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Iron in PDB 1iqc: Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea

Protein crystallography data

The structure of Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea, PDB code: 1iqc was solved by H.Shimizu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 88.134, 55.111, 144.000, 90.00, 103.60, 90.00
R / Rfree (%) 22.2 / 25.7

Other elements in 1iqc:

The structure of Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Calcium (Ca) 5 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea (pdb code 1iqc). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea, PDB code: 1iqc:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 1iqc

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Iron binding site 1 out of 8 in the Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea


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 Di-Heme Peroxidase From Nitrosomonas Europaea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:13.0
occ:1.00
FE A:HEC401 0.0 13.0 1.0
NC A:HEC401 2.0 13.7 1.0
NA A:HEC401 2.0 15.8 1.0
NB A:HEC401 2.0 11.4 1.0
ND A:HEC401 2.0 14.4 1.0
NE2 A:HIS43 2.1 11.6 1.0
O A:HOH1680 2.3 18.6 1.0
C1C A:HEC401 3.0 10.5 1.0
C4B A:HEC401 3.0 12.0 1.0
C4D A:HEC401 3.0 14.2 1.0
C4C A:HEC401 3.0 12.8 1.0
C1A A:HEC401 3.0 12.2 1.0
C1D A:HEC401 3.0 12.5 1.0
C4A A:HEC401 3.1 12.9 1.0
CD2 A:HIS43 3.1 14.5 1.0
C1B A:HEC401 3.1 11.0 1.0
CE1 A:HIS43 3.1 11.4 1.0
CHC A:HEC401 3.4 13.8 1.0
CHA A:HEC401 3.4 10.9 1.0
CHD A:HEC401 3.4 11.0 1.0
CHB A:HEC401 3.4 11.1 1.0
NE2 A:GLN92 4.1 15.8 1.0
ND1 A:HIS43 4.2 9.4 1.0
CG A:HIS43 4.2 10.9 1.0
C2C A:HEC401 4.2 11.7 1.0
C3C A:HEC401 4.3 12.8 1.0
C3B A:HEC401 4.3 12.5 1.0
C3D A:HEC401 4.3 12.6 1.0
C2A A:HEC401 4.3 13.8 1.0
C3A A:HEC401 4.3 13.9 1.0
C2B A:HEC401 4.3 10.9 1.0
C2D A:HEC401 4.3 16.6 1.0
O A:HOH1479 4.7 41.3 1.0
CB A:PRO96 4.9 21.4 1.0
CG A:PRO96 5.0 25.3 1.0

Iron binding site 2 out of 8 in 1iqc

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Iron binding site 2 out of 8 in the Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea


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 Di-Heme Peroxidase From Nitrosomonas Europaea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:15.7
occ:1.00
FE A:HEC402 0.0 15.7 1.0
ND A:HEC402 2.0 15.5 1.0
NB A:HEC402 2.0 17.9 1.0
NC A:HEC402 2.0 19.1 1.0
NA A:HEC402 2.0 15.2 1.0
NE2 A:HIS187 2.1 12.1 1.0
SD A:MET258 2.3 20.6 1.0
C1D A:HEC402 3.0 16.8 1.0
C4B A:HEC402 3.0 16.9 1.0
C4D A:HEC402 3.0 13.3 1.0
C1C A:HEC402 3.0 17.4 1.0
C4C A:HEC402 3.0 18.1 1.0
C1A A:HEC402 3.0 14.3 1.0
C1B A:HEC402 3.0 16.7 1.0
C4A A:HEC402 3.1 18.1 1.0
CD2 A:HIS187 3.1 10.7 1.0
CE1 A:HIS187 3.1 13.2 1.0
CHC A:HEC402 3.4 17.1 1.0
CHD A:HEC402 3.4 17.4 1.0
CHA A:HEC402 3.4 14.7 1.0
CG A:MET258 3.4 17.5 1.0
CHB A:HEC402 3.5 16.8 1.0
CE A:MET258 3.6 16.2 1.0
ND1 A:HIS187 4.2 15.6 1.0
CG A:HIS187 4.2 14.4 1.0
C3D A:HEC402 4.2 15.6 1.0
C2D A:HEC402 4.2 19.5 1.0
C3B A:HEC402 4.3 16.3 1.0
C2B A:HEC402 4.3 18.6 1.0
C3C A:HEC402 4.3 15.8 1.0
C2C A:HEC402 4.3 15.7 1.0
C2A A:HEC402 4.3 12.4 1.0
C3A A:HEC402 4.3 15.8 1.0
CB A:MET258 4.4 20.3 1.0

Iron binding site 3 out of 8 in 1iqc

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Iron binding site 3 out of 8 in the Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea


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 Di-Heme Peroxidase From Nitrosomonas Europaea within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:19.1
occ:1.00
FE B:HEC401 0.0 19.1 1.0
ND B:HEC401 1.9 20.4 1.0
NB B:HEC401 2.0 18.6 1.0
NC B:HEC401 2.0 17.9 1.0
NA B:HEC401 2.0 18.0 1.0
O B:HOH1609 2.1 25.8 1.0
NE2 B:HIS43 2.1 21.2 1.0
C1D B:HEC401 3.0 19.8 1.0
C4C B:HEC401 3.0 22.5 1.0
C4D B:HEC401 3.0 15.2 1.0
C1B B:HEC401 3.0 19.6 1.0
C4A B:HEC401 3.0 17.2 1.0
C4B B:HEC401 3.0 16.2 1.0
C1A B:HEC401 3.1 17.6 1.0
C1C B:HEC401 3.1 20.5 1.0
CD2 B:HIS43 3.1 21.0 1.0
CE1 B:HIS43 3.2 20.8 1.0
CHD B:HEC401 3.4 19.7 1.0
CHB B:HEC401 3.4 16.7 1.0
CHA B:HEC401 3.4 14.6 1.0
CHC B:HEC401 3.5 17.3 1.0
NE2 B:GLN92 4.0 14.3 1.0
CG B:HIS43 4.2 23.6 1.0
C2D B:HEC401 4.2 18.6 1.0
C3D B:HEC401 4.2 19.0 1.0
ND1 B:HIS43 4.2 22.1 1.0
C3A B:HEC401 4.3 19.4 1.0
C2B B:HEC401 4.3 20.1 1.0
C3B B:HEC401 4.3 19.6 1.0
C2A B:HEC401 4.3 16.7 1.0
C2C B:HEC401 4.3 19.9 1.0
C3C B:HEC401 4.3 20.2 1.0
O B:HOH1413 4.3 26.4 1.0
CG B:PRO96 4.4 22.6 1.0
CD B:GLN92 4.9 17.7 1.0

Iron binding site 4 out of 8 in 1iqc

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Iron binding site 4 out of 8 in the Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea


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 Di-Heme Peroxidase From Nitrosomonas Europaea within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:28.3
occ:1.00
FE B:HEC402 0.0 28.3 1.0
NA B:HEC402 2.0 31.3 1.0
NB B:HEC402 2.0 32.3 1.0
ND B:HEC402 2.0 26.1 1.0
NC B:HEC402 2.0 29.6 1.0
NE2 B:HIS187 2.1 28.1 1.0
SD B:MET258 2.3 35.6 1.0
CD2 B:HIS187 3.0 29.3 1.0
C1A B:HEC402 3.0 31.8 1.0
C4D B:HEC402 3.0 26.1 1.0
C4A B:HEC402 3.0 32.8 1.0
C4B B:HEC402 3.0 33.9 1.0
C1B B:HEC402 3.1 35.4 1.0
C1C B:HEC402 3.1 29.2 1.0
C1D B:HEC402 3.1 26.8 1.0
C4C B:HEC402 3.1 30.9 1.0
CE1 B:HIS187 3.1 26.9 1.0
CHA B:HEC402 3.4 29.3 1.0
CHC B:HEC402 3.4 32.4 1.0
CHB B:HEC402 3.4 36.6 1.0
CG B:MET258 3.5 32.9 1.0
CHD B:HEC402 3.5 26.3 1.0
CE B:MET258 3.7 27.0 1.0
CG B:HIS187 4.2 30.3 1.0
ND1 B:HIS187 4.2 27.0 1.0
C3A B:HEC402 4.3 34.3 1.0
C2A B:HEC402 4.3 32.8 1.0
C3B B:HEC402 4.3 34.4 1.0
C2B B:HEC402 4.3 37.1 1.0
C3D B:HEC402 4.3 26.6 1.0
C2D B:HEC402 4.3 25.8 1.0
C2C B:HEC402 4.3 31.3 1.0
C3C B:HEC402 4.3 28.8 1.0
CB B:MET258 4.4 32.3 1.0

Iron binding site 5 out of 8 in 1iqc

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Iron binding site 5 out of 8 in the Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea


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 Di-Heme Peroxidase From Nitrosomonas Europaea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:14.2
occ:1.00
FE C:HEC401 0.0 14.2 1.0
NB C:HEC401 1.9 11.1 1.0
ND C:HEC401 2.0 14.5 1.0
NA C:HEC401 2.0 12.3 1.0
NC C:HEC401 2.0 13.3 1.0
NE2 C:HIS43 2.1 12.9 1.0
O C:HOH689 2.3 20.5 1.0
C4B C:HEC401 3.0 10.5 1.0
C4D C:HEC401 3.0 11.3 1.0
C1D C:HEC401 3.0 13.5 1.0
C1B C:HEC401 3.0 11.1 1.0
C1A C:HEC401 3.0 12.6 1.0
C4A C:HEC401 3.0 11.6 1.0
C4C C:HEC401 3.0 13.5 1.0
CD2 C:HIS43 3.0 13.6 1.0
C1C C:HEC401 3.1 10.1 1.0
CE1 C:HIS43 3.1 16.1 1.0
CHD C:HEC401 3.4 14.4 1.0
CHA C:HEC401 3.4 16.2 1.0
CHC C:HEC401 3.4 14.7 1.0
CHB C:HEC401 3.4 12.4 1.0
NE2 C:GLN92 4.0 15.8 1.0
ND1 C:HIS43 4.2 11.1 1.0
CG C:HIS43 4.2 12.4 1.0
C3B C:HEC401 4.2 13.2 1.0
C2D C:HEC401 4.2 13.8 1.0
C3D C:HEC401 4.2 15.6 1.0
C2B C:HEC401 4.2 13.1 1.0
C3A C:HEC401 4.3 13.8 1.0
C3C C:HEC401 4.3 13.8 1.0
C2A C:HEC401 4.3 14.9 1.0
C2C C:HEC401 4.3 11.8 1.0
O C:HOH485 4.5 28.7 1.0
CB C:PRO96 4.9 18.6 1.0
CD C:GLN92 4.9 16.5 1.0
CG C:PRO96 5.0 19.4 1.0

Iron binding site 6 out of 8 in 1iqc

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Iron binding site 6 out of 8 in the Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe402

b:14.2
occ:1.00
FE C:HEC402 0.0 14.2 1.0
NB C:HEC402 2.0 13.6 1.0
ND C:HEC402 2.0 16.9 1.0
NA C:HEC402 2.0 14.3 1.0
NC C:HEC402 2.0 13.6 1.0
NE2 C:HIS187 2.1 12.2 1.0
SD C:MET258 2.3 19.1 1.0
CD2 C:HIS187 3.0 19.0 1.0
C1B C:HEC402 3.0 15.4 1.0
C4B C:HEC402 3.0 16.9 1.0
C1D C:HEC402 3.0 14.3 1.0
C4A C:HEC402 3.0 12.9 1.0
C4D C:HEC402 3.0 11.4 1.0
C4C C:HEC402 3.0 16.0 1.0
C1C C:HEC402 3.0 16.2 1.0
C1A C:HEC402 3.1 14.2 1.0
CE1 C:HIS187 3.1 14.4 1.0
CHB C:HEC402 3.4 11.5 1.0
CHD C:HEC402 3.4 11.7 1.0
CHC C:HEC402 3.4 14.8 1.0
CHA C:HEC402 3.4 12.0 1.0
CG C:MET258 3.5 14.5 1.0
CE C:MET258 3.5 14.7 1.0
CG C:HIS187 4.2 12.5 1.0
ND1 C:HIS187 4.2 12.8 1.0
C2B C:HEC402 4.3 14.7 1.0
C3D C:HEC402 4.3 12.0 1.0
C3B C:HEC402 4.3 15.5 1.0
C2D C:HEC402 4.3 16.1 1.0
C3A C:HEC402 4.3 12.1 1.0
C2A C:HEC402 4.3 12.2 1.0
C2C C:HEC402 4.3 20.5 1.0
C3C C:HEC402 4.3 16.2 1.0
CB C:MET258 4.4 15.8 1.0

Iron binding site 7 out of 8 in 1iqc

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Iron binding site 7 out of 8 in the Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:30.9
occ:1.00
FE D:HEC401 0.0 30.9 1.0
NC D:HEC401 2.0 37.4 1.0
ND D:HEC401 2.0 35.7 1.0
NB D:HEC401 2.0 36.1 1.0
NA D:HEC401 2.0 35.6 1.0
NE2 D:HIS43 2.1 28.7 1.0
O D:HOH2540 2.2 31.1 1.0
CD2 D:HIS43 3.0 31.2 1.0
C1C D:HEC401 3.0 38.6 1.0
C4B D:HEC401 3.0 39.4 1.0
C4D D:HEC401 3.0 37.1 1.0
C4C D:HEC401 3.0 37.4 1.0
C1A D:HEC401 3.0 36.6 1.0
C1D D:HEC401 3.1 37.5 1.0
C4A D:HEC401 3.1 37.0 1.0
C1B D:HEC401 3.1 38.0 1.0
CE1 D:HIS43 3.1 33.7 1.0
CHC D:HEC401 3.4 38.9 1.0
CHA D:HEC401 3.4 37.9 1.0
CHD D:HEC401 3.4 38.4 1.0
CHB D:HEC401 3.4 39.5 1.0
CG D:HIS43 4.1 34.0 1.0
ND1 D:HIS43 4.2 28.2 1.0
NE2 D:GLN92 4.2 41.6 1.0
C2C D:HEC401 4.3 40.5 1.0
C2D D:HEC401 4.3 36.9 1.0
C2B D:HEC401 4.3 38.1 1.0
C3D D:HEC401 4.3 37.4 1.0
C3C D:HEC401 4.3 37.7 1.0
C3B D:HEC401 4.3 39.8 1.0
C2A D:HEC401 4.3 39.1 1.0
C3A D:HEC401 4.3 38.4 1.0
CG D:PRO96 4.4 49.9 1.0

Iron binding site 8 out of 8 in 1iqc

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Iron binding site 8 out of 8 in the Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe402

b:27.0
occ:1.00
FE D:HEC402 0.0 27.0 1.0
ND D:HEC402 1.9 11.8 1.0
NB D:HEC402 2.0 30.9 1.0
NA D:HEC402 2.0 30.7 1.0
NC D:HEC402 2.0 25.2 1.0
NE2 D:HIS187 2.1 33.3 1.0
SD D:MET258 2.4 34.7 1.0
C4D D:HEC402 3.0 34.5 1.0
C4B D:HEC402 3.0 30.9 1.0
C1D D:HEC402 3.0 31.0 1.0
C1A D:HEC402 3.0 31.4 1.0
CD2 D:HIS187 3.0 39.5 1.0
C1B D:HEC402 3.0 32.5 1.0
C4A D:HEC402 3.1 28.7 1.0
C1C D:HEC402 3.1 31.0 1.0
C4C D:HEC402 3.1 28.3 1.0
CE1 D:HIS187 3.1 38.9 1.0
CG D:MET258 3.3 31.6 1.0
CHA D:HEC402 3.4 30.0 1.0
CHC D:HEC402 3.4 34.6 1.0
CHB D:HEC402 3.4 33.1 1.0
CHD D:HEC402 3.5 25.3 1.0
CE D:MET258 3.9 31.7 1.0
CB D:MET258 4.2 34.7 1.0
CG D:HIS187 4.2 41.2 1.0
ND1 D:HIS187 4.2 42.5 1.0
C3D D:HEC402 4.2 32.2 1.0
C2D D:HEC402 4.2 31.5 1.0
C3B D:HEC402 4.2 33.6 1.0
C2B D:HEC402 4.3 33.4 1.0
C2A D:HEC402 4.3 28.7 1.0
C3A D:HEC402 4.3 30.4 1.0
C2C D:HEC402 4.3 33.2 1.0
C3C D:HEC402 4.3 31.0 1.0

Reference:

H.Shimizu, D.J.Schuller, W.N.Lanzilotta, M.Sundaramoorthy, D.M.Arciero, A.B.Hooper, T.L.Poulos. Crystal Structure of Nitrosomonas Europaea Cytochrome C Peroxidase and the Structural Basis For Ligand Switching in Bacterial Di-Heme Peroxidases Biochemistry V. 40 13483 2001.
ISSN: ISSN 0006-2960
PubMed: 11695895
DOI: 10.1021/BI011481H
Page generated: Sat Aug 3 08:07:27 2024

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