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Iron in PDB 2vxh: The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen

Enzymatic activity of The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen

All present enzymatic activity of The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen:
1.13.11.49;

Protein crystallography data

The structure of The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen, PDB code: 2vxh was solved by D.C.De Geus, E.A.J.Thomassen, P.L.Hagedoorn, N.S.Pannu, J.P.Abrahams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.68 / 2.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 164.458, 169.335, 60.792, 90.00, 90.00, 90.00
R / Rfree (%) 21.87 / 25.486

Iron Binding Sites:

The binding sites of Iron atom in the The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen (pdb code 2vxh). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen, PDB code: 2vxh:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 2vxh

Go back to Iron Binding Sites List in 2vxh
Iron binding site 1 out of 6 in the The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1001

b:18.4
occ:1.00
FE A:HEM1001 0.0 18.4 1.0
NE2 A:HIS170 2.1 21.5 1.0
NA A:HEM1001 2.1 17.4 1.0
N A:SCN1002 2.1 20.9 1.0
NC A:HEM1001 2.1 17.1 1.0
ND A:HEM1001 2.1 17.2 1.0
NB A:HEM1001 2.1 18.0 1.0
CE1 A:HIS170 2.9 23.8 1.0
C1A A:HEM1001 3.1 16.6 1.0
C4A A:HEM1001 3.1 17.4 1.0
C4C A:HEM1001 3.1 16.8 1.0
C1D A:HEM1001 3.1 18.6 1.0
C1B A:HEM1001 3.1 17.8 1.0
C1C A:HEM1001 3.1 14.4 1.0
C4D A:HEM1001 3.1 16.9 1.0
C4B A:HEM1001 3.1 16.7 1.0
CD2 A:HIS170 3.2 22.2 1.0
C A:SCN1002 3.3 19.8 1.0
CHD A:HEM1001 3.4 16.5 1.0
CHA A:HEM1001 3.4 15.6 1.0
CHB A:HEM1001 3.5 18.4 1.0
CHC A:HEM1001 3.5 15.8 1.0
ND1 A:HIS170 4.0 23.4 1.0
CG A:HIS170 4.2 24.7 1.0
C2A A:HEM1001 4.3 17.9 1.0
C3A A:HEM1001 4.3 16.8 1.0
C3C A:HEM1001 4.3 16.7 1.0
C2C A:HEM1001 4.3 16.5 1.0
C2B A:HEM1001 4.3 18.6 1.0
C3B A:HEM1001 4.3 19.1 1.0
C2D A:HEM1001 4.4 18.7 1.0
C3D A:HEM1001 4.4 17.3 1.0
NE A:ARG183 4.4 24.9 1.0
NH2 A:ARG183 4.5 25.0 1.0
CZ A:ARG183 4.9 26.5 1.0
S A:SCN1002 4.9 22.3 1.0

Iron binding site 2 out of 6 in 2vxh

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Iron binding site 2 out of 6 in the The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1001

b:18.2
occ:1.00
FE B:HEM1001 0.0 18.2 1.0
N B:SCN1002 2.0 19.2 1.0
NE2 B:HIS170 2.1 22.4 1.0
NA B:HEM1001 2.1 19.1 1.0
NC B:HEM1001 2.1 19.4 1.0
ND B:HEM1001 2.1 19.6 1.0
NB B:HEM1001 2.1 18.8 1.0
CE1 B:HIS170 2.9 23.4 1.0
C1A B:HEM1001 3.1 19.4 1.0
C4C B:HEM1001 3.1 19.1 1.0
C1D B:HEM1001 3.1 19.9 1.0
C4D B:HEM1001 3.1 19.7 1.0
C4A B:HEM1001 3.1 18.9 1.0
C1C B:HEM1001 3.1 18.8 1.0
C1B B:HEM1001 3.1 17.3 1.0
C4B B:HEM1001 3.1 17.6 1.0
CD2 B:HIS170 3.2 22.9 1.0
C B:SCN1002 3.2 18.8 1.0
CHD B:HEM1001 3.4 18.9 1.0
CHA B:HEM1001 3.4 19.5 1.0
CHB B:HEM1001 3.5 17.9 1.0
CHC B:HEM1001 3.5 18.9 1.0
ND1 B:HIS170 4.1 23.4 1.0
CG B:HIS170 4.2 24.4 1.0
C3C B:HEM1001 4.3 18.5 1.0
C2A B:HEM1001 4.3 18.8 1.0
C2C B:HEM1001 4.3 18.6 1.0
C3A B:HEM1001 4.3 18.8 1.0
C2D B:HEM1001 4.3 19.6 1.0
C2B B:HEM1001 4.3 17.1 1.0
C3B B:HEM1001 4.3 17.5 1.0
C3D B:HEM1001 4.3 20.3 1.0
NH1 B:ARG183 4.6 27.4 1.0
S B:SCN1002 4.9 20.6 1.0
CD B:ARG183 4.9 23.0 1.0

Iron binding site 3 out of 6 in 2vxh

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Iron binding site 3 out of 6 in the The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1001

b:18.3
occ:1.00
FE C:HEM1001 0.0 18.3 1.0
NA C:HEM1001 2.1 19.7 1.0
NB C:HEM1001 2.1 19.6 1.0
N C:SCN1002 2.1 20.9 1.0
NC C:HEM1001 2.1 18.5 1.0
NE2 C:HIS170 2.1 20.5 1.0
ND C:HEM1001 2.1 19.1 1.0
CE1 C:HIS170 2.9 22.7 1.0
C1A C:HEM1001 3.1 20.6 1.0
C4B C:HEM1001 3.1 18.9 1.0
C4D C:HEM1001 3.1 18.7 1.0
C1C C:HEM1001 3.1 18.5 1.0
C4C C:HEM1001 3.1 19.2 1.0
C1D C:HEM1001 3.1 19.7 1.0
C1B C:HEM1001 3.1 19.4 1.0
C4A C:HEM1001 3.1 20.4 1.0
CD2 C:HIS170 3.2 23.6 1.0
C C:SCN1002 3.2 20.7 1.0
CHA C:HEM1001 3.4 20.0 1.0
CHC C:HEM1001 3.4 18.2 1.0
CHD C:HEM1001 3.5 17.9 1.0
CHB C:HEM1001 3.5 19.1 1.0
ND1 C:HIS170 4.1 22.1 1.0
CG C:HIS170 4.2 24.3 1.0
C3B C:HEM1001 4.3 20.8 1.0
C2A C:HEM1001 4.3 20.9 1.0
C2C C:HEM1001 4.3 18.9 1.0
NE C:ARG183 4.3 26.6 1.0
C3D C:HEM1001 4.3 18.7 1.0
C3C C:HEM1001 4.3 19.2 1.0
C2B C:HEM1001 4.3 21.1 1.0
C3A C:HEM1001 4.3 20.0 1.0
C2D C:HEM1001 4.3 19.9 1.0
NH2 C:ARG183 4.5 26.8 1.0
CZ C:ARG183 4.9 26.9 1.0
S C:SCN1002 4.9 22.9 1.0

Iron binding site 4 out of 6 in 2vxh

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Iron binding site 4 out of 6 in the The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1001

b:25.1
occ:1.00
FE D:HEM1001 0.0 25.1 1.0
N D:SCN1002 2.0 18.7 1.0
NB D:HEM1001 2.0 24.8 1.0
NC D:HEM1001 2.1 24.0 1.0
NA D:HEM1001 2.1 25.8 1.0
ND D:HEM1001 2.1 23.6 1.0
NE2 D:HIS170 2.2 23.8 1.0
C4B D:HEM1001 3.0 24.8 1.0
C1C D:HEM1001 3.0 23.3 1.0
C1A D:HEM1001 3.1 24.6 1.0
C1B D:HEM1001 3.1 26.0 1.0
C4D D:HEM1001 3.1 24.3 1.0
CE1 D:HIS170 3.1 23.9 1.0
C4A D:HEM1001 3.1 26.3 1.0
C4C D:HEM1001 3.1 22.9 1.0
C1D D:HEM1001 3.1 24.5 1.0
C D:SCN1002 3.1 18.6 1.0
CD2 D:HIS170 3.3 23.9 1.0
CHC D:HEM1001 3.4 24.8 1.0
CHA D:HEM1001 3.4 25.4 1.0
CHB D:HEM1001 3.5 25.1 1.0
CHD D:HEM1001 3.5 22.6 1.0
ND1 D:HIS170 4.2 24.6 1.0
C3B D:HEM1001 4.3 25.4 1.0
C2B D:HEM1001 4.3 25.3 1.0
C2C D:HEM1001 4.3 22.8 1.0
C2A D:HEM1001 4.3 26.2 1.0
C3C D:HEM1001 4.3 22.2 1.0
C3D D:HEM1001 4.3 24.1 1.0
C3A D:HEM1001 4.3 25.6 1.0
C2D D:HEM1001 4.4 23.0 1.0
CG D:HIS170 4.4 25.2 1.0
NH1 D:ARG183 4.5 27.3 1.0
S D:SCN1002 4.8 20.3 1.0
CD D:ARG183 4.9 23.1 1.0

Iron binding site 5 out of 6 in 2vxh

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Iron binding site 5 out of 6 in the The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe1001

b:17.6
occ:1.00
FE E:HEM1001 0.0 17.6 1.0
N E:SCN1002 1.9 17.1 1.0
NB E:HEM1001 2.1 19.4 1.0
ND E:HEM1001 2.1 16.2 1.0
NC E:HEM1001 2.1 17.2 1.0
NA E:HEM1001 2.1 18.2 1.0
NE2 E:HIS170 2.2 20.2 1.0
CE1 E:HIS170 3.0 22.8 1.0
C1B E:HEM1001 3.1 20.5 1.0
C1D E:HEM1001 3.1 17.7 1.0
C4B E:HEM1001 3.1 19.1 1.0
C E:SCN1002 3.1 16.8 1.0
C4D E:HEM1001 3.1 17.3 1.0
C1C E:HEM1001 3.1 16.8 1.0
C4C E:HEM1001 3.1 17.7 1.0
C4A E:HEM1001 3.1 19.3 1.0
C1A E:HEM1001 3.2 17.8 1.0
CD2 E:HIS170 3.3 21.3 1.0
CHD E:HEM1001 3.4 17.0 1.0
CHC E:HEM1001 3.4 16.7 1.0
CHB E:HEM1001 3.5 19.6 1.0
CHA E:HEM1001 3.5 16.0 1.0
ND1 E:HIS170 4.1 22.4 1.0
C2B E:HEM1001 4.3 22.1 1.0
C3B E:HEM1001 4.3 20.7 1.0
NE E:ARG183 4.3 24.7 1.0
CG E:HIS170 4.3 23.3 1.0
C2D E:HEM1001 4.3 16.9 1.0
C3D E:HEM1001 4.3 15.9 1.0
C2C E:HEM1001 4.3 17.4 1.0
C3C E:HEM1001 4.3 17.5 1.0
C3A E:HEM1001 4.4 19.6 1.0
C2A E:HEM1001 4.4 18.7 1.0
NH2 E:ARG183 4.5 23.8 1.0
S E:SCN1002 4.8 17.6 1.0
CZ E:ARG183 4.8 25.6 1.0

Iron binding site 6 out of 6 in 2vxh

Go back to Iron Binding Sites List in 2vxh
Iron binding site 6 out of 6 in the The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe1001

b:23.8
occ:1.00
FE F:HEM1001 0.0 23.8 1.0
NB F:HEM1001 2.0 25.2 1.0
N F:SCN1002 2.1 22.9 1.0
NA F:HEM1001 2.1 26.6 1.0
ND F:HEM1001 2.1 25.2 1.0
NE2 F:HIS170 2.1 22.7 1.0
NC F:HEM1001 2.1 24.5 1.0
CE1 F:HIS170 3.0 23.5 1.0
C1B F:HEM1001 3.0 25.5 1.0
C4B F:HEM1001 3.0 25.7 1.0
C4D F:HEM1001 3.1 24.0 1.0
C4A F:HEM1001 3.1 26.6 1.0
CD2 F:HIS170 3.1 23.3 1.0
C1D F:HEM1001 3.1 24.2 1.0
C1A F:HEM1001 3.1 26.1 1.0
C1C F:HEM1001 3.1 24.5 1.0
C4C F:HEM1001 3.1 24.9 1.0
C F:SCN1002 3.2 21.6 1.0
CHB F:HEM1001 3.4 25.4 1.0
CHC F:HEM1001 3.4 25.2 1.0
CHA F:HEM1001 3.5 24.6 1.0
CHD F:HEM1001 3.5 24.0 1.0
ND1 F:HIS170 4.1 24.1 1.0
CG F:HIS170 4.2 24.1 1.0
NH1 F:ARG183 4.2 27.5 1.0
C2B F:HEM1001 4.2 25.6 1.0
C3B F:HEM1001 4.3 25.6 1.0
C3D F:HEM1001 4.3 24.2 1.0
C3A F:HEM1001 4.3 26.6 1.0
C2D F:HEM1001 4.3 25.1 1.0
C2A F:HEM1001 4.3 26.5 1.0
C2C F:HEM1001 4.4 25.2 1.0
C3C F:HEM1001 4.4 25.7 1.0
CD F:ARG183 4.9 23.5 1.0
S F:SCN1002 4.9 22.6 1.0

Reference:

D.C.De Geus, E.A.J.Thomassen, P.L.Hagedoorn, N.S.Pannu, E.Van Duijn, J.P.Abrahams. Crystal Structure of Chlorite Dismutase, A Detoxifying Enzyme Producing Molecular Oxygen J.Mol.Biol. V. 387 192 2009.
ISSN: ISSN 0022-2836
PubMed: 19361444
DOI: 10.1016/J.JMB.2009.01.036
Page generated: Sun Dec 13 14:54:33 2020

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