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Cadmium in PDB 4czq: Crystal Structure of the Extralong Fungal Manganese Peroxidase From Ceriporiopsis Subvermispora in Complex with Cadmium

Enzymatic activity of Crystal Structure of the Extralong Fungal Manganese Peroxidase From Ceriporiopsis Subvermispora in Complex with Cadmium

All present enzymatic activity of Crystal Structure of the Extralong Fungal Manganese Peroxidase From Ceriporiopsis Subvermispora in Complex with Cadmium:
1.11.1.13;

Protein crystallography data

The structure of Crystal Structure of the Extralong Fungal Manganese Peroxidase From Ceriporiopsis Subvermispora in Complex with Cadmium, PDB code: 4czq was solved by F.J.Medrano, A.Romero, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.349 / 1.20
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 108.620, 108.620, 68.320, 90.00, 90.00, 90.00
R / Rfree (%) 15.09 / 16.19

Other elements in 4czq:

The structure of Crystal Structure of the Extralong Fungal Manganese Peroxidase From Ceriporiopsis Subvermispora in Complex with Cadmium also contains other interesting chemical elements:

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

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of the Extralong Fungal Manganese Peroxidase From Ceriporiopsis Subvermispora in Complex with Cadmium (pdb code 4czq). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Crystal Structure of the Extralong Fungal Manganese Peroxidase From Ceriporiopsis Subvermispora in Complex with Cadmium, PDB code: 4czq:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 4czq

Go back to Cadmium Binding Sites List in 4czq
Cadmium binding site 1 out of 3 in the Crystal Structure of the Extralong Fungal Manganese Peroxidase From Ceriporiopsis Subvermispora in Complex with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of the Extralong Fungal Manganese Peroxidase From Ceriporiopsis Subvermispora in Complex with Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1373

b:14.9
occ:1.00
 O1D A:HEM1372 2.3 15.2 1.0
OE2 A:GLU39 2.3 17.4 1.0
OD2 A:ASP179 2.3 17.5 1.0
OE2 A:GLU35 2.3 15.3 1.0
O A:HOH2075 2.4 16.4 1.0
O A:HOH2068 2.4 15.3 1.0
CGD A:HEM1372 3.1 14.4 1.0
CD A:GLU39 3.2 17.0 1.0
CD A:GLU35 3.2 14.5 1.0
HG2 A:GLU39 3.2 18.8 1.0
CG A:ASP179 3.2 17.1 1.0
OE1 A:GLU35 3.4 15.2 1.0
OD1 A:ASP179 3.6 16.8 1.0
CG A:GLU39 3.6 15.6 1.0
O2D A:HEM1372 3.7 14.9 1.0
HG3 A:GLU39 3.8 18.8 1.0
HBD A:HEM1372 3.9 16.4 1.0
O A:HOH2070 4.0 36.6 1.0
CBD A:HEM1372 4.1 13.7 1.0
OE1 A:GLU39 4.1 17.1 1.0
O A:HOH2076 4.2 24.7 1.0
O A:HOH2067 4.2 14.2 1.0
O A:HOH2069 4.4 19.7 1.0
O A:ARG177 4.4 14.2 1.0
HB2 A:ASP179 4.4 19.6 1.0
O2A A:HEM1372 4.5 15.5 1.0
HB2 A:ARG177 4.5 16.1 1.0
CB A:ASP179 4.5 16.3 1.0
HBDA A:HEM1372 4.6 16.4 1.0
CG A:GLU35 4.6 14.1 1.0
H32 A:GOL1376 4.6 42.2 1.0
HG3 A:GLU35 4.6 16.9 1.0
H A:ASP179 4.7 17.9 1.0
H2 A:GOL1376 4.7 49.0 1.0
HH11 A:ARG42 4.7 23.5 1.0
O A:HOH2080 4.8 22.8 1.0
H31 A:GOL1376 4.9 42.2 1.0
HG2 A:GLU35 5.0 16.9 1.0
HA A:ALA187 5.0 18.7 1.0
HB2 A:HIS38 5.0 15.3 1.0

Cadmium binding site 2 out of 3 in 4czq

Go back to Cadmium Binding Sites List in 4czq
Cadmium binding site 2 out of 3 in the Crystal Structure of the Extralong Fungal Manganese Peroxidase From Ceriporiopsis Subvermispora in Complex with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of the Extralong Fungal Manganese Peroxidase From Ceriporiopsis Subvermispora in Complex with Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1374

b:19.2
occ:0.41
 OD2 A:ASP85 2.3 22.5 1.0
O A:HOH2151 2.5 25.3 1.0
O A:HOH2070 2.5 36.6 1.0
O A:HOH2076 2.5 24.7 1.0
O A:HOH2262 2.7 30.3 1.0
CG A:ASP85 3.2 21.4 1.0
O A:HOH2263 3.5 42.1 1.0
OD1 A:ASP85 3.6 22.6 1.0
HE2 A:LYS180 3.9 26.0 1.0
O1 A:GOL1376 4.0 41.1 1.0
O A:HOH2069 4.0 19.7 1.0
HA2 A:GLY82 4.1 20.2 1.0
OD2 A:ASP179 4.3 17.5 1.0
HB2 A:ASP85 4.3 22.4 1.0
O A:HOH2152 4.3 49.1 1.0
O A:GLY82 4.4 16.8 1.0
CB A:ASP85 4.4 18.7 1.0
HZ2 A:LYS180 4.5 27.8 1.0
HB3 A:ASP179 4.5 19.6 1.0
HB2 A:ASP179 4.5 19.6 1.0
O A:HOH2080 4.6 22.8 1.0
OD1 A:ASP84 4.6 20.0 1.0
HZ1 A:LYS180 4.6 27.8 1.0
OD2 A:ASP363 4.7 30.0 1.0
HO1 A:GOL1376 4.7 49.3 1.0
O A:HOH2444 4.7 40.0 1.0
CE A:LYS180 4.7 21.7 1.0
H12 A:GOL1376 4.7 53.3 1.0
HA3 A:GLY82 4.8 20.2 1.0
H2 A:GOL1376 4.8 49.0 1.0
OE2 A:GLU39 4.8 17.4 1.0
CA A:GLY82 4.8 16.8 1.0
NZ A:LYS180 4.8 23.2 1.0
CB A:ASP179 4.9 16.3 1.0
HB3 A:ASP85 4.9 22.4 1.0
H A:ASP85 4.9 19.9 1.0
C1 A:GOL1376 4.9 44.4 1.0
CG A:ASP179 4.9 17.1 1.0

Cadmium binding site 3 out of 3 in 4czq

Go back to Cadmium Binding Sites List in 4czq
Cadmium binding site 3 out of 3 in the Crystal Structure of the Extralong Fungal Manganese Peroxidase From Ceriporiopsis Subvermispora in Complex with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of the Extralong Fungal Manganese Peroxidase From Ceriporiopsis Subvermispora in Complex with Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1375

b:27.2
occ:0.53
 OD2 A:ASP363 2.4 30.0 1.0
OD1 A:ASP363 2.5 30.3 1.0
O A:HOH2442 2.6 45.1 1.0
O A:HOH2263 2.7 42.1 1.0
CG A:ASP363 2.8 29.8 1.0
O A:HOH2152 3.1 49.1 1.0
HZ2 A:LYS180 3.3 27.8 1.0
O A:HOH2441 3.6 51.1 1.0
NZ A:LYS180 4.0 23.2 1.0
O A:HOH2151 4.0 25.3 1.0
HZ1 A:LYS180 4.1 27.8 1.0
HZ3 A:LYS180 4.2 27.8 1.0
O A:HOH2440 4.3 33.2 1.0
CB A:ASP363 4.3 29.3 1.0
HD3 A:PRO365 4.4 55.6 1.0
HB3 A:ASP363 4.6 35.2 1.0
HD2 A:PRO365 4.6 55.6 1.0
OD2 A:ASP84 4.6 22.9 1.0
HB2 A:ASP363 4.7 35.2 1.0
H A:ASP363 4.7 30.6 1.0
O A:HOH2262 4.9 30.3 1.0
CD A:PRO365 4.9 46.3 1.0
O A:HOH2154 5.0 42.5 1.0
C A:ASP363 5.0 33.0 1.0

Reference:

E.Fernandez-Fueyo, S.Acebes, F.J.Ruiz-Duenas, M.J.Martinez, A.Romero, F.J.Medrano, V.Guallar, A.T.Martinez. Structural Implications of the C-Terminal Tail in the Catalytic and Stability Properties of Manganese Peroxidases From Ligninolytic Fungi Acta Crystallogr.,Sect.D V. 70 3253 2014.
ISSN: ISSN 0907-4449
PubMed: 25478843
DOI: 10.1107/S1399004714022755
Page generated: Sat Dec 12 08:24:20 2020

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