Atomistry » Calcium » PDB 7ytq-7zci » 7ywv
Atomistry »
  Calcium »
    PDB 7ytq-7zci »
      7ywv »

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: Thu Jul 10 02:45:56 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy