Iron in PDB 6fxj: Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III

The structure of Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III, PDB code: 6fxj was solved by S.Hofbauer, V.Pfanzagl, G.Mlynek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.89 / 1.79
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.870, 129.110, 77.920, 90.00, 105.96, 90.00
R / Rfree (%)	18.6 / 21.4

The structure of Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Sodium	(Na)	7 atoms

The binding sites of Iron atom in the Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III (pdb code 6fxj). 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 Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III, PDB code: 6fxj:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:84.4 occ:1.00 FE A:FEC302 0.0 84.4 1.0 ND A:FEC302 2.0 35.9 1.0 NC A:FEC302 2.0 42.6 1.0 NA A:FEC302 2.0 36.2 1.0 NB A:FEC302 2.1 36.7 1.0 OE1 A:GLN187 2.3 33.9 0.4 NE2 A:HIS174 2.5 25.0 1.0 C4D A:FEC302 3.0 37.9 1.0 C1A A:FEC302 3.0 38.8 1.0 C1C A:FEC302 3.0 48.2 1.0 C4B A:FEC302 3.0 43.4 1.0 C1D A:FEC302 3.0 39.0 1.0 C4C A:FEC302 3.1 44.8 1.0 C4A A:FEC302 3.1 39.1 1.0 C1B A:FEC302 3.1 40.3 1.0 CHA A:FEC302 3.3 36.3 1.0 CHC A:FEC302 3.3 45.9 1.0 CD2 A:HIS174 3.4 25.6 1.0 CD A:GLN187 3.4 33.3 0.4 CHD A:FEC302 3.4 40.8 1.0 HD11 A:ILE189 3.5 50.0 0.6 HD2 A:HIS174 3.5 30.9 1.0 CE1 A:HIS174 3.5 25.2 1.0 CHB A:FEC302 3.5 37.7 1.0 HE22 A:GLN187 3.6 41.2 0.4 HE1 A:HIS174 3.6 30.4 1.0 HD11 A:ILE189 3.7 50.7 0.4 HG3 A:GLN187 3.8 40.8 0.6 HG13 A:ILE189 3.9 42.3 0.4 NE2 A:GLN187 3.9 34.3 0.4 HG13 A:ILE189 3.9 42.3 0.6 HE1 A:MET219 4.1 39.4 1.0 CD1 A:ILE189 4.2 41.6 0.6 C3D A:FEC302 4.2 38.0 1.0 HD12 A:ILE189 4.2 50.0 0.6 C2C A:FEC302 4.2 50.5 1.0 C2A A:FEC302 4.2 38.5 1.0 C2D A:FEC302 4.2 37.4 1.0 C3A A:FEC302 4.3 39.4 1.0 C3C A:FEC302 4.3 48.4 1.0 C3B A:FEC302 4.3 43.6 1.0 C2B A:FEC302 4.3 43.0 1.0 CD1 A:ILE189 4.4 42.2 0.4 CG1 A:ILE189 4.5 35.1 0.4 CG1 A:ILE189 4.5 35.1 0.6 HG3 A:GLN187 4.5 40.2 0.4 CG A:HIS174 4.6 25.5 1.0 ND1 A:HIS174 4.6 24.5 1.0 CG A:GLN187 4.6 33.4 0.4 HG12 A:ILE189 4.6 42.3 0.4 HD12 A:ILE189 4.6 50.7 0.4 CG A:GLN187 4.7 33.9 0.6 HE21 A:GLN187 4.8 41.2 0.4 HG12 A:ILE189 4.8 42.3 0.6 CE A:MET219 4.9 32.7 1.0 HE2 A:MET219 4.9 39.4 1.0

Iron binding site 2 out of 5 in the Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:56.7 occ:0.93 FE B:FEC302 0.0 56.7 0.9 ND B:FEC302 2.0 55.6 0.9 NC B:FEC302 2.0 60.8 0.9 NA B:FEC302 2.0 53.6 0.9 NB B:FEC302 2.1 57.4 0.9 C4D B:FEC302 2.9 53.9 0.9 C1A B:FEC302 3.0 51.8 0.9 C1C B:FEC302 3.0 63.8 0.9 C4B B:FEC302 3.0 59.8 0.9 C4C B:FEC302 3.0 61.0 0.9 C1D B:FEC302 3.0 55.7 0.9 C4A B:FEC302 3.1 53.0 0.9 HD2 B:HIS174 3.1 56.6 1.0 NE2 B:HIS174 3.1 46.6 1.0 C1B B:FEC302 3.1 58.8 0.9 CHA B:FEC302 3.3 52.4 0.9 CHC B:FEC302 3.3 61.4 0.9 CD2 B:HIS174 3.4 47.1 1.0 CHD B:FEC302 3.4 57.5 0.9 CHB B:FEC302 3.5 56.8 0.9 HG13 B:ILE189 3.7 36.5 1.0 HD11 B:ILE189 3.8 36.9 1.0 HG3 B:GLN187 4.0 57.5 1.0 HE1 B:MET219 4.2 59.7 1.0 C3D B:FEC302 4.2 54.6 0.9 C2A B:FEC302 4.2 50.9 0.9 C2C B:FEC302 4.2 67.0 0.9 C2D B:FEC302 4.2 54.8 0.9 C3C B:FEC302 4.2 65.2 0.9 C3A B:FEC302 4.2 50.0 0.9 C3B B:FEC302 4.3 62.0 0.9 CE1 B:HIS174 4.3 47.5 1.0 C2B B:FEC302 4.3 61.1 0.9 CD1 B:ILE189 4.4 30.7 1.0 CG1 B:ILE189 4.5 30.3 1.0 HD12 B:ILE189 4.5 36.9 1.0 CG B:HIS174 4.7 47.4 1.0 HG12 B:ILE189 4.7 36.5 1.0 HE1 B:HIS174 4.7 57.1 1.0 HE2 B:MET219 4.8 59.7 1.0 CE B:MET219 4.9 49.7 1.0 CG B:GLN187 4.9 47.8 1.0

Iron binding site 3 out of 5 in the Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe301 b:78.0 occ:0.80 FE C:FEC301 0.0 78.0 0.8 ND C:FEC301 2.0 71.9 0.8 NC C:FEC301 2.0 72.7 0.8 NA C:FEC301 2.0 71.5 0.8 NB C:FEC301 2.1 77.8 0.8 C1A C:FEC301 3.0 71.8 0.8 C4D C:FEC301 3.0 71.3 0.8 C1D C:FEC301 3.0 72.4 0.8 C4C C:FEC301 3.0 73.3 0.8 C4B C:FEC301 3.1 74.6 0.8 C1C C:FEC301 3.1 73.1 0.8 HD2 C:HIS174 3.1 56.7 1.0 C4A C:FEC301 3.1 72.6 0.8 C1B C:FEC301 3.1 78.0 0.8 CHA C:FEC301 3.3 71.3 0.8 CHC C:FEC301 3.4 72.3 0.8 CHD C:FEC301 3.4 71.1 0.8 CHB C:FEC301 3.5 75.5 0.8 NE2 C:HIS174 3.6 46.0 1.0 CD2 C:HIS174 3.6 47.2 1.0 HG13 C:ILE189 3.8 37.4 1.0 C2A C:FEC301 4.2 71.7 0.8 C2D C:FEC301 4.2 71.4 0.8 C3D C:FEC301 4.2 70.5 0.8 C3A C:FEC301 4.2 71.0 0.8 C3C C:FEC301 4.3 75.2 0.8 C2C C:FEC301 4.3 75.7 0.8 HG3 C:GLN187 4.3 65.7 1.0 C3B C:FEC301 4.3 78.0 0.8 C2B C:FEC301 4.3 80.9 0.8 HD11 C:ILE189 4.3 38.3 1.0 CG1 C:ILE189 4.6 31.1 1.0 HA2 C:GLY175 4.7 51.8 1.0 HE1 C:MET219 4.7 64.4 1.0 HG12 C:ILE189 4.8 37.4 1.0 CE1 C:HIS174 4.9 46.4 1.0 CD1 C:ILE189 4.9 31.8 1.0 CG C:HIS174 4.9 45.7 1.0 HD12 C:ILE189 5.0 38.3 1.0

Iron binding site 4 out of 5 in the Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe302 b:33.2 occ:1.00 FE D:FEC302 0.0 33.2 1.0 ND D:FEC302 2.0 30.4 1.0 NC D:FEC302 2.0 34.4 1.0 NA D:FEC302 2.0 32.2 1.0 NB D:FEC302 2.0 30.4 1.0 NE2 D:HIS174 2.3 26.0 1.0 C4D D:FEC302 3.0 30.4 1.0 C1A D:FEC302 3.0 32.2 1.0 C1C D:FEC302 3.0 34.9 1.0 C4B D:FEC302 3.0 32.1 1.0 C1D D:FEC302 3.0 31.5 1.0 C4C D:FEC302 3.0 34.5 1.0 C4A D:FEC302 3.1 31.4 1.0 C1B D:FEC302 3.1 30.5 1.0 CE1 D:HIS174 3.3 27.4 1.0 CHA D:FEC302 3.3 31.4 1.0 CD2 D:HIS174 3.3 28.2 1.0 CHC D:FEC302 3.4 34.3 1.0 HE1 D:HIS174 3.4 33.0 1.0 CHD D:FEC302 3.4 34.2 1.0 HD2 D:HIS174 3.5 33.9 1.0 CHB D:FEC302 3.5 30.2 1.0 HD11 D:ILE189 3.6 71.3 1.0 HG3 D:GLN187 3.8 52.8 0.7 HE1 D:MET219 4.0 36.4 1.0 HG13 D:ILE189 4.1 56.0 1.0 C3D D:FEC302 4.2 31.4 1.0 HG3 D:GLN187 4.2 54.3 0.3 C2D D:FEC302 4.2 31.3 1.0 C2C D:FEC302 4.2 38.5 1.0 C2A D:FEC302 4.2 34.5 1.0 C3C D:FEC302 4.3 37.5 1.0 C3A D:FEC302 4.3 33.1 1.0 C3B D:FEC302 4.3 34.3 1.0 C2B D:FEC302 4.3 32.7 1.0 CD1 D:ILE189 4.3 59.3 1.0 ND1 D:HIS174 4.4 26.7 1.0 HD12 D:ILE189 4.4 71.3 1.0 CG D:HIS174 4.5 26.0 1.0 CG1 D:ILE189 4.7 46.6 1.0 HE2 D:MET219 4.7 36.4 1.0 CG D:GLN187 4.7 43.9 0.7 CE D:MET219 4.7 30.3 1.0 HG12 D:ILE189 4.9 56.0 1.0 HB2 D:GLN187 4.9 49.7 0.3

Iron binding site 5 out of 5 in the Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe302 b:47.2 occ:0.96 FE E:FEC302 0.0 47.2 1.0 ND E:FEC302 2.0 45.0 1.0 NC E:FEC302 2.0 50.9 1.0 NA E:FEC302 2.0 46.8 1.0 NB E:FEC302 2.1 51.1 1.0 NE2 E:HIS174 2.5 35.0 1.0 C4D E:FEC302 3.0 43.6 1.0 C1A E:FEC302 3.0 46.2 1.0 C1C E:FEC302 3.0 52.7 1.0 C1D E:FEC302 3.0 44.8 1.0 C4B E:FEC302 3.0 53.1 1.0 C4C E:FEC302 3.0 51.1 1.0 C4A E:FEC302 3.1 48.5 1.0 C1B E:FEC302 3.1 53.4 1.0 HD2 E:HIS174 3.3 42.4 1.0 CD2 E:HIS174 3.3 35.2 1.0 CHA E:FEC302 3.3 44.4 1.0 CHC E:FEC302 3.4 52.3 1.0 CHD E:FEC302 3.4 47.9 1.0 CHB E:FEC302 3.5 51.6 1.0 CE1 E:HIS174 3.6 34.8 1.0 HG13 E:ILE189 3.7 33.8 1.0 O E:HOH543 3.8 47.9 1.0 HE1 E:HIS174 3.9 41.9 1.0 HD11 E:ILE189 4.0 35.3 1.0 HG3 E:GLN187 4.1 62.6 1.0 C3D E:FEC302 4.2 42.1 1.0 C2A E:FEC302 4.2 48.3 1.0 C2C E:FEC302 4.2 56.0 1.0 C2D E:FEC302 4.2 42.1 1.0 C3A E:FEC302 4.3 47.6 1.0 C3C E:FEC302 4.3 53.7 1.0 HE1 E:MET219 4.3 57.4 1.0 C3B E:FEC302 4.3 57.2 1.0 C2B E:FEC302 4.3 55.3 1.0 CG1 E:ILE189 4.5 28.1 1.0 CG E:HIS174 4.5 35.4 1.0 CD1 E:ILE189 4.6 29.4 1.0 ND1 E:HIS174 4.7 34.9 1.0 HG12 E:ILE189 4.7 33.8 1.0 HD12 E:ILE189 4.7 35.3 1.0 HE2 E:MET219 4.8 57.4 1.0 CE E:MET219 5.0 47.7 1.0

L.Milazzo, T.Gabler, D.Puhringer, Z.Jandova, D.Maresch, H.Michlits, V.Pfanzagl, K.Djinovic-Carugo, C.Oostenbrink, P.G.Furtmuller, C.Obinger, G.Smulevich, S.Hofbauer. Redox Cofactor Rotates During Its Stepwise Decarboxylation: Molecular Mechanism of Conversion of Coproheme to Hemeb. Acs Catalysis V. 9 6766 2019.
ISSN: ESSN 2155-5435
PubMed: 31423350
DOI: 10.1021/ACSCATAL.9B00963