Iron in PDB 5loq: Structure of Coproheme Bound Hemq From Listeria Monocytogenes

The structure of Structure of Coproheme Bound Hemq From Listeria Monocytogenes, PDB code: 5loq was solved by D.Puehringer, G.Mlynek, S.Hofbauer, K.Djinovic-Carugo, C.Obinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.00 / 1.69
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.687, 129.369, 77.916, 90.00, 105.52, 90.00
R / Rfree (%)	18.4 / 21.5

The structure of Structure of Coproheme Bound Hemq From Listeria Monocytogenes also contains other interesting chemical elements:

Sodium

(Na)

5 atoms

The binding sites of Iron atom in the Structure of Coproheme Bound Hemq From Listeria Monocytogenes (pdb code 5loq). 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 Bound Hemq From Listeria Monocytogenes, PDB code: 5loq:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the Structure of Coproheme Bound Hemq From Listeria Monocytogenes


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 Bound Hemq From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:46.9 occ:0.94 FE A:FEC302 0.0 46.9 0.9 NA A:FEC302 2.0 45.6 0.9 NC A:FEC302 2.0 49.5 0.9 ND A:FEC302 2.0 54.4 0.9 NB A:FEC302 2.1 42.5 0.9 NE2 A:HIS174 2.4 44.5 1.0 C4A A:FEC302 3.0 44.6 0.9 C1A A:FEC302 3.0 49.0 0.9 C4D A:FEC302 3.0 59.8 0.9 C4C A:FEC302 3.0 54.2 0.9 C1D A:FEC302 3.0 59.6 0.9 C1C A:FEC302 3.0 50.6 0.9 C1B A:FEC302 3.1 42.2 0.9 C4B A:FEC302 3.1 42.2 0.9 CHB A:FEC302 3.3 43.3 0.9 CD2 A:HIS174 3.4 45.7 1.0 CHA A:FEC302 3.4 54.5 0.9 CHD A:FEC302 3.4 57.4 0.9 CHC A:FEC302 3.4 46.2 0.9 HD2 A:HIS174 3.4 54.9 1.0 CE1 A:HIS174 3.5 43.8 1.0 HD11 A:ILE189 3.6 47.8 1.0 HE1 A:HIS174 3.6 52.6 1.0 HG13 A:ILE189 3.8 46.8 1.0 HG3 A:GLN187 3.9 67.1 1.0 C3A A:FEC302 4.1 46.2 0.9 HE1 A:MET219 4.2 56.4 1.0 C2A A:FEC302 4.2 47.3 0.9 HHA A:FEC302 4.2 65.5 0.9 C2D A:FEC302 4.2 66.4 0.9 C3C A:FEC302 4.2 55.6 0.9 C3D A:FEC302 4.2 70.0 0.9 C2C A:FEC302 4.2 56.6 0.9 HHB A:FEC302 4.3 52.0 0.9 HHD A:FEC302 4.3 68.9 0.9 CD1 A:ILE189 4.3 39.8 1.0 C2B A:FEC302 4.3 42.1 0.9 C3B A:FEC302 4.3 40.4 0.9 HHC A:FEC302 4.4 55.5 0.9 CG1 A:ILE189 4.4 38.9 1.0 HD12 A:ILE189 4.4 47.8 1.0 CG A:HIS174 4.5 43.6 1.0 ND1 A:HIS174 4.6 43.7 1.0 HG12 A:ILE189 4.6 46.8 1.0 HE21 A:GLN187 4.6 86.3 1.0 HE2 A:MET219 4.8 56.4 1.0 CG A:GLN187 4.9 55.9 1.0 CE A:MET219 4.9 47.0 1.0

Iron binding site 2 out of 5 in the Structure of Coproheme Bound Hemq From Listeria Monocytogenes


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 Bound Hemq From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:70.2 occ:0.94 FE B:FEC302 0.0 70.2 0.9 ND B:FEC302 2.0 68.9 0.9 NC B:FEC302 2.0 70.8 0.9 NA B:FEC302 2.0 74.1 0.9 NB B:FEC302 2.1 68.5 0.9 NE2 B:HIS174 2.7 63.9 1.0 C1A B:FEC302 3.0 75.0 0.9 C4D B:FEC302 3.0 69.7 0.9 C4A B:FEC302 3.0 78.7 0.9 C1D B:FEC302 3.0 69.2 0.9 C1C B:FEC302 3.0 72.7 0.9 C4C B:FEC302 3.0 72.4 0.9 C4B B:FEC302 3.1 67.9 0.9 C1B B:FEC302 3.1 69.9 0.9 CHA B:FEC302 3.3 71.1 0.9 CHD B:FEC302 3.4 70.7 0.9 CHC B:FEC302 3.4 70.0 0.9 CHB B:FEC302 3.4 74.5 0.9 HD2 B:HIS174 3.4 77.2 1.0 CD2 B:HIS174 3.5 64.3 1.0 HG13 B:ILE189 3.7 46.0 1.0 CE1 B:HIS174 3.8 63.7 1.0 HD11 B:ILE189 3.8 46.9 1.0 HE1 B:HIS174 4.0 76.5 1.0 HG3 B:GLN187 4.0 57.6 1.0 C2A B:FEC302 4.2 80.9 0.9 C3A B:FEC302 4.2 86.6 0.9 HHA B:FEC302 4.2 85.4 0.9 C3D B:FEC302 4.2 70.9 0.9 C2D B:FEC302 4.2 68.8 0.9 C2C B:FEC302 4.2 78.6 0.9 C3C B:FEC302 4.2 76.5 0.9 HHD B:FEC302 4.3 84.9 0.9 HHC B:FEC302 4.3 84.1 0.9 HHB B:FEC302 4.3 89.4 0.9 C3B B:FEC302 4.3 66.3 0.9 C2B B:FEC302 4.3 67.8 0.9 CG1 B:ILE189 4.4 38.3 1.0 CD1 B:ILE189 4.4 39.0 1.0 HE21 B:GLN187 4.5 75.3 1.0 HD12 B:ILE189 4.5 46.9 1.0 HE1 B:MET219 4.7 62.9 1.0 HG12 B:ILE189 4.7 46.0 1.0 CG B:HIS174 4.7 61.4 1.0 HE2 B:MET219 4.8 62.9 1.0 ND1 B:HIS174 4.8 63.0 1.0 CG B:GLN187 5.0 47.9 1.0

Iron binding site 3 out of 5 in the Structure of Coproheme Bound Hemq From Listeria Monocytogenes


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 Bound Hemq From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe302 b:68.9 occ:0.83 FE C:FEC302 0.0 68.9 0.8 ND C:FEC302 2.0 72.3 0.8 NC C:FEC302 2.0 70.8 0.8 NA C:FEC302 2.0 66.9 0.8 NB C:FEC302 2.1 65.1 0.8 C4D C:FEC302 3.0 73.7 0.8 C1A C:FEC302 3.0 68.2 0.8 C1D C:FEC302 3.0 74.7 0.8 NE2 C:HIS174 3.0 56.0 1.0 C4C C:FEC302 3.0 73.4 0.8 C4A C:FEC302 3.1 65.6 0.8 C1C C:FEC302 3.1 70.8 0.8 HD2 C:HIS174 3.1 68.3 1.0 C4B C:FEC302 3.1 64.4 0.8 C1B C:FEC302 3.1 63.1 0.8 CHA C:FEC302 3.3 70.8 0.8 CD2 C:HIS174 3.4 56.9 1.0 CHD C:FEC302 3.4 74.3 0.8 CHC C:FEC302 3.4 67.7 0.8 CHB C:FEC302 3.4 63.8 0.8 HG13 C:ILE189 3.9 43.0 1.0 HD11 C:ILE189 4.1 43.9 1.0 C3D C:FEC302 4.2 77.2 0.8 C2D C:FEC302 4.2 76.3 0.8 C2A C:FEC302 4.2 67.1 0.8 C3A C:FEC302 4.2 66.9 0.8 HHA C:FEC302 4.3 85.1 0.8 C3C C:FEC302 4.3 74.4 0.8 C2C C:FEC302 4.3 73.6 0.8 HHD C:FEC302 4.3 89.2 0.8 CE1 C:HIS174 4.3 55.3 1.0 HHC C:FEC302 4.3 81.2 0.8 C3B C:FEC302 4.3 60.2 0.8 HHB C:FEC302 4.3 76.6 0.8 C2B C:FEC302 4.4 60.7 0.8 HG3 C:GLN187 4.4 71.0 1.0 HE1 C:MET219 4.5 71.6 1.0 CG1 C:ILE189 4.7 35.8 1.0 CD1 C:ILE189 4.7 36.5 1.0 HE1 C:HIS174 4.7 66.4 1.0 CG C:HIS174 4.7 54.0 1.0 HD12 C:ILE189 4.7 43.9 1.0 HE2 C:MET219 4.7 71.6 1.0 HG12 C:ILE189 4.9 43.0 1.0 HA2 C:GLY175 5.0 57.8 1.0

Iron binding site 4 out of 5 in the Structure of Coproheme Bound Hemq From Listeria Monocytogenes


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 Bound Hemq From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe302 b:42.3 occ:0.92 FE D:FEC302 0.0 42.3 0.9 NA D:FEC302 2.0 38.7 0.9 ND D:FEC302 2.0 49.4 0.9 NC D:FEC302 2.0 51.7 0.9 NB D:FEC302 2.1 40.4 0.9 NE2 D:HIS174 2.5 37.6 1.0 C4A D:FEC302 3.0 37.4 0.9 C1A D:FEC302 3.0 40.0 0.9 C4D D:FEC302 3.0 52.2 0.9 C1D D:FEC302 3.0 54.5 0.9 C4C D:FEC302 3.0 57.5 0.9 C1C D:FEC302 3.1 57.1 0.9 C4B D:FEC302 3.1 42.4 0.9 C1B D:FEC302 3.1 38.0 0.9 CHA D:FEC302 3.3 46.1 0.9 CD2 D:HIS174 3.4 38.4 1.0 HD2 D:HIS174 3.4 46.1 1.0 CHB D:FEC302 3.4 37.6 0.9 CHD D:FEC302 3.4 56.0 0.9 CHC D:FEC302 3.4 49.8 0.9 CE1 D:HIS174 3.6 37.3 1.0 HD11 D:ILE189 3.7 40.0 1.0 HG13 D:ILE189 3.8 38.2 1.0 HE1 D:HIS174 3.8 44.9 1.0 HG3 D:GLN187 4.0 50.8 1.0 C3A D:FEC302 4.1 39.1 0.9 C2A D:FEC302 4.2 38.7 0.9 C3D D:FEC302 4.2 61.8 0.9 HHA D:FEC302 4.2 55.4 0.9 C2D D:FEC302 4.2 58.4 0.9 HE1 D:MET219 4.2 51.4 1.0 C3C D:FEC302 4.3 65.8 0.9 C2C D:FEC302 4.3 70.5 0.9 HHB D:FEC302 4.3 45.2 0.9 HHD D:FEC302 4.3 67.3 0.9 C3B D:FEC302 4.3 39.1 0.9 HHC D:FEC302 4.3 59.8 0.9 C2B D:FEC302 4.4 38.0 0.9 CD1 D:ILE189 4.4 33.3 1.0 CG1 D:ILE189 4.4 31.8 1.0 HD12 D:ILE189 4.5 40.0 1.0 CG D:HIS174 4.6 36.9 1.0 HG12 D:ILE189 4.6 38.2 1.0 ND1 D:HIS174 4.6 37.0 1.0 HE21 D:GLN187 4.8 64.9 1.0 HE2 D:MET219 4.8 51.4 1.0 CE D:MET219 4.9 42.8 1.0 CG D:GLN187 5.0 42.3 1.0

Iron binding site 5 out of 5 in the Structure of Coproheme Bound Hemq From Listeria Monocytogenes


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 Bound Hemq From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe302 b:72.7 occ:0.93 FE E:FEC302 0.0 72.7 0.9 ND E:FEC302 2.0 74.0 0.9 NC E:FEC302 2.0 77.4 0.9 NA E:FEC302 2.0 70.7 0.9 NB E:FEC302 2.1 69.5 0.9 NE2 E:HIS174 2.6 51.3 1.0 C1A E:FEC302 3.0 71.8 0.9 C4D E:FEC302 3.0 75.3 0.9 C4A E:FEC302 3.0 70.6 0.9 C1D E:FEC302 3.0 76.8 0.9 C4C E:FEC302 3.0 80.8 0.9 C1C E:FEC302 3.0 80.8 0.9 C4B E:FEC302 3.1 70.7 0.9 C1B E:FEC302 3.1 68.0 0.9 CHA E:FEC302 3.3 73.4 0.9 HD2 E:HIS174 3.4 62.8 1.0 CD2 E:HIS174 3.4 52.3 1.0 CHC E:FEC302 3.4 75.7 0.9 CHD E:FEC302 3.4 78.8 0.9 CHB E:FEC302 3.4 69.3 0.9 HG13 E:ILE189 3.7 37.8 1.0 CE1 E:HIS174 3.7 50.7 1.0 HE1 E:HIS174 3.9 60.9 1.0 HD11 E:ILE189 4.0 37.8 1.0 HE21 E:GLN187 4.1 86.2 1.0 HG3 E:GLN187 4.1 69.0 1.0 C2A E:FEC302 4.2 71.7 0.9 C3A E:FEC302 4.2 71.9 0.9 HE1 E:MET219 4.2 53.0 1.0 C2D E:FEC302 4.2 77.6 0.9 C3D E:FEC302 4.2 79.2 0.9 C3C E:FEC302 4.3 85.9 0.9 HHA E:FEC302 4.3 88.1 0.9 C2C E:FEC302 4.3 89.1 0.9 C3B E:FEC302 4.3 67.4 0.9 HHC E:FEC302 4.3 90.9 0.9 HHB E:FEC302 4.3 83.3 0.9 HHD E:FEC302 4.3 94.6 0.9 C2B E:FEC302 4.3 66.0 0.9 CG1 E:ILE189 4.5 31.4 1.0 CD1 E:ILE189 4.6 31.5 1.0 CG E:HIS174 4.6 50.5 1.0 HG12 E:ILE189 4.7 37.8 1.0 HD12 E:ILE189 4.7 37.8 1.0 NE2 E:GLN187 4.7 71.8 1.0 ND1 E:HIS174 4.7 50.8 1.0 HA2 E:GLY175 4.9 56.5 1.0 HE2 E:MET219 4.9 53.0 1.0 CE E:MET219 5.0 44.1 1.0

S.Hofbauer, G.Mlynek, L.Milazzo, D.Puhringer, D.Maresch, I.Schaffner, P.G.Furtmuller, G.Smulevich, K.Djinovic-Carugo, C.Obinger. Hydrogen Peroxide-Mediated Conversion of Coproheme to Heme B By Hemq-Lessons From the First Crystal Structure and Kinetic Studies. Febs J. V. 283 4386 2016.
ISSN: ISSN 1742-4658
PubMed: 27758026
DOI: 10.1111/FEBS.13930