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Iron in PDB 4m08: Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V

Enzymatic activity of Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V

All present enzymatic activity of Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V:
1.13.11.49;

Protein crystallography data

The structure of Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V, PDB code: 4m08 was solved by K.Gysel, A.Hagmueller, K.Djinovic-Carugo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.15 / 2.80
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 145.830, 145.830, 137.225, 90.00, 90.00, 120.00
R / Rfree (%) 22.1 / 28

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V (pdb code 4m08). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V, PDB code: 4m08:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 4m08

Go back to Iron Binding Sites List in 4m08
Iron binding site 1 out of 5 in the Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:45.0
occ:1.00
FE A:HEM301 0.0 45.0 1.0
NC A:HEM301 2.0 26.9 1.0
NA A:HEM301 2.1 30.9 1.0
NB A:HEM301 2.1 36.8 1.0
ND A:HEM301 2.1 36.3 1.0
N3 A:IMD306 2.5 29.0 1.0
NE2 A:HIS160 2.5 56.6 1.0
C2 A:IMD306 2.8 36.2 1.0
C4C A:HEM301 3.0 43.4 1.0
C1C A:HEM301 3.1 45.9 1.0
C4A A:HEM301 3.1 29.8 1.0
C1B A:HEM301 3.1 55.8 1.0
C1A A:HEM301 3.1 29.9 1.0
C4B A:HEM301 3.1 43.8 1.0
C1D A:HEM301 3.1 31.3 1.0
C4D A:HEM301 3.1 44.1 1.0
CD2 A:HIS160 3.3 51.1 1.0
CHB A:HEM301 3.4 44.4 1.0
CHD A:HEM301 3.4 37.6 1.0
CHC A:HEM301 3.4 42.6 1.0
CHA A:HEM301 3.5 35.8 1.0
CE1 A:HIS160 3.6 73.7 1.0
C4 A:IMD306 3.8 36.4 1.0
N1 A:IMD306 4.1 53.3 1.0
C3C A:HEM301 4.3 36.9 1.0
C2C A:HEM301 4.3 41.6 1.0
C2B A:HEM301 4.3 58.6 1.0
C3A A:HEM301 4.3 39.4 1.0
C2A A:HEM301 4.3 40.8 1.0
C3B A:HEM301 4.3 56.0 1.0
C2D A:HEM301 4.4 34.9 1.0
C3D A:HEM301 4.4 39.8 1.0
CG A:HIS160 4.5 59.8 1.0
C5 A:IMD306 4.5 48.7 1.0
ND1 A:HIS160 4.6 74.6 1.0

Iron binding site 2 out of 5 in 4m08

Go back to Iron Binding Sites List in 4m08
Iron binding site 2 out of 5 in the Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:29.8
occ:1.00
FE B:HEM301 0.0 29.8 1.0
NA B:HEM301 2.0 17.1 1.0
NB B:HEM301 2.1 43.9 1.0
NC B:HEM301 2.1 30.9 1.0
ND B:HEM301 2.1 33.4 1.0
NE2 B:HIS160 2.3 19.1 1.0
N3 B:IMD305 2.5 16.9 1.0
C4 B:IMD305 2.9 23.4 1.0
C1A B:HEM301 3.0 23.4 1.0
C4A B:HEM301 3.0 31.9 1.0
C4B B:HEM301 3.1 45.2 1.0
C1B B:HEM301 3.1 30.0 1.0
C4D B:HEM301 3.1 30.3 1.0
C1C B:HEM301 3.1 31.4 1.0
C4C B:HEM301 3.1 32.7 1.0
C1D B:HEM301 3.1 32.4 1.0
CE1 B:HIS160 3.3 30.7 1.0
CD2 B:HIS160 3.4 21.0 1.0
CHA B:HEM301 3.4 35.2 1.0
CHB B:HEM301 3.4 34.5 1.0
CHC B:HEM301 3.4 40.2 1.0
CHD B:HEM301 3.5 30.2 1.0
C2 B:IMD305 3.8 49.4 1.0
C3B B:HEM301 4.3 33.2 1.0
C2A B:HEM301 4.3 32.1 1.0
C3A B:HEM301 4.3 17.4 1.0
C2B B:HEM301 4.3 25.7 1.0
C5 B:IMD305 4.3 30.1 1.0
C2C B:HEM301 4.3 30.8 1.0
C3C B:HEM301 4.3 27.8 1.0
C3D B:HEM301 4.3 24.3 1.0
C2D B:HEM301 4.4 24.4 1.0
ND1 B:HIS160 4.4 38.6 1.0
CG B:HIS160 4.5 18.4 1.0
N1 B:IMD305 4.7 25.8 1.0

Iron binding site 3 out of 5 in 4m08

Go back to Iron Binding Sites List in 4m08
Iron binding site 3 out of 5 in the Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe302

b:23.1
occ:1.00
FE C:HEM302 0.0 23.1 1.0
NA C:HEM302 2.0 30.4 1.0
NC C:HEM302 2.1 15.5 1.0
NB C:HEM302 2.1 13.1 1.0
ND C:HEM302 2.1 36.5 1.0
NE2 C:HIS160 2.4 22.4 1.0
N3 C:IMD305 2.5 13.9 1.0
C2 C:IMD305 2.9 26.7 1.0
C1A C:HEM302 3.1 33.0 1.0
C4A C:HEM302 3.1 30.7 1.0
C4C C:HEM302 3.1 24.9 1.0
C1D C:HEM302 3.1 24.5 1.0
C4D C:HEM302 3.1 33.4 1.0
C4B C:HEM302 3.1 26.4 1.0
C1C C:HEM302 3.1 16.9 1.0
C1B C:HEM302 3.1 19.5 1.0
CD2 C:HIS160 3.3 28.3 1.0
CE1 C:HIS160 3.3 28.4 1.0
CHD C:HEM302 3.4 31.9 1.0
CHA C:HEM302 3.4 30.8 1.0
CHB C:HEM302 3.4 36.0 1.0
CHC C:HEM302 3.5 12.9 1.0
C4 C:IMD305 3.6 31.8 1.0
N1 C:IMD305 4.1 32.9 1.0
C2A C:HEM302 4.3 28.5 1.0
C3A C:HEM302 4.3 15.3 1.0
C3C C:HEM302 4.3 12.7 1.0
C2D C:HEM302 4.3 38.9 1.0
C2C C:HEM302 4.3 24.7 1.0
C3D C:HEM302 4.3 32.8 1.0
C3B C:HEM302 4.3 42.0 1.0
C2B C:HEM302 4.3 35.6 1.0
C5 C:IMD305 4.4 45.0 1.0
ND1 C:HIS160 4.4 36.7 1.0
CG C:HIS160 4.4 28.1 1.0

Iron binding site 4 out of 5 in 4m08

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Iron binding site 4 out of 5 in the Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe301

b:53.5
occ:1.00
FE D:HEM301 0.0 53.5 1.0
NA D:HEM301 2.0 61.2 1.0
NB D:HEM301 2.1 57.3 1.0
NC D:HEM301 2.1 60.3 1.0
ND D:HEM301 2.1 59.0 1.0
NE2 D:HIS160 2.5 45.5 1.0
N1 D:IMD304 2.6 73.3 1.0
C2 D:IMD304 2.9 75.8 1.0
C4A D:HEM301 3.1 70.2 1.0
C1B D:HEM301 3.1 61.2 1.0
C1A D:HEM301 3.1 65.5 1.0
C4C D:HEM301 3.1 57.3 1.0
C4B D:HEM301 3.1 66.1 1.0
C1D D:HEM301 3.1 53.4 1.0
C4D D:HEM301 3.1 69.4 1.0
C1C D:HEM301 3.1 49.8 1.0
CD2 D:HIS160 3.4 51.4 1.0
CHB D:HEM301 3.4 72.8 1.0
CHD D:HEM301 3.4 57.3 1.0
CHA D:HEM301 3.5 70.9 1.0
CHC D:HEM301 3.5 55.6 1.0
CE1 D:HIS160 3.5 53.5 1.0
C5 D:IMD304 3.6 76.0 1.0
N3 D:IMD304 4.0 87.1 1.0
C3A D:HEM301 4.3 67.9 1.0
C2B D:HEM301 4.3 58.4 1.0
C2A D:HEM301 4.3 71.8 1.0
C3B D:HEM301 4.3 65.7 1.0
C3C D:HEM301 4.3 46.2 1.0
C4 D:IMD304 4.3 83.5 1.0
C2D D:HEM301 4.3 45.1 1.0
C2C D:HEM301 4.3 41.0 1.0
C3D D:HEM301 4.3 63.2 1.0
CG D:HIS160 4.6 51.8 1.0
ND1 D:HIS160 4.6 56.9 1.0

Iron binding site 5 out of 5 in 4m08

Go back to Iron Binding Sites List in 4m08
Iron binding site 5 out of 5 in the Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe301

b:62.5
occ:1.00
FE E:HEM301 0.0 62.5 1.0
NC E:HEM301 2.1 62.0 1.0
NB E:HEM301 2.1 74.4 1.0
ND E:HEM301 2.1 47.3 1.0
NA E:HEM301 2.1 56.5 1.0
NE2 E:HIS160 2.5 53.3 1.0
N1 E:IMD304 2.5 88.3 1.0
C5 E:IMD304 2.9 87.5 1.0
C4D E:HEM301 3.1 59.1 1.0
C4C E:HEM301 3.1 55.6 1.0
C1D E:HEM301 3.1 56.6 1.0
C4B E:HEM301 3.1 68.8 1.0
C1C E:HEM301 3.1 61.5 1.0
C1A E:HEM301 3.1 58.6 1.0
C1B E:HEM301 3.1 70.9 1.0
C4A E:HEM301 3.1 63.0 1.0
CD2 E:HIS160 3.2 63.6 1.0
CHA E:HEM301 3.4 59.0 1.0
CHD E:HEM301 3.4 49.5 1.0
CHC E:HEM301 3.4 60.4 1.0
CHB E:HEM301 3.5 68.3 1.0
C2 E:IMD304 3.6 87.9 1.0
CE1 E:HIS160 3.6 70.1 1.0
C4 E:IMD304 4.1 87.4 1.0
C3C E:HEM301 4.3 54.2 1.0
C2C E:HEM301 4.3 61.8 1.0
C3D E:HEM301 4.3 67.2 1.0
C3B E:HEM301 4.3 64.5 1.0
C2B E:HEM301 4.3 65.1 1.0
C2A E:HEM301 4.3 62.6 1.0
C3A E:HEM301 4.3 66.0 1.0
C2D E:HEM301 4.3 63.0 1.0
N3 E:IMD304 4.4 90.9 1.0
CG E:HIS160 4.4 75.2 1.0
ND1 E:HIS160 4.6 76.6 1.0

Reference:

S.Hofbauer, K.Gysel, M.Bellei, A.Hagmuller, I.Schaffner, G.Mlynek, J.Kostan, K.F.Pirker, H.Daims, P.G.Furtmuller, G.Battistuzzi, K.Djinovic-Carugo, C.Obinger. Manipulating Conserved Heme Cavity Residues of Chlorite Dismutase: Effect on Structure, Redox Chemistry, and Reactivity. Biochemistry V. 53 77 2014.
ISSN: ISSN 0006-2960
PubMed: 24364531
DOI: 10.1021/BI401042Z
Page generated: Tue Aug 5 12:37:24 2025

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