Atomistry » Iron » PDB 8r9f-8rgq » 8re3
Atomistry »
  Iron »
    PDB 8r9f-8rgq »
      8re3 »

Iron in PDB 8re3: Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) Mutant M190G From Deinoccoccus Radiodurans

Protein crystallography data

The structure of Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) Mutant M190G From Deinoccoccus Radiodurans, PDB code: 8re3 was solved by B.A.Salgueiro, K.Frade, C.Frazao, P.Matias, E.Moe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.74 / 1.51
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.09, 97.697, 116.037, 90, 90, 90
R / Rfree (%) 16.7 / 19.5

Other elements in 8re3:

The structure of Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) Mutant M190G From Deinoccoccus Radiodurans also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) Mutant M190G From Deinoccoccus Radiodurans (pdb code 8re3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) Mutant M190G From Deinoccoccus Radiodurans, PDB code: 8re3:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 8re3

Go back to Iron Binding Sites List in 8re3
Iron binding site 1 out of 2 in the Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) Mutant M190G From Deinoccoccus Radiodurans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) Mutant M190G From Deinoccoccus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:16.1
occ:1.00
FE A:HEM501 0.0 16.1 1.0
ND A:HEM501 2.0 16.1 1.0
NA A:HEM501 2.0 17.7 1.0
NC A:HEM501 2.0 13.8 1.0
O A:OH502 2.0 20.5 1.0
NB A:HEM501 2.0 18.4 1.0
NE2 A:HIS324 2.1 17.5 1.0
C1C A:HEM501 3.0 14.8 1.0
C4B A:HEM501 3.0 16.4 1.0
C1A A:HEM501 3.0 18.0 1.0
C1D A:HEM501 3.0 17.9 1.0
C4D A:HEM501 3.0 18.5 1.0
C4A A:HEM501 3.1 21.8 1.0
C4C A:HEM501 3.1 17.0 1.0
CD2 A:HIS324 3.1 20.1 1.0
CE1 A:HIS324 3.1 20.9 1.0
C1B A:HEM501 3.1 19.2 1.0
HD2 A:HIS324 3.3 24.3 1.0
HE1 A:HIS324 3.3 25.3 1.0
CHC A:HEM501 3.4 16.6 1.0
CHA A:HEM501 3.4 17.7 1.0
CHD A:HEM501 3.4 16.7 1.0
CHB A:HEM501 3.5 16.4 1.0
HH11 A:ARG348 3.6 33.5 1.0
O A:OH503 3.7 26.4 1.0
HG3 A:MET328 4.0 25.6 1.0
NH1 A:ARG348 4.1 27.8 1.0
HD2 A:ARG348 4.1 30.3 1.0
ND1 A:HIS324 4.2 21.2 1.0
CG A:HIS324 4.2 19.1 1.0
HD3 A:ARG348 4.2 30.3 1.0
C2D A:HEM501 4.3 17.9 1.0
C3D A:HEM501 4.3 17.5 1.0
C3A A:HEM501 4.3 20.0 1.0
C2A A:HEM501 4.3 18.8 1.0
C2C A:HEM501 4.3 16.3 1.0
C3C A:HEM501 4.3 15.7 1.0
C3B A:HEM501 4.3 17.6 1.0
C2B A:HEM501 4.3 20.2 1.0
HHC A:HEM501 4.3 20.0 1.0
HHA A:HEM501 4.4 21.4 1.0
HHD A:HEM501 4.4 20.2 1.0
HH12 A:ARG348 4.4 33.5 1.0
HHB A:HEM501 4.5 19.8 1.0
CD A:ARG348 4.6 25.1 1.0
HZ A:PHE375 4.7 21.8 1.0
HE1 A:PHE375 4.7 24.1 1.0
CZ A:ARG348 4.8 24.8 1.0
NE A:ARG348 4.9 25.5 1.0
CZ A:PHE375 5.0 18.1 1.0
CG A:MET328 5.0 21.1 1.0
CE1 A:PHE375 5.0 19.9 1.0
HD1 A:HIS324 5.0 25.6 1.0

Iron binding site 2 out of 2 in 8re3

Go back to Iron Binding Sites List in 8re3
Iron binding site 2 out of 2 in the Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) Mutant M190G From Deinoccoccus Radiodurans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) Mutant M190G From Deinoccoccus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:14.7
occ:1.00
FE B:HEM501 0.0 14.7 1.0
NB B:HEM501 2.0 13.0 1.0
NA B:HEM501 2.0 17.0 1.0
NC B:HEM501 2.0 15.4 1.0
ND B:HEM501 2.0 15.4 1.0
NE2 B:HIS324 2.1 15.4 1.0
O B:OH502 2.1 19.4 1.0
C4B B:HEM501 3.0 14.0 1.0
C1C B:HEM501 3.0 15.4 1.0
C1A B:HEM501 3.0 17.6 1.0
CD2 B:HIS324 3.0 17.6 1.0
C1B B:HEM501 3.1 16.6 1.0
C4A B:HEM501 3.1 15.8 1.0
C4D B:HEM501 3.1 15.5 1.0
C4C B:HEM501 3.1 17.1 1.0
C1D B:HEM501 3.1 15.8 1.0
CE1 B:HIS324 3.1 18.2 1.0
HD2 B:HIS324 3.2 21.2 1.0
HE1 B:HIS324 3.3 22.0 1.0
CHC B:HEM501 3.4 14.7 1.0
CHA B:HEM501 3.4 18.4 1.0
CHD B:HEM501 3.5 13.2 1.0
CHB B:HEM501 3.5 15.0 1.0
O B:OH503 3.7 28.9 1.0
HH11 B:ARG348 3.7 34.5 1.0
HG3 B:MET328 4.0 24.6 1.0
HD2 B:ARG348 4.2 34.7 1.0
ND1 B:HIS324 4.2 20.7 1.0
CG B:HIS324 4.2 17.3 1.0
C3B B:HEM501 4.2 16.6 1.0
C2A B:HEM501 4.2 16.7 1.0
C2B B:HEM501 4.3 15.1 1.0
C3A B:HEM501 4.3 15.1 1.0
C2C B:HEM501 4.3 15.1 1.0
NH1 B:ARG348 4.3 28.6 1.0
C3C B:HEM501 4.3 15.8 1.0
HD3 B:ARG348 4.3 34.7 1.0
C2D B:HEM501 4.3 16.3 1.0
C3D B:HEM501 4.3 18.1 1.0
HHC B:HEM501 4.3 17.8 1.0
HHA B:HEM501 4.4 22.2 1.0
HHD B:HEM501 4.4 16.0 1.0
HHB B:HEM501 4.4 18.1 1.0
HE1 B:PHE375 4.6 24.8 1.0
HZ B:PHE375 4.6 21.4 1.0
HH12 B:ARG348 4.6 34.5 1.0
CD B:ARG348 4.6 28.8 1.0
CE1 B:PHE375 4.9 20.6 1.0
CZ B:PHE375 4.9 17.7 1.0
CG B:MET328 5.0 20.4 1.0
CZ B:ARG348 5.0 30.9 1.0
HD1 B:HIS324 5.0 25.0 1.0

Reference:

K.Frade, C.M.Silveira, B.A.Salgueiro, S.Mendes, L.O.Martins, C.Frazao, S.Todorovic, E.Moe. Biochemical, Biophysical, and Structural Analysis of An Unusual Dyp From the Extremophile Deinococcus Radiodurans. Molecules V. 29 2024.
ISSN: ESSN 1420-3049
PubMed: 38257271
DOI: 10.3390/MOLECULES29020358
Page generated: Sat Aug 10 16:56:23 2024

Last articles

Mg in 4Y52
Mg in 4Y30
Mg in 4Y2V
Mg in 4Y2X
Mg in 4Y2Y
Mg in 4Y2U
Mg in 4Y2T
Mg in 4Y2Q
Mg in 4Y2R
Mg in 4Y2S
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy