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Calcium 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:

Cadmium (Cd) 3 atoms
Iron (Fe) 1 atom

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the Extralong Fungal Manganese Peroxidase From Ceriporiopsis Subvermispora in Complex with Cadmium, PDB code: 4czq:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 4czq

Go back to Calcium Binding Sites List in 4czq
Calcium binding site 1 out of 2 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 Calcium with other atoms in the Ca 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:Ca1370

b:11.3
occ:1.00
 O A:THR174 2.4 12.5 1.0
O A:THR193 2.4 12.2 1.0
OD2 A:ASP191 2.5 12.6 1.0
OG1 A:THR174 2.5 11.9 1.0
OD1 A:ASP198 2.5 12.5 1.0
OG1 A:THR193 2.5 12.8 1.0
O A:THR196 2.5 12.1 1.0
OD1 A:ASP191 2.7 12.7 1.0
CG A:ASP191 2.9 12.4 1.0
C A:THR193 3.3 12.7 1.0
C A:THR174 3.3 11.7 1.0
H A:ASP198 3.4 14.4 1.0
HA A:THR174 3.4 14.4 1.0
CG A:ASP198 3.4 12.7 1.0
CB A:THR193 3.5 13.0 1.0
CB A:THR174 3.6 11.3 1.0
CA A:THR174 3.7 12.0 1.0
HB A:THR193 3.7 15.6 1.0
H A:THR193 3.7 15.5 1.0
HB2 A:GLN200 3.7 15.8 1.0
C A:THR196 3.7 11.7 1.0
H A:THR196 3.7 15.4 1.0
HB A:THR196 3.7 16.5 1.0
OD2 A:ASP198 3.8 12.8 1.0
CA A:THR193 3.9 12.8 1.0
HA A:PRO194 3.9 15.8 1.0
HG21 A:THR174 4.1 13.9 1.0
N A:THR193 4.2 12.9 1.0
N A:ASP198 4.2 12.0 1.0
N A:PRO194 4.3 13.0 1.0
HB A:THR174 4.3 13.5 1.0
HG21 A:ILE175 4.4 15.4 1.0
CG2 A:THR174 4.4 11.6 1.0
HA A:PHE197 4.4 14.3 1.0
H A:ILE201 4.4 14.7 1.0
N A:THR196 4.4 12.8 1.0
CB A:ASP191 4.4 12.5 1.0
H A:GLN200 4.5 15.0 1.0
CA A:THR196 4.5 12.5 1.0
O A:ASP198 4.5 12.5 1.0
CA A:PRO194 4.5 13.1 1.0
HA A:ILE175 4.5 15.1 1.0
N A:ILE175 4.5 11.8 1.0
CB A:THR196 4.5 13.8 1.0
O A:HOH2253 4.7 19.6 1.0
CB A:GLN200 4.7 13.1 1.0
CB A:ASP198 4.7 12.4 1.0
HG23 A:ILE175 4.7 15.4 1.0
HG22 A:THR174 4.7 13.9 1.0
HB2 A:ASP191 4.7 15.0 1.0
N A:PHE197 4.8 11.7 1.0
HA A:THR193 4.8 15.3 1.0
HB3 A:ASP191 4.8 15.0 1.0
CA A:ASP198 4.8 12.3 1.0
C A:ASP198 4.8 12.4 1.0
CG2 A:THR193 4.9 13.8 1.0
HB A:ILE201 4.9 16.8 1.0
HG2 A:GLN200 4.9 15.6 1.0
CA A:PHE197 4.9 12.0 1.0
CG2 A:ILE175 5.0 12.8 1.0

Calcium binding site 2 out of 2 in 4czq

Go back to Calcium Binding Sites List in 4czq
Calcium binding site 2 out of 2 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 Calcium with other atoms in the Ca 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:Ca1371

b:14.8
occ:1.00
 O A:HOH2095 2.3 15.9 1.0
OD1 A:ASP47 2.3 16.7 1.0
OD1 A:ASP64 2.4 15.6 1.0
O A:ASP47 2.4 15.3 1.0
O A:HOH2086 2.4 15.6 1.0
O A:GLY62 2.4 15.6 1.0
OG A:SER66 2.5 16.8 1.0
HA A:ASP47 3.2 17.9 1.0
H A:SER66 3.3 20.2 1.0
C A:ASP47 3.3 14.5 1.0
H A:ASP64 3.3 18.4 1.0
CG A:ASP47 3.4 15.6 1.0
CG A:ASP64 3.5 16.2 1.0
HB3 A:SER66 3.6 20.3 1.0
HB1 A:ALA50 3.6 19.4 1.0
CB A:SER66 3.6 16.9 1.0
C A:GLY62 3.6 15.0 1.0
CA A:ASP47 3.7 14.9 1.0
OD2 A:ASP64 4.0 17.3 1.0
N A:SER66 4.0 16.9 1.0
N A:ASP64 4.1 15.3 1.0
H A:MET67 4.1 21.0 1.0
CB A:ASP47 4.1 15.4 1.0
O A:HOH2122 4.2 16.9 1.0
H A:GLY62 4.2 19.6 1.0
OD2 A:ASP47 4.3 15.9 1.0
HA A:ALA63 4.3 18.5 1.0
H A:GLY65 4.3 19.5 1.0
HG2 A:MET67 4.3 22.6 1.0
HA2 A:GLY62 4.3 18.7 1.0
HB2 A:SER66 4.3 20.3 1.0
CA A:GLY62 4.3 15.6 1.0
N A:GLY62 4.3 16.3 1.0
CA A:SER66 4.4 17.0 1.0
HA A:ALA48 4.5 17.4 1.0
OE1 A:GLU74 4.5 18.3 1.0
N A:ALA48 4.5 14.5 1.0
CB A:ALA50 4.5 16.2 1.0
N A:GLY65 4.6 16.3 1.0
O A:ALA50 4.6 16.5 1.0
OE2 A:GLU74 4.6 18.8 1.0
CB A:ASP64 4.6 16.6 1.0
H A:ALA50 4.6 18.6 1.0
N A:ALA63 4.6 15.1 1.0
HB3 A:ALA136 4.7 21.5 1.0
N A:MET67 4.7 17.5 1.0
H A:GLY61 4.7 19.9 1.0
HB3 A:ASP47 4.8 18.5 1.0
O A:HIS46 4.8 15.8 1.0
CA A:ASP64 4.8 16.3 1.0
HB2 A:ASP47 4.8 18.5 1.0
CA A:ALA63 4.8 15.4 1.0
C A:ASP64 4.9 16.8 1.0
HB3 A:ASP64 4.9 20.0 1.0
HB2 A:ALA50 4.9 19.4 1.0
HB3 A:ALA50 5.0 19.4 1.0
CA A:ALA48 5.0 14.5 1.0
C A:GLY61 5.0 16.2 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 Jul 13 23:20:05 2024

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