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Iron in PDB 3nn3: Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii R173A Mutant

Enzymatic activity of Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii R173A Mutant

All present enzymatic activity of Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii R173A Mutant:
1.13.11.49;

Protein crystallography data

The structure of Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii R173A Mutant, PDB code: 3nn3 was solved by J.Kostan, B.Sjoeblom, F.Maixner, G.Mlynek, P.G.Furtmueller, C.Obinger, M.Wagner, H.Daims, K.Djinovic-Carugo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.39 / 2.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 139.740, 113.620, 120.520, 90.00, 118.94, 90.00
R / Rfree (%) 21.2 / 25.4

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii R173A Mutant (pdb code 3nn3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii R173A Mutant, PDB code: 3nn3:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 3nn3

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Iron binding site 1 out of 5 in the Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii R173A Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii R173A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe239

b:50.1
occ:1.00
FE A:HEM239 0.0 50.1 1.0
NC A:HEM239 1.9 46.5 1.0
NB A:HEM239 2.0 48.1 1.0
ND A:HEM239 2.0 46.1 1.0
NA A:HEM239 2.1 48.2 1.0
NE2 A:HIS160 2.2 60.5 1.0
C4B A:HEM239 3.0 49.0 1.0
C4C A:HEM239 3.0 45.6 1.0
C1C A:HEM239 3.0 46.3 1.0
C1D A:HEM239 3.0 46.0 1.0
C4D A:HEM239 3.0 45.1 1.0
C1B A:HEM239 3.0 49.0 1.0
O A:HOH245 3.1 51.9 1.0
C1A A:HEM239 3.1 47.5 1.0
C4A A:HEM239 3.1 48.5 1.0
CE1 A:HIS160 3.2 59.7 1.0
CD2 A:HIS160 3.2 61.5 1.0
CHC A:HEM239 3.3 47.6 1.0
CHD A:HEM239 3.3 45.9 1.0
CHA A:HEM239 3.4 46.7 1.0
CHB A:HEM239 3.5 48.9 1.0
C3C A:HEM239 4.2 45.6 1.0
C3B A:HEM239 4.2 49.8 1.0
C2C A:HEM239 4.2 45.8 1.0
C2B A:HEM239 4.2 49.4 1.0
C2D A:HEM239 4.2 43.7 1.0
C3D A:HEM239 4.2 46.5 1.0
ND1 A:HIS160 4.3 59.2 1.0
CG A:HIS160 4.3 60.3 1.0
C2A A:HEM239 4.3 48.1 1.0
C3A A:HEM239 4.4 47.4 1.0

Iron binding site 2 out of 5 in 3nn3

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Iron binding site 2 out of 5 in the Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii R173A Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii R173A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe239

b:46.5
occ:1.00
FE B:HEM239 0.0 46.5 1.0
NC B:HEM239 1.9 40.9 1.0
NA B:HEM239 2.0 41.1 1.0
NB B:HEM239 2.0 42.8 1.0
ND B:HEM239 2.0 39.9 1.0
NE2 B:HIS160 2.2 56.4 1.0
C4C B:HEM239 3.0 41.5 1.0
C4D B:HEM239 3.0 39.0 1.0
C1A B:HEM239 3.0 42.1 1.0
C4B B:HEM239 3.0 43.7 1.0
C1D B:HEM239 3.0 40.7 1.0
C4A B:HEM239 3.0 43.5 1.0
C1C B:HEM239 3.0 42.6 1.0
C1B B:HEM239 3.0 45.1 1.0
O B:HOH247 3.0 53.6 1.0
CD2 B:HIS160 3.1 56.9 1.0
CE1 B:HIS160 3.2 55.1 1.0
CHA B:HEM239 3.3 41.3 1.0
CHD B:HEM239 3.4 42.2 1.0
CHC B:HEM239 3.4 43.2 1.0
CHB B:HEM239 3.4 44.3 1.0
C3C B:HEM239 4.2 41.6 1.0
C3D B:HEM239 4.2 42.3 1.0
C2A B:HEM239 4.2 42.6 1.0
C3B B:HEM239 4.2 46.5 1.0
C3A B:HEM239 4.2 41.6 1.0
C2C B:HEM239 4.2 42.2 1.0
C2B B:HEM239 4.3 46.7 1.0
C2D B:HEM239 4.3 39.6 1.0
ND1 B:HIS160 4.3 56.2 1.0
CG B:HIS160 4.3 56.8 1.0
CE B:MET157 4.9 62.4 1.0

Iron binding site 3 out of 5 in 3nn3

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Iron binding site 3 out of 5 in the Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii R173A Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii R173A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe239

b:50.8
occ:1.00
FE C:HEM239 0.0 50.8 1.0
NB C:HEM239 1.9 45.8 1.0
NA C:HEM239 2.0 45.6 1.0
ND C:HEM239 2.0 44.1 1.0
NC C:HEM239 2.0 45.3 1.0
NE2 C:HIS160 2.3 58.8 1.0
O C:HOH245 2.9 52.3 1.0
C1B C:HEM239 2.9 46.2 1.0
C4A C:HEM239 3.0 46.4 1.0
C1A C:HEM239 3.0 45.7 1.0
C4B C:HEM239 3.0 46.5 1.0
C4C C:HEM239 3.0 44.9 1.0
C4D C:HEM239 3.0 44.4 1.0
C1D C:HEM239 3.0 44.2 1.0
C1C C:HEM239 3.1 45.8 1.0
CE1 C:HIS160 3.1 57.1 1.0
CD2 C:HIS160 3.3 57.9 1.0
CHB C:HEM239 3.3 46.2 1.0
CHD C:HEM239 3.4 44.0 1.0
CHA C:HEM239 3.4 45.0 1.0
CHC C:HEM239 3.5 45.9 1.0
C2B C:HEM239 4.1 47.6 1.0
C3B C:HEM239 4.2 46.7 1.0
C2A C:HEM239 4.2 45.2 1.0
ND1 C:HIS160 4.2 55.9 1.0
C3A C:HEM239 4.2 45.0 1.0
C3C C:HEM239 4.3 43.9 1.0
C3D C:HEM239 4.3 44.8 1.0
C2D C:HEM239 4.3 43.3 1.0
C2C C:HEM239 4.3 44.9 1.0
CG C:HIS160 4.3 56.5 1.0

Iron binding site 4 out of 5 in 3nn3

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Iron binding site 4 out of 5 in the Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii R173A Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii R173A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe239

b:51.1
occ:1.00
FE D:HEM239 0.0 51.1 1.0
NA D:HEM239 1.9 50.5 1.0
NB D:HEM239 2.0 50.4 1.0
ND D:HEM239 2.0 48.5 1.0
NC D:HEM239 2.1 49.5 1.0
NE2 D:HIS160 2.2 58.5 1.0
C1A D:HEM239 3.0 50.3 1.0
C1B D:HEM239 3.0 51.3 1.0
C4A D:HEM239 3.0 50.3 1.0
C4D D:HEM239 3.0 48.2 1.0
C4B D:HEM239 3.0 50.8 1.0
C4C D:HEM239 3.1 48.8 1.0
C1D D:HEM239 3.1 48.4 1.0
CE1 D:HIS160 3.1 57.0 1.0
C1C D:HEM239 3.1 49.8 1.0
CD2 D:HIS160 3.2 58.6 1.0
O D:HOH245 3.3 58.1 1.0
CHA D:HEM239 3.3 49.9 1.0
CHB D:HEM239 3.4 50.6 1.0
CHD D:HEM239 3.4 48.4 1.0
CHC D:HEM239 3.5 50.4 1.0
C2A D:HEM239 4.2 50.8 1.0
C2B D:HEM239 4.2 52.6 1.0
C3B D:HEM239 4.2 51.1 1.0
C3A D:HEM239 4.2 50.4 1.0
ND1 D:HIS160 4.2 55.6 1.0
C3D D:HEM239 4.3 48.5 1.0
C3C D:HEM239 4.3 49.5 1.0
C2D D:HEM239 4.3 47.4 1.0
C2C D:HEM239 4.3 49.9 1.0
CG D:HIS160 4.3 56.3 1.0

Iron binding site 5 out of 5 in 3nn3

Go back to Iron Binding Sites List in 3nn3
Iron binding site 5 out of 5 in the Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii R173A Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii R173A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe239

b:46.9
occ:1.00
FE E:HEM239 0.0 46.9 1.0
NC E:HEM239 1.9 39.1 1.0
NA E:HEM239 2.0 39.8 1.0
NB E:HEM239 2.0 41.3 1.0
ND E:HEM239 2.1 39.2 1.0
NE2 E:HIS160 2.3 58.3 1.0
C4C E:HEM239 2.8 42.7 1.0
C4A E:HEM239 3.0 42.8 1.0
C1C E:HEM239 3.0 41.3 1.0
C1B E:HEM239 3.0 42.1 1.0
C1D E:HEM239 3.0 39.7 1.0
C1A E:HEM239 3.0 42.6 1.0
C4B E:HEM239 3.1 42.3 1.0
O E:HOH243 3.1 45.8 1.0
C4D E:HEM239 3.1 39.7 1.0
CD2 E:HIS160 3.2 58.6 1.0
CE1 E:HIS160 3.2 57.5 1.0
CHD E:HEM239 3.3 41.5 1.0
CHB E:HEM239 3.3 42.9 1.0
CHC E:HEM239 3.4 42.0 1.0
CHA E:HEM239 3.5 42.0 1.0
C3C E:HEM239 4.1 41.4 1.0
C2C E:HEM239 4.1 40.0 1.0
C3A E:HEM239 4.2 41.2 1.0
C2B E:HEM239 4.2 45.9 1.0
C2A E:HEM239 4.2 40.8 1.0
C3B E:HEM239 4.3 45.3 1.0
C2D E:HEM239 4.3 41.1 1.0
ND1 E:HIS160 4.3 57.8 1.0
C3D E:HEM239 4.4 43.1 1.0
CG E:HIS160 4.4 59.1 1.0

Reference:

J.Kostan, B.Sjoeblom, F.Maixner, G.Mlynek, P.G.Furtmueller, C.Obinger, M.Wagner, H.Daims, K.Djinovic-Carugo. Structural and Functional Characterisation of the Chlorite Dismutase From the Nitrite-Oxidizing Bacterium "Candidatus Nitrospira Defluvii": Identification of A Catalytically Important Amino Acid Residue J.Struct.Biol. V. 172 331 2010.
ISSN: ISSN 1047-8477
PubMed: 20600954
DOI: 10.1016/J.JSB.2010.06.014
Page generated: Sun Dec 13 15:14:44 2020

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