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Iron in PDB 4cab: The Refined Structure of Catalase DR1998 From Deinococcus Radiodurans at 2.6 A Resolution

Enzymatic activity of The Refined Structure of Catalase DR1998 From Deinococcus Radiodurans at 2.6 A Resolution

All present enzymatic activity of The Refined Structure of Catalase DR1998 From Deinococcus Radiodurans at 2.6 A Resolution:
1.11.1.6;

Protein crystallography data

The structure of The Refined Structure of Catalase DR1998 From Deinococcus Radiodurans at 2.6 A Resolution, PDB code: 4cab was solved by P.T.Borges, C.S.Miranda, S.P.Santos, C.Frazao, C.V.Romao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.402 / 2.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 97.326, 311.875, 145.628, 90.00, 90.00, 90.00
R / Rfree (%) 23.63 / 23.63

Other elements in 4cab:

The structure of The Refined Structure of Catalase DR1998 From Deinococcus Radiodurans at 2.6 A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 10 atoms

Iron Binding Sites:

The binding sites of Iron atom in the The Refined Structure of Catalase DR1998 From Deinococcus Radiodurans at 2.6 A Resolution (pdb code 4cab). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the The Refined Structure of Catalase DR1998 From Deinococcus Radiodurans at 2.6 A Resolution, PDB code: 4cab:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4cab

Go back to Iron Binding Sites List in 4cab
Iron binding site 1 out of 4 in the The Refined Structure of Catalase DR1998 From Deinococcus Radiodurans at 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Refined Structure of Catalase DR1998 From Deinococcus Radiodurans at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe537

b:21.7
occ:1.00
 FE A:HEM537 0.0 21.7 1.0
NA A:HEM537 2.0 22.1 1.0
NB A:HEM537 2.1 22.1 1.0
ND A:HEM537 2.1 21.4 1.0
NC A:HEM537 2.1 21.5 1.0
OH A:TYR369 2.6 19.6 1.0
C4A A:HEM537 3.0 22.4 1.0
C1B A:HEM537 3.1 22.4 1.0
C1A A:HEM537 3.1 22.0 1.0
C4B A:HEM537 3.1 22.1 1.0
C1D A:HEM537 3.1 21.1 1.0
C4D A:HEM537 3.1 21.5 1.0
C4C A:HEM537 3.1 21.1 1.0
C1C A:HEM537 3.1 21.5 1.0
CZ A:TYR369 3.4 19.2 1.0
CHB A:HEM537 3.4 22.5 1.0
CHA A:HEM537 3.4 21.8 1.0
CHD A:HEM537 3.4 20.9 1.0
CHC A:HEM537 3.5 21.9 1.0
CE1 A:TYR369 3.7 18.8 1.0
C3A A:HEM537 4.3 22.5 1.0
C2B A:HEM537 4.3 22.7 1.0
C2A A:HEM537 4.3 22.3 1.0
C3B A:HEM537 4.3 22.3 1.0
C2D A:HEM537 4.3 20.9 1.0
C3C A:HEM537 4.3 21.0 1.0
C3D A:HEM537 4.3 21.2 1.0
C2C A:HEM537 4.3 21.2 1.0
NE A:ARG365 4.3 18.1 1.0
CE2 A:TYR369 4.5 19.3 1.0
NH2 A:ARG365 4.5 17.8 1.0
CZ A:PHE172 4.5 19.6 1.0
O A:HOH2025 4.7 26.7 1.0
CG2 A:VAL80 4.8 16.7 1.0
CZ A:ARG365 4.8 18.2 1.0
CD1 A:TYR369 4.9 18.4 1.0
CE1 A:PHE172 4.9 20.2 1.0
NE2 A:HIS81 5.0 18.8 1.0

Iron binding site 2 out of 4 in 4cab

Go back to Iron Binding Sites List in 4cab
Iron binding site 2 out of 4 in the The Refined Structure of Catalase DR1998 From Deinococcus Radiodurans at 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Refined Structure of Catalase DR1998 From Deinococcus Radiodurans at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe537

b:18.7
occ:1.00
 FE B:HEM537 0.0 18.7 1.0
NA B:HEM537 2.0 19.2 1.0
NB B:HEM537 2.1 18.7 1.0
ND B:HEM537 2.1 18.8 1.0
NC B:HEM537 2.1 18.3 1.0
OH B:TYR369 2.2 21.2 1.0
C4A B:HEM537 3.0 19.4 1.0
C1D B:HEM537 3.1 18.6 1.0
C1B B:HEM537 3.1 18.9 1.0
C1A B:HEM537 3.1 19.5 1.0
C4C B:HEM537 3.1 18.1 1.0
C4D B:HEM537 3.1 19.1 1.0
C4B B:HEM537 3.1 18.4 1.0
C1C B:HEM537 3.1 18.0 1.0
CZ B:TYR369 3.1 21.0 1.0
CHB B:HEM537 3.4 19.2 1.0
CHD B:HEM537 3.4 18.2 1.0
CHA B:HEM537 3.4 19.5 1.0
CHC B:HEM537 3.5 18.1 1.0
CE1 B:TYR369 3.5 20.2 1.0
CE2 B:TYR369 4.2 21.5 1.0
C3A B:HEM537 4.3 19.7 1.0
C2A B:HEM537 4.3 19.8 1.0
C2B B:HEM537 4.3 18.7 1.0
C3B B:HEM537 4.3 18.4 1.0
C2D B:HEM537 4.3 18.7 1.0
C3C B:HEM537 4.3 17.7 1.0
C2C B:HEM537 4.3 17.7 1.0
C3D B:HEM537 4.3 19.1 1.0
NE B:ARG365 4.3 21.3 1.0
NH2 B:ARG365 4.5 21.6 1.0
CZ B:PHE172 4.6 19.3 1.0
CD1 B:TYR369 4.8 23.1 1.0
CG2 B:VAL80 4.8 18.8 1.0
CZ B:ARG365 4.8 21.7 1.0
O B:HOH2015 4.9 27.3 1.0

Iron binding site 3 out of 4 in 4cab

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Iron binding site 3 out of 4 in the The Refined Structure of Catalase DR1998 From Deinococcus Radiodurans at 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Refined Structure of Catalase DR1998 From Deinococcus Radiodurans at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe537

b:19.4
occ:1.00
 FE C:HEM537 0.0 19.4 1.0
NC C:HEM537 2.0 19.6 1.0
ND C:HEM537 2.1 18.5 1.0
NA C:HEM537 2.1 19.1 1.0
NB C:HEM537 2.1 20.2 1.0
OH C:TYR369 2.4 16.7 1.0
C4C C:HEM537 3.0 19.3 1.0
C1D C:HEM537 3.1 18.3 1.0
C1C C:HEM537 3.1 20.2 1.0
C4B C:HEM537 3.1 20.8 1.0
C1B C:HEM537 3.1 20.6 1.0
C4A C:HEM537 3.1 19.6 1.0
C1A C:HEM537 3.1 18.5 1.0
C4D C:HEM537 3.1 17.9 1.0
CZ C:TYR369 3.2 16.8 1.0
CHD C:HEM537 3.4 20.6 1.0
CHC C:HEM537 3.4 20.7 1.0
CHB C:HEM537 3.5 20.3 1.0
CHA C:HEM537 3.5 18.0 1.0
CE1 C:TYR369 3.6 16.2 1.0
CE2 C:TYR369 4.1 17.5 1.0
C3C C:HEM537 4.2 19.8 1.0
C2C C:HEM537 4.3 20.4 1.0
C3B C:HEM537 4.3 21.9 1.0
C2B C:HEM537 4.3 21.3 1.0
C2D C:HEM537 4.3 17.7 1.0
C3A C:HEM537 4.3 19.2 1.0
C2A C:HEM537 4.3 18.6 1.0
C3D C:HEM537 4.3 17.4 1.0
NE C:ARG365 4.4 17.7 1.0
CZ C:PHE172 4.6 13.6 1.0
NH2 C:ARG365 4.6 17.3 1.0
CD1 C:TYR369 4.8 16.4 1.0
CG2 C:VAL80 4.8 17.5 1.0
O C:HOH2022 4.8 13.3 1.0
CZ C:ARG365 4.9 17.8 1.0

Iron binding site 4 out of 4 in 4cab

Go back to Iron Binding Sites List in 4cab
Iron binding site 4 out of 4 in the The Refined Structure of Catalase DR1998 From Deinococcus Radiodurans at 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Refined Structure of Catalase DR1998 From Deinococcus Radiodurans at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe537

b:21.4
occ:1.00
 FE D:HEM537 0.0 21.4 1.0
NC D:HEM537 2.1 21.6 1.0
NA D:HEM537 2.1 21.0 1.0
ND D:HEM537 2.1 21.2 1.0
NB D:HEM537 2.1 21.6 1.0
OH D:TYR369 2.3 20.0 1.0
C4C D:HEM537 3.1 21.6 1.0
C1D D:HEM537 3.1 21.1 1.0
C1C D:HEM537 3.1 21.9 1.0
C1A D:HEM537 3.1 20.6 1.0
C4D D:HEM537 3.1 20.6 1.0
C4B D:HEM537 3.1 21.9 1.0
C4A D:HEM537 3.1 21.1 1.0
C1B D:HEM537 3.1 21.6 1.0
CZ D:TYR369 3.2 19.6 1.0
CHD D:HEM537 3.4 21.4 1.0
CHA D:HEM537 3.4 22.6 1.0
CHC D:HEM537 3.4 22.0 1.0
CHB D:HEM537 3.5 21.4 1.0
CE1 D:TYR369 3.6 19.2 1.0
CE2 D:TYR369 4.2 19.7 1.0
C3C D:HEM537 4.3 22.0 1.0
C2C D:HEM537 4.3 22.2 1.0
C2D D:HEM537 4.3 20.8 1.0
C3B D:HEM537 4.3 22.2 1.0
C3A D:HEM537 4.3 20.8 1.0
C2A D:HEM537 4.3 20.5 1.0
C2B D:HEM537 4.3 22.0 1.0
C3D D:HEM537 4.3 21.6 1.0
NE D:ARG365 4.4 21.2 1.0
CZ D:PHE172 4.5 20.5 1.0
NH2 D:ARG365 4.7 21.3 1.0
O D:HOH2018 4.7 21.3 1.0
CG2 D:VAL80 4.8 19.3 1.0
CD1 D:TYR369 4.8 18.8 1.0
CZ D:ARG365 5.0 21.5 1.0
CE1 D:PHE172 5.0 21.0 1.0

Reference:

P.T.Borges, C.Frazao, C.S.Miranda, M.A.Carrondo, C.V.Romao. Structure of the Mono-Functional Heme Catalase DR1998 From Deinococcus Radiodurans Febs J. 2014.
ISSN: ESSN 1742-4658
PubMed: 24975828
DOI: 10.1111/FEBS.12895
Page generated: Sun Dec 13 15:29:53 2020

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