Calcium in PDB 7ywv: Eugenol Oxidase From Rhodococcus Jostii: Mutant S81H, D151E, A423M, H434Y, S394V, Q425S, I445D, S518P

Enzymatic activity of Eugenol Oxidase From Rhodococcus Jostii: Mutant S81H, D151E, A423M, H434Y, S394V, Q425S, I445D, S518P

All present enzymatic activity of Eugenol Oxidase From Rhodococcus Jostii: Mutant S81H, D151E, A423M, H434Y, S394V, Q425S, I445D, S518P:
1.1.3.38;

Protein crystallography data

The structure of Eugenol Oxidase From Rhodococcus Jostii: Mutant S81H, D151E, A423M, H434Y, S394V, Q425S, I445D, S518P, PDB code: 7ywv 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) 49.30 / 2.40
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 114.191, 142.402, 288.521, 90, 100.41, 90
R / Rfree (%) 22.2 / 26.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Eugenol Oxidase From Rhodococcus Jostii: Mutant S81H, D151E, A423M, H434Y, S394V, Q425S, I445D, S518P (pdb code 7ywv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Eugenol Oxidase From Rhodococcus Jostii: Mutant S81H, D151E, A423M, H434Y, S394V, Q425S, I445D, S518P, PDB code: 7ywv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 7ywv

Go back to Calcium Binding Sites List in 7ywv
Calcium binding site 1 out of 5 in the Eugenol Oxidase From Rhodococcus Jostii: Mutant S81H, D151E, A423M, H434Y, S394V, Q425S, I445D, S518P


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Eugenol Oxidase From Rhodococcus Jostii: Mutant S81H, D151E, A423M, H434Y, S394V, Q425S, I445D, S518P within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:79.3
occ:1.00
 O A:HOH702 2.3 48.9 1.0
O A:HOH740 2.4 30.3 1.0
OD2 A:ASP249 2.4 70.1 1.0
CG A:ASP249 3.3 61.8 1.0
OD1 A:ASP249 3.5 65.4 1.0
NZ A:LYS309 4.1 61.2 1.0
OE2 A:GLU306 4.4 52.4 1.0
OE1 A:GLU306 4.6 56.8 1.0
NZ A:LYS250 4.6 59.4 1.0
CB A:ASP249 4.7 53.5 1.0
CD A:GLU306 4.8 52.2 1.0
O A:ASP249 4.9 53.1 1.0

Calcium binding site 2 out of 5 in 7ywv

Go back to Calcium Binding Sites List in 7ywv
Calcium binding site 2 out of 5 in the Eugenol Oxidase From Rhodococcus Jostii: Mutant S81H, D151E, A423M, H434Y, S394V, Q425S, I445D, S518P


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Eugenol Oxidase From Rhodococcus Jostii: Mutant S81H, D151E, A423M, H434Y, S394V, Q425S, I445D, S518P within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca603

b:47.1
occ:1.00
 OE2 B:GLU64 2.0 49.6 1.0
OD1 C:ASP400 2.2 42.5 1.0
O B:HOH720 2.6 24.6 1.0
CD B:GLU64 3.1 46.2 1.0
CG C:ASP400 3.2 42.7 1.0
OD2 C:ASP400 3.5 45.9 1.0
CG B:GLU64 3.7 43.6 1.0
OE1 B:GLU64 4.1 49.2 1.0
NZ A:LYS119 4.2 45.6 1.0
OD2 C:ASP259 4.3 50.1 1.0
OD1 C:ASP259 4.4 46.5 1.0
CB C:ARG402 4.5 55.0 1.0
CB C:ASP400 4.6 42.3 1.0
OD1 B:ASP68 4.6 45.3 1.0
OD2 B:ASP68 4.7 57.5 1.0
N C:ARG402 4.7 45.8 1.0
CG C:ASP259 4.7 43.1 1.0
N C:GLY401 4.8 42.6 1.0

Calcium binding site 3 out of 5 in 7ywv

Go back to Calcium Binding Sites List in 7ywv
Calcium binding site 3 out of 5 in the Eugenol Oxidase From Rhodococcus Jostii: Mutant S81H, D151E, A423M, H434Y, S394V, Q425S, I445D, S518P


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Eugenol Oxidase From Rhodococcus Jostii: Mutant S81H, D151E, A423M, H434Y, S394V, Q425S, I445D, S518P within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca604

b:52.7
occ:1.00
 OD1 B:ASP400 2.1 61.4 1.0
O B:HOH725 2.6 41.8 1.0
CG B:ASP400 3.2 53.4 1.0
OD2 B:ASP400 3.5 53.6 1.0
OD2 B:ASP259 4.0 48.5 1.0
NZ E:LYS119 4.0 51.2 1.0
OD1 B:ASP259 4.0 62.2 1.0
CG B:ASP259 4.4 52.9 1.0
CB B:ASP400 4.5 51.9 1.0
CB B:ARG402 4.6 64.8 1.0
N B:ARG402 4.6 51.4 1.0
N B:GLY401 4.7 42.4 1.0

Calcium binding site 4 out of 5 in 7ywv

Go back to Calcium Binding Sites List in 7ywv
Calcium binding site 4 out of 5 in the Eugenol Oxidase From Rhodococcus Jostii: Mutant S81H, D151E, A423M, H434Y, S394V, Q425S, I445D, S518P


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Eugenol Oxidase From Rhodococcus Jostii: Mutant S81H, D151E, A423M, H434Y, S394V, Q425S, I445D, S518P within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca603

b:55.9
occ:1.00
 OE2 C:GLU64 2.0 64.1 1.0
OD1 G:ASP400 2.4 65.5 1.0
CD C:GLU64 3.1 56.5 1.0
CG G:ASP400 3.4 64.3 1.0
OD2 G:ASP400 3.8 81.4 1.0
CG C:GLU64 3.8 52.6 1.0
NZ D:LYS119 4.1 60.3 1.0
OD2 G:ASP259 4.1 57.5 1.0
OE1 C:GLU64 4.1 53.7 1.0
OD2 C:ASP68 4.2 58.0 1.0
OD1 G:ASP259 4.2 68.7 1.0
CG G:ASP259 4.5 60.2 1.0
OD1 C:ASP68 4.6 52.5 1.0
CB G:ASP400 4.7 55.8 1.0
CD G:ARG402 4.8 100.8 1.0
CG C:ASP68 4.9 54.4 1.0
CG G:ARG402 5.0 90.1 1.0

Calcium binding site 5 out of 5 in 7ywv

Go back to Calcium Binding Sites List in 7ywv
Calcium binding site 5 out of 5 in the Eugenol Oxidase From Rhodococcus Jostii: Mutant S81H, D151E, A423M, H434Y, S394V, Q425S, I445D, S518P


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Eugenol Oxidase From Rhodococcus Jostii: Mutant S81H, D151E, A423M, H434Y, S394V, Q425S, I445D, S518P within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca603

b:58.0
occ:1.00
 OD1 E:ASP400 2.2 55.8 1.0
OE2 A:GLU64 2.2 59.1 1.0
O E:HOH720 3.0 40.9 1.0
CG E:ASP400 3.2 53.9 1.0
CD A:GLU64 3.2 58.9 1.0
OD2 E:ASP400 3.5 56.2 1.0
CG A:GLU64 3.7 57.2 1.0
NZ B:LYS119 4.1 46.8 1.0
OD1 E:ASP259 4.2 56.4 1.0
OE1 A:GLU64 4.3 64.0 1.0
OD2 E:ASP259 4.5 52.8 1.0
CB E:ASP400 4.5 54.6 1.0
OD1 A:ASP68 4.6 38.7 1.0
CG E:ASP259 4.7 50.3 1.0
CB E:ARG402 4.8 73.1 1.0
N E:ARG402 4.8 55.0 1.0
OD2 A:ASP68 4.9 48.6 1.0
N E:GLY401 4.9 51.0 1.0

Reference:

Y.Guo, L.Alvigini, M.Trajkovic, L.Alonso-Cotchico, E.Monza, S.Savino, I.Maric, A.Mattevi, M.W.Fraaije. Structure- and Computational-Aided Engineering of An Oxidase to Produce Isoeugenol From A Lignin-Derived Compound. Nat Commun V. 13 7195 2022.
ISSN: ESSN 2041-1723
PubMed: 36418310
DOI: 10.1038/S41467-022-34912-3
Page generated: Tue Apr 4 19:18:02 2023

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