Iron in PDB 4wd4: Crystal Structure of Human HO1 H25R

All present enzymatic activity of Crystal Structure of Human HO1 H25R:
1.14.99.3;

The structure of Crystal Structure of Human HO1 H25R, PDB code: 4wd4 was solved by J.M.M.Caaveiro, K.Morante, P.Sigala, K.Tsumoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.10 / 2.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.080, 54.410, 122.280, 90.00, 99.09, 90.00
R / Rfree (%)	20.3 / 25.9

The binding sites of Iron atom in the Crystal Structure of Human HO1 H25R (pdb code 4wd4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Human HO1 H25R, PDB code: 4wd4:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Human HO1 H25R


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 Human HO1 H25R within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe300 b:70.0 occ:1.00 FE A:HEM300 0.0 70.0 1.0 ND A:HEM300 1.9 69.4 1.0 NA A:HEM300 2.0 79.4 1.0 NB A:HEM300 2.1 70.9 1.0 NC A:HEM300 2.1 63.0 1.0 C1D A:HEM300 2.9 65.0 1.0 C4D A:HEM300 2.9 73.4 1.0 OE2 A:GLU29 3.0 77.8 1.0 C1A A:HEM300 3.0 83.9 1.0 C4A A:HEM300 3.0 83.9 1.0 C4B A:HEM300 3.1 67.9 1.0 C1B A:HEM300 3.1 71.4 1.0 C4C A:HEM300 3.1 59.3 1.0 C1C A:HEM300 3.1 59.9 1.0 CHA A:HEM300 3.4 78.5 1.0 CHD A:HEM300 3.4 61.3 1.0 CHC A:HEM300 3.5 64.0 1.0 CHB A:HEM300 3.5 75.8 1.0 CD A:GLU29 4.1 85.6 1.0 C2D A:HEM300 4.2 66.9 1.0 C3D A:HEM300 4.2 74.1 1.0 C3A A:HEM300 4.2 91.9 1.0 C2A A:HEM300 4.2 91.5 1.0 C3C A:HEM300 4.3 55.6 1.0 C2B A:HEM300 4.3 67.5 1.0 C2C A:HEM300 4.3 53.5 1.0 C3B A:HEM300 4.3 66.1 1.0 O A:GLY139 4.4 48.8 1.0 CG A:GLU29 4.6 82.3 1.0 CA A:GLY143 4.7 66.3 1.0 CA A:GLY139 4.8 50.3 1.0 CD A:ARG25 4.8 76.5 1.0 N A:GLY143 4.8 66.6 1.0 C A:GLY139 4.9 51.3 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Human HO1 H25R


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 Human HO1 H25R within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:98.6 occ:1.00 FE B:HEM301 0.0 98.6 1.0 ND B:HEM301 1.9 97.9 1.0 NA B:HEM301 2.0 99.6 1.0 NC B:HEM301 2.1 97.0 1.0 NB B:HEM301 2.1 98.8 1.0 C1D B:HEM301 2.9 0.7 1.0 C4D B:HEM301 2.9 98.4 1.0 C1A B:HEM301 3.0 96.9 1.0 C4C B:HEM301 3.1 97.8 1.0 C4A B:HEM301 3.1 0.1 1.0 C4B B:HEM301 3.1 91.9 1.0 C1B B:HEM301 3.1 0.5 1.0 C1C B:HEM301 3.1 91.9 1.0 OE2 B:GLU29 3.2 59.7 1.0 CHA B:HEM301 3.4 98.0 1.0 CHD B:HEM301 3.4 99.5 1.0 CHC B:HEM301 3.5 88.1 1.0 CHB B:HEM301 3.5 0.8 1.0 C2D B:HEM301 4.2 0.2 1.0 C3D B:HEM301 4.2 0.5 1.0 C2A B:HEM301 4.2 93.5 1.0 CD B:GLU29 4.2 64.9 1.0 C3A B:HEM301 4.3 97.7 1.0 C2C B:HEM301 4.3 95.2 1.0 C3C B:HEM301 4.3 95.6 1.0 C2B B:HEM301 4.3 96.1 1.0 C3B B:HEM301 4.4 93.6 1.0 O B:GLY139 4.5 34.1 1.0 CG B:GLU29 4.6 66.7 1.0 CA B:GLY139 4.8 34.6 1.0 CA B:GLY143 4.9 42.4 1.0 C B:GLY139 5.0 34.5 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Human HO1 H25R


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 Human HO1 H25R within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe300 b:63.3 occ:1.00 FE C:HEM300 0.0 63.3 1.0 ND C:HEM300 1.9 63.6 1.0 NA C:HEM300 2.0 67.8 1.0 NB C:HEM300 2.1 60.2 1.0 NC C:HEM300 2.1 60.7 1.0 C1D C:HEM300 2.9 61.9 1.0 C4D C:HEM300 3.0 65.0 1.0 OE2 C:GLU29 3.0 84.6 1.0 C4A C:HEM300 3.0 69.0 1.0 C1A C:HEM300 3.0 73.4 1.0 C4B C:HEM300 3.0 60.2 1.0 C1B C:HEM300 3.1 61.5 1.0 C4C C:HEM300 3.1 61.1 1.0 C1C C:HEM300 3.1 57.1 1.0 CHA C:HEM300 3.4 69.2 1.0 CHD C:HEM300 3.4 62.5 1.0 CHB C:HEM300 3.4 65.1 1.0 CHC C:HEM300 3.4 58.0 1.0 CD C:GLU29 4.0 83.8 1.0 C2D C:HEM300 4.2 60.1 1.0 C3A C:HEM300 4.2 74.4 1.0 C2A C:HEM300 4.2 79.7 1.0 C3D C:HEM300 4.2 64.9 1.0 C3C C:HEM300 4.3 56.5 1.0 C2B C:HEM300 4.3 60.1 1.0 C2C C:HEM300 4.3 55.4 1.0 C3B C:HEM300 4.3 61.9 1.0 O C:GLY139 4.3 39.5 1.0 CG C:GLU29 4.5 82.7 1.0 CA C:GLY143 4.7 75.2 1.0 OG C:SER142 4.7 63.3 1.0 N C:GLY143 4.8 69.3 1.0 CA C:GLY139 4.8 45.5 1.0 CD C:ARG25 4.9 83.4 1.0 C C:GLY139 4.9 44.3 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Human HO1 H25R


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 Human HO1 H25R within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:0.2 occ:1.00 FE D:HEM301 0.0 0.2 1.0 ND D:HEM301 1.9 0.1 1.0 NA D:HEM301 2.0 0.4 1.0 NB D:HEM301 2.1 0.4 1.0 NC D:HEM301 2.1 0.8 1.0 C1D D:HEM301 2.9 1.0 1.0 C4D D:HEM301 3.0 0.9 1.0 C4B D:HEM301 3.0 95.7 1.0 C1A D:HEM301 3.1 0.1 1.0 C4A D:HEM301 3.1 0.5 1.0 C4C D:HEM301 3.1 99.8 1.0 C1B D:HEM301 3.1 0.1 1.0 C1C D:HEM301 3.1 89.6 1.0 OE2 D:GLU29 3.3 80.9 1.0 CHD D:HEM301 3.4 0.1 1.0 CHA D:HEM301 3.4 0.4 1.0 CHC D:HEM301 3.5 90.0 1.0 CHB D:HEM301 3.5 0.2 1.0 C2D D:HEM301 4.2 0.4 1.0 C3D D:HEM301 4.2 0.1 1.0 C3A D:HEM301 4.3 0.9 1.0 C2A D:HEM301 4.3 0.0 1.0 C2B D:HEM301 4.3 98.8 1.0 C3C D:HEM301 4.3 85.9 1.0 C3B D:HEM301 4.3 95.5 1.0 C2C D:HEM301 4.3 79.8 1.0 CD D:GLU29 4.4 85.1 1.0 O D:GLY139 4.4 35.9 1.0 CA D:GLY139 4.7 37.9 1.0 CG D:GLU29 4.8 81.1 1.0 CD D:ARG25 4.8 68.5 1.0 C D:GLY139 4.9 36.8 1.0 CA D:GLY143 4.9 45.8 1.0 N D:GLY143 5.0 42.8 1.0

P.A.Sigala, K.Morante, K.Tsumoto, J.M.Caaveiro, D.E.Goldberg. In-Cell Enzymology to Probe His-Heme Ligation in Heme Oxygenase Catalysis Biochemistry V. 55 4836 2016.
ISSN: ISSN 0006-2960
PubMed: 27490825
DOI: 10.1021/ACS.BIOCHEM.6B00562