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Iron in PDB 4gph: Structure of Hmuo, Heme Oxygenase From Corynebacterium Diphtheriae, in Complex with the Putative Reaction Intermediates Between FE3+- Biliverdin and Biliverdin (Data Set IV)

Enzymatic activity of Structure of Hmuo, Heme Oxygenase From Corynebacterium Diphtheriae, in Complex with the Putative Reaction Intermediates Between FE3+- Biliverdin and Biliverdin (Data Set IV)

All present enzymatic activity of Structure of Hmuo, Heme Oxygenase From Corynebacterium Diphtheriae, in Complex with the Putative Reaction Intermediates Between FE3+- Biliverdin and Biliverdin (Data Set IV):
1.14.99.3;

Protein crystallography data

The structure of Structure of Hmuo, Heme Oxygenase From Corynebacterium Diphtheriae, in Complex with the Putative Reaction Intermediates Between FE3+- Biliverdin and Biliverdin (Data Set IV), PDB code: 4gph was solved by M.Unno, M.Ikeda-Saito, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.065, 62.966, 107.728, 90.00, 100.78, 90.00
R / Rfree (%) 16.5 / 20.5

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Hmuo, Heme Oxygenase From Corynebacterium Diphtheriae, in Complex with the Putative Reaction Intermediates Between FE3+- Biliverdin and Biliverdin (Data Set IV) (pdb code 4gph). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Structure of Hmuo, Heme Oxygenase From Corynebacterium Diphtheriae, in Complex with the Putative Reaction Intermediates Between FE3+- Biliverdin and Biliverdin (Data Set IV), PDB code: 4gph:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 4gph

Go back to Iron Binding Sites List in 4gph
Iron binding site 1 out of 2 in the Structure of Hmuo, Heme Oxygenase From Corynebacterium Diphtheriae, in Complex with the Putative Reaction Intermediates Between FE3+- Biliverdin and Biliverdin (Data Set IV)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Hmuo, Heme Oxygenase From Corynebacterium Diphtheriae, in Complex with the Putative Reaction Intermediates Between FE3+- Biliverdin and Biliverdin (Data Set IV) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:49.1
occ:0.30
 NA A:BLA3002 1.6 27.8 0.3
NA A:BLA3002 1.6 37.3 0.7
NB A:BLA3002 2.0 25.2 0.3
O A:HOH3161 2.2 16.4 0.3
NB A:BLA3002 2.2 40.5 0.7
ND A:BLA3002 2.2 63.8 0.7
ND A:BLA3002 2.3 56.2 0.3
NC A:BLA3002 2.3 58.7 0.3
C4A A:BLA3002 2.6 22.4 0.3
C1A A:BLA3002 2.7 41.3 0.7
NC A:BLA3002 2.7 63.4 0.7
C4A A:BLA3002 2.7 33.8 0.7
C1B A:BLA3002 2.7 21.0 0.3
C1A A:BLA3002 2.8 31.2 0.3
C1B A:BLA3002 3.0 34.5 0.7
CHB A:BLA3002 3.0 21.7 0.3
C4D A:BLA3002 3.1 66.6 0.7
CHA A:BLA3002 3.1 55.6 0.7
C4B A:BLA3002 3.1 30.4 0.3
C4D A:BLA3002 3.2 59.0 0.3
CHB A:BLA3002 3.2 32.7 0.7
C4B A:BLA3002 3.2 45.0 0.7
CHA A:BLA3002 3.2 46.5 0.3
C1C A:BLA3002 3.3 60.7 0.3
C1D A:BLA3002 3.4 71.5 0.3
C4C A:BLA3002 3.4 71.0 0.3
C1D A:BLA3002 3.4 78.2 0.7
CHD A:BLA3002 3.6 75.1 0.3
OB A:BLA3002 3.6 38.4 0.3
OB A:BLA3002 3.6 52.2 0.7
OC A:BLA3002 3.6 57.2 0.3
NE2 A:HIS20 3.7 43.5 1.0
C4C A:BLA3002 3.7 76.6 0.7
CHD A:BLA3002 3.7 80.6 0.7
C1C A:BLA3002 3.7 65.7 0.7
C3A A:BLA3002 3.9 21.4 0.3
C2A A:BLA3002 3.9 39.8 0.7
C2A A:BLA3002 3.9 28.0 0.3
C3A A:BLA3002 3.9 32.0 0.7
CE1 A:HIS20 4.0 42.7 1.0
C2B A:BLA3002 4.0 23.8 0.3
OC A:BLA3002 4.0 62.2 0.7
C2B A:BLA3002 4.1 38.5 0.7
C3B A:BLA3002 4.2 28.9 0.3
C3B A:BLA3002 4.3 44.0 0.7
O A:HOH3173 4.3 36.0 1.0
CA A:GLY135 4.3 27.9 1.0
O A:GLY135 4.4 28.6 1.0
C3D A:BLA3002 4.4 85.9 0.7
C3D A:BLA3002 4.5 78.7 0.3
C2D A:BLA3002 4.6 85.9 0.3
C2D A:BLA3002 4.6 93.3 0.7
C2C A:BLA3002 4.6 72.4 0.3
C3C A:BLA3002 4.6 80.0 0.3
CD2 A:HIS20 4.8 43.5 1.0
N A:GLY139 4.8 39.2 1.0
C A:GLY135 4.8 25.8 1.0
CA A:GLY139 4.9 41.3 1.0
C3C A:BLA3002 4.9 86.1 0.7
C2C A:BLA3002 5.0 78.5 0.7

Iron binding site 2 out of 2 in 4gph

Go back to Iron Binding Sites List in 4gph
Iron binding site 2 out of 2 in the Structure of Hmuo, Heme Oxygenase From Corynebacterium Diphtheriae, in Complex with the Putative Reaction Intermediates Between FE3+- Biliverdin and Biliverdin (Data Set IV)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Hmuo, Heme Oxygenase From Corynebacterium Diphtheriae, in Complex with the Putative Reaction Intermediates Between FE3+- Biliverdin and Biliverdin (Data Set IV) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe901

b:55.0
occ:0.40
 NB C:BLA902 1.9 29.3 0.3
NA C:BLA902 1.9 25.1 0.3
NA C:BLA902 1.9 29.5 0.7
NB C:BLA902 2.0 35.0 0.7
ND C:BLA902 2.0 25.1 0.3
ND C:BLA902 2.0 27.7 0.7
NC C:BLA902 2.4 28.4 0.3
NC C:BLA902 2.5 32.2 0.7
O3 C:ASC903 2.6 29.7 1.0
C4B C:BLA902 2.9 31.9 0.3
C1B C:BLA902 2.9 30.0 0.3
C4D C:BLA902 2.9 26.8 0.3
C1B C:BLA902 2.9 36.2 0.7
C1A C:BLA902 2.9 27.8 0.3
C4D C:BLA902 2.9 30.2 0.7
C4B C:BLA902 3.0 38.1 0.7
C4A C:BLA902 3.0 33.3 0.7
C1A C:BLA902 3.0 31.9 0.7
C4A C:BLA902 3.0 28.1 0.3
C1D C:BLA902 3.0 27.3 0.7
C1D C:BLA902 3.0 25.2 0.3
CHA C:BLA902 3.2 27.9 0.3
OB C:BLA902 3.2 33.2 0.3
CHA C:BLA902 3.3 32.3 0.7
OB C:BLA902 3.3 38.3 0.7
CHB C:BLA902 3.3 39.5 0.7
C4C C:BLA902 3.3 26.3 0.3
C3 C:ASC903 3.3 37.6 1.0
CHB C:BLA902 3.3 31.1 0.3
CHD C:BLA902 3.4 26.1 0.3
C4C C:BLA902 3.4 27.2 0.7
CHD C:BLA902 3.4 28.5 0.7
C1C C:BLA902 3.4 29.8 0.3
C1C C:BLA902 3.6 32.1 0.7
OC C:BLA902 3.8 41.5 0.7
OC C:BLA902 3.9 30.6 0.3
C2 C:ASC903 4.0 32.7 1.0
CA C:GLY735 4.0 21.7 1.0
C3B C:BLA902 4.1 34.3 0.3
C2B C:BLA902 4.1 34.4 0.3
C3B C:BLA902 4.1 40.6 0.7
C2B C:BLA902 4.1 41.8 0.7
C3D C:BLA902 4.1 28.7 0.7
C3D C:BLA902 4.2 26.8 0.3
C3A C:BLA902 4.2 33.9 0.7
C2A C:BLA902 4.2 28.6 0.3
C2A C:BLA902 4.2 30.7 0.7
C3A C:BLA902 4.2 29.8 0.3
O2 C:ASC903 4.2 33.7 1.0
C4 C:ASC903 4.2 39.6 1.0
C2D C:BLA902 4.2 27.6 0.7
C2D C:BLA902 4.3 25.6 0.3
NE2 C:HIS620 4.3 33.5 1.0
O C:GLY735 4.3 21.9 1.0
C3C C:BLA902 4.5 28.3 0.3
C3C C:BLA902 4.6 30.1 0.7
C2C C:BLA902 4.6 30.0 0.3
C C:GLY735 4.7 21.1 1.0
C2C C:BLA902 4.7 33.1 0.7
CB C:SER738 4.7 22.0 1.0
CE1 C:HIS620 4.8 31.6 1.0
N C:GLY739 4.9 20.2 1.0

Reference:

M.Unno, A.Ardevol, C.Rovira, M.Ikeda-Saito. Crystal Structures of the Substrate-Free and the Product-Bound Forms of Hmuo, A Heme Oxygenase From Corynebacterium Diphtheriae To Be Published.
Page generated: Tue Aug 5 10:45:20 2025

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