33.5 1.0
CB C:ASP400 4.8 24.7 1.0
CG C:ASP259 4.8 24.9 1.0
N C:ARG402 4.9 26.4 1.0
CB C:ARG402 4.9 26.3 1.0
N C:GLY401 4.9 19.1 1.0
CD C:ARG402 5.0 44.2 1.0

Calcium binding site 5 out of 12 in 8bap

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Calcium binding site 5 out of 12 in the Eugenol Oxidase (Eugo) From Rhodococcus Jostii RHA1, Eightfold Mutant Active on Propanol Syringol


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Eugenol Oxidase (Eugo) From Rhodococcus Jostii RHA1, Eightfold Mutant Active on Propanol Syringol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca603

b:33.9
occ:1.00
 OD1 D:ASP400 2.4 36.8 1.0
OE1 G:GLU64 2.6 39.9 1.0
CG D:ASP400 3.4 25.1 1.0
CD G:GLU64 3.7 47.6 1.0
OD2 D:ASP400 3.8 25.1 1.0
NZ A:LYS119 4.1 28.5 1.0
CG G:GLU64 4.2 33.7 1.0
OD1 D:ASP259 4.3 27.9 1.0
OD2 D:ASP259 4.4 25.0 1.0
OD2 G:ASP68 4.4 49.6 1.0
CB G:GLU64 4.6 31.4 1.0
OE2 G:GLU64 4.7 48.3 1.0
N D:ARG402 4.7 31.6 1.0
CB D:ASP400 4.7 30.2 1.0
OD1 G:ASP68 4.7 38.9 1.0
CG D:ASP259 4.8 30.4 1.0
CB D:ARG402 4.8 36.3 1.0
N D:GLY401 4.8 27.9 1.0

Calcium binding site 6 out of 12 in 8bap

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Calcium binding site 6 out of 12 in the Eugenol Oxidase (Eugo) From Rhodococcus Jostii RHA1, Eightfold Mutant Active on Propanol Syringol


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Eugenol Oxidase (Eugo) From Rhodococcus Jostii RHA1, Eightfold Mutant Active on Propanol Syringol within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca603

b:31.2
occ:1.00
 OD1 H:ASP400 2.4 20.1 1.0
OE2 E:GLU64 2.8 28.7 1.0
O H:HOH725 2.9 22.8 1.0
CD E:GLU64 3.1 27.9 1.0
CG H:ASP400 3.3 20.7 1.0
OD2 H:ASP400 3.6 25.1 1.0
CG E:GLU64 3.6 29.3 1.0
NZ C:LYS119 3.7 21.6 1.0
OE1 E:GLU64 3.8 32.2 1.0
CD H:ARG402 4.0 49.9 1.0
NH1 H:ARG402 4.2 46.1 1.0
OD1 H:ASP259 4.3 23.3 1.0
OD2 H:ASP259 4.4 24.1 1.0
NE H:ARG402 4.5 61.0 1.0
CZ H:ARG402 4.6 54.9 1.0
OD2 E:ASP68 4.7 26.6 1.0
CB H:ASP400 4.7 21.4 1.0
CG H:ASP259 4.7 21.8 1.0
N H:ARG402 4.8 24.0 1.0
CB H:ARG402 4.8 20.7 1.0
N H:GLY401 4.8 18.5 1.0
CE C:LYS119 4.9 21.5 1.0
OD1 E:ASP68 4.9 36.3 1.0
CG H:ARG402 5.0 33.9 1.0

Calcium binding site 7 out of 12 in 8bap

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Calcium binding site 7 out of 12 in the Eugenol Oxidase (Eugo) From Rhodococcus Jostii RHA1, Eightfold Mutant Active on Propanol Syringol


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Eugenol Oxidase (Eugo) From Rhodococcus Jostii RHA1, Eightfold Mutant Active on Propanol Syringol within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca603

b:35.9
occ:1.00
 O F:HOH719 2.5 27.6 1.0
OD1 F:ASP400 2.5 33.5 1.0
O F:HOH722 2.6 24.8 1.0
CG F:ASP400 3.4 30.6 1.0
OD2 F:ASP400 3.6 22.1 1.0
OD1 F:ASP259 3.9 25.0 1.0
OD2 F:ASP259 4.0 28.6 1.0
CD F:ARG402 4.3 60.8 1.0
CG F:ASP259 4.3 30.0 1.0
N F:GLY401 4.7 28.3 1.0
N F:ARG402 4.7 28.6 1.0
CB F:ASP400 4.8 31.0 1.0
CG F:ARG402 4.9 52.5 1.0
CB F:ARG402 5.0 41.3 1.0

Calcium binding site 8 out of 12 in 8bap

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Calcium binding site 8 out of 12 in the Eugenol Oxidase (Eugo) From Rhodococcus Jostii RHA1, Eightfold Mutant Active on Propanol Syringol


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Eugenol Oxidase (Eugo) From Rhodococcus Jostii RHA1, Eightfold Mutant Active on Propanol Syringol within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca603

b:39.6
occ:1.00
 OE2 D:GLU64 2.4 30.6 1.0
OD1 J:ASP400 2.4 32.1 1.0
O J:HOH744 2.8 20.6 1.0
CD D:GLU64 3.1 38.4 1.0
NH1 J:ARG402 3.2 54.5 1.0
CZ J:ARG402 3.3 60.8 1.0
CG J:ASP400 3.5 25.7 1.0
CG D:GLU64 3.5 33.4 1.0
NH2 J:ARG402 3.7 59.4 1.0
OD2 J:ASP400 3.8 33.4 1.0
NE J:ARG402 3.8 66.9 1.0
NZ B:LYS119 3.9 21.6 1.0
OE1 D:GLU64 4.1 37.7 1.0
OD1 J:ASP259 4.3 23.4 1.0
CD J:ARG402 4.3 55.8 1.0
OD2 J:ASP259 4.5 33.9 1.0
OD2 D:ASP68 4.6 35.5 1.0
CG J:ASP259 4.7 27.7 1.0
CB J:ASP400 4.8 26.8 1.0
OD1 D:ASP68 4.8 36.4 1.0
N J:GLY401 4.9 26.4 1.0
CB D:GLU64 4.9 26.2 1.0
N J:ARG402 5.0 27.4 1.0
CE B:LYS119 5.0 24.2 1.0

Calcium binding site 9 out of 12 in 8bap

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Calcium binding site 9 out of 12 in the Eugenol Oxidase (Eugo) From Rhodococcus Jostii RHA1, Eightfold Mutant Active on Propanol Syringol


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Eugenol Oxidase (Eugo) From Rhodococcus Jostii RHA1, Eightfold Mutant Active on Propanol Syringol within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca603

b:37.5
occ:1.00
 OE2 L:GLU64 2.0 47.3 1.0
CD L:GLU64 2.8 35.3 1.0
CG L:GLU64 3.6 31.4 1.0
OE1 L:GLU64 3.7 38.8 1.0
NZ F:LYS119 3.8 24.5 1.0
CE F:LYS119 4.6 26.4 1.0
OD2 L:ASP68 4.8 39.1 1.0

Calcium binding site 10 out of 12 in 8bap

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Calcium binding site 10 out of 12 in the Eugenol Oxidase (Eugo) From Rhodococcus Jostii RHA1, Eightfold Mutant Active on Propanol Syringol


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Eugenol Oxidase (Eugo) From Rhodococcus Jostii RHA1, Eightfold Mutant Active on Propanol Syringol within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ca603

b:41.4
occ:1.00
 OE2 F:GLU64 2.0 39.6 1.0
OD1 M:ASP400 2.5 29.9 1.0
NH1 M:ARG402 2.8 56.3 1.0
CD F:GLU64 3.1 38.2 1.0
CG M:ASP400 3.4 31.7 1.0
OD2 M:ASP400 3.7 43.0 1.0
CG F:GLU64 3.8 29.3 1.0
CZ M:ARG402 3.9 63.0 1.0
OE1 F:GLU64 4.0 33.5 1.0
NZ L:LYS119 4.0 22.8 1.0
OD1 M:ASP259 4.1 34.1 1.0
OD2 M:ASP259 4.2 34.1 1.0
CD M:ARG402 4.3 49.9 1.0
NE M:ARG402 4.5 65.8 1.0
CG M:ASP259 4.5 41.2 1.0
OD2 F:ASP68 4.6 38.3 1.0
OD1 F:ASP68 4.8 26.7 1.0
N M:GLY401 4.8 38.7 1.0
NH2 M:ARG402 4.8 54.8 1.0
CB M:ASP400 4.8 31.7 1.0
N M:ARG402 4.9 37.3 1.0
CE L:LYS119 4.9 22.2 1.0
CB M:ARG402 5.0 39.7 1.0

Reference:

Y.Guo, L.Alvigini, M.Saifuddin, B.Ashley, M.Trajkovic, L.Alonso-Cotchico, A.Mattevi, M.W.Fraaije. One-Pot Biocatalytic Synthesis of Rac-Syringaresinol From A Lignin-Derived Phenol Acs Catalysis 2023.
ISSN: ESSN 2155-5435
Page generated: Fri Jul 19 07:15:49 2024

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