Iron in PDB 8quo: Cryo-Em Structure of Coproheme Decarboxylase From Corynebacterium Diphtheriae in Complex with Heme B

The binding sites of Iron atom in the Cryo-Em Structure of Coproheme Decarboxylase From Corynebacterium Diphtheriae in Complex with Heme B (pdb code 8quo). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Cryo-Em Structure of Coproheme Decarboxylase From Corynebacterium Diphtheriae in Complex with Heme B, PDB code: 8quo:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the Cryo-Em Structure of Coproheme Decarboxylase From Corynebacterium Diphtheriae in Complex with Heme B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of Coproheme Decarboxylase From Corynebacterium Diphtheriae in Complex with Heme B within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:102.9 occ:1.00 FE A:HEM301 0.0 102.9 1.0 NC A:HEM301 2.1 84.0 1.0 ND A:HEM301 2.1 84.4 1.0 NA A:HEM301 2.1 92.0 1.0 NB A:HEM301 2.1 88.6 1.0 NE2 A:HIS158 2.2 82.9 1.0 C1B A:HEM301 3.0 85.5 1.0 C4C A:HEM301 3.0 78.7 1.0 C4B A:HEM301 3.0 80.7 1.0 C1C A:HEM301 3.0 78.7 1.0 C1D A:HEM301 3.0 77.9 1.0 C4A A:HEM301 3.1 91.0 1.0 CE1 A:HIS158 3.1 79.2 1.0 C4D A:HEM301 3.1 79.3 1.0 C1A A:HEM301 3.1 88.7 1.0 CD2 A:HIS158 3.3 78.8 1.0 CHB A:HEM301 3.4 87.1 1.0 CHD A:HEM301 3.4 74.1 1.0 CHC A:HEM301 3.4 78.2 1.0 CHA A:HEM301 3.5 79.5 1.0 OG1 A:THR172 4.2 82.4 1.0 C2B A:HEM301 4.2 81.0 1.0 C3B A:HEM301 4.2 79.5 1.0 ND1 A:HIS158 4.2 81.4 1.0 C2C A:HEM301 4.2 78.6 1.0 C3C A:HEM301 4.2 78.3 1.0 C2D A:HEM301 4.3 78.4 1.0 C3A A:HEM301 4.3 94.5 1.0 C3D A:HEM301 4.3 80.1 1.0 C2A A:HEM301 4.3 95.5 1.0 CG A:HIS158 4.4 79.8 1.0

Iron binding site 2 out of 5 in the Cryo-Em Structure of Coproheme Decarboxylase From Corynebacterium Diphtheriae in Complex with Heme B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of Coproheme Decarboxylase From Corynebacterium Diphtheriae in Complex with Heme B within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:102.5 occ:1.00 FE B:HEM301 0.0 102.5 1.0 NC B:HEM301 2.0 83.8 1.0 NA B:HEM301 2.0 92.1 1.0 ND B:HEM301 2.1 82.2 1.0 NB B:HEM301 2.1 87.2 1.0 NE2 B:HIS158 2.2 81.8 1.0 C1B B:HEM301 3.0 84.8 1.0 C4B B:HEM301 3.0 79.8 1.0 C4C B:HEM301 3.0 79.7 1.0 C1C B:HEM301 3.0 78.3 1.0 C4A B:HEM301 3.1 90.7 1.0 C1D B:HEM301 3.1 75.8 1.0 C1A B:HEM301 3.1 89.2 1.0 C4D B:HEM301 3.1 79.6 1.0 CE1 B:HIS158 3.1 77.3 1.0 CD2 B:HIS158 3.3 78.8 1.0 CHB B:HEM301 3.4 86.8 1.0 CHD B:HEM301 3.4 73.8 1.0 CHC B:HEM301 3.4 77.6 1.0 CHA B:HEM301 3.4 81.3 1.0 OG1 B:THR172 4.2 80.5 1.0 C2B B:HEM301 4.2 82.1 1.0 C3B B:HEM301 4.2 80.4 1.0 C2C B:HEM301 4.2 80.2 1.0 C3C B:HEM301 4.2 81.3 1.0 ND1 B:HIS158 4.3 79.9 1.0 C3A B:HEM301 4.3 94.6 1.0 C2A B:HEM301 4.3 94.7 1.0 C2D B:HEM301 4.3 77.8 1.0 C3D B:HEM301 4.3 80.7 1.0 CG B:HIS158 4.4 77.9 1.0

Iron binding site 3 out of 5 in the Cryo-Em Structure of Coproheme Decarboxylase From Corynebacterium Diphtheriae in Complex with Heme B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em Structure of Coproheme Decarboxylase From Corynebacterium Diphtheriae in Complex with Heme B within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe301 b:101.9 occ:1.00 FE C:HEM301 0.0 101.9 1.0 ND C:HEM301 2.0 83.9 1.0 NC C:HEM301 2.1 82.6 1.0 NA C:HEM301 2.1 90.7 1.0 NB C:HEM301 2.1 87.4 1.0 NE2 C:HIS158 2.2 81.1 1.0 C1B C:HEM301 3.0 84.3 1.0 CE1 C:HIS158 3.0 76.8 1.0 C4B C:HEM301 3.0 80.2 1.0 C4C C:HEM301 3.0 79.8 1.0 C1D C:HEM301 3.0 76.5 1.0 C4A C:HEM301 3.1 88.1 1.0 C1C C:HEM301 3.1 78.8 1.0 C4D C:HEM301 3.1 80.9 1.0 C1A C:HEM301 3.1 90.5 1.0 CD2 C:HIS158 3.3 77.3 1.0 CHB C:HEM301 3.4 84.4 1.0 CHD C:HEM301 3.4 75.1 1.0 CHC C:HEM301 3.4 78.4 1.0 CHA C:HEM301 3.5 83.2 1.0 OG1 C:THR172 4.2 79.2 1.0 C2B C:HEM301 4.2 83.0 1.0 C3B C:HEM301 4.2 81.8 1.0 ND1 C:HIS158 4.2 78.3 1.0 C3C C:HEM301 4.2 81.7 1.0 C2C C:HEM301 4.2 80.3 1.0 C2D C:HEM301 4.3 76.8 1.0 C3A C:HEM301 4.3 92.8 1.0 C3D C:HEM301 4.3 79.2 1.0 C2A C:HEM301 4.3 96.0 1.0 CG C:HIS158 4.4 77.3 1.0

Iron binding site 4 out of 5 in the Cryo-Em Structure of Coproheme Decarboxylase From Corynebacterium Diphtheriae in Complex with Heme B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure of Coproheme Decarboxylase From Corynebacterium Diphtheriae in Complex with Heme B within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:105.2 occ:1.00 FE D:HEM301 0.0 105.2 1.0 ND D:HEM301 2.0 84.0 1.0 NC D:HEM301 2.1 83.1 1.0 NA D:HEM301 2.1 90.2 1.0 NB D:HEM301 2.1 87.5 1.0 NE2 D:HIS158 2.2 83.4 1.0 C1B D:HEM301 3.0 84.7 1.0 C4C D:HEM301 3.0 79.8 1.0 C1D D:HEM301 3.0 76.2 1.0 C4A D:HEM301 3.0 87.8 1.0 C4B D:HEM301 3.1 77.7 1.0 C1C D:HEM301 3.1 78.6 1.0 C4D D:HEM301 3.1 80.6 1.0 CE1 D:HIS158 3.1 79.5 1.0 C1A D:HEM301 3.1 87.6 1.0 CD2 D:HIS158 3.3 76.8 1.0 CHB D:HEM301 3.4 85.1 1.0 CHD D:HEM301 3.4 73.6 1.0 CHC D:HEM301 3.4 77.7 1.0 CHA D:HEM301 3.4 82.3 1.0 OG1 D:THR172 4.2 82.6 1.0 C2B D:HEM301 4.2 81.7 1.0 C3B D:HEM301 4.2 78.7 1.0 ND1 D:HIS158 4.2 81.8 1.0 C3C D:HEM301 4.3 81.1 1.0 C2C D:HEM301 4.3 80.3 1.0 C2D D:HEM301 4.3 78.2 1.0 C3A D:HEM301 4.3 91.1 1.0 C3D D:HEM301 4.3 80.4 1.0 C2A D:HEM301 4.3 92.6 1.0 CG D:HIS158 4.4 78.6 1.0

Iron binding site 5 out of 5 in the Cryo-Em Structure of Coproheme Decarboxylase From Corynebacterium Diphtheriae in Complex with Heme B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cryo-Em Structure of Coproheme Decarboxylase From Corynebacterium Diphtheriae in Complex with Heme B within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe301 b:106.8 occ:1.00 FE E:HEM301 0.0 106.8 1.0 NC E:HEM301 2.0 83.2 1.0 ND E:HEM301 2.1 82.9 1.0 NA E:HEM301 2.1 89.6 1.0 NB E:HEM301 2.1 86.8 1.0 NE2 E:HIS158 2.2 79.5 1.0 C1B E:HEM301 3.0 82.7 1.0 C4C E:HEM301 3.0 79.1 1.0 C4B E:HEM301 3.0 78.3 1.0 C1D E:HEM301 3.0 76.5 1.0 C1C E:HEM301 3.0 77.4 1.0 C4A E:HEM301 3.1 88.0 1.0 CE1 E:HIS158 3.1 76.7 1.0 C4D E:HEM301 3.1 79.7 1.0 C1A E:HEM301 3.1 86.8 1.0 CD2 E:HIS158 3.3 75.0 1.0 CHB E:HEM301 3.4 84.7 1.0 CHD E:HEM301 3.4 74.8 1.0 CHC E:HEM301 3.4 76.5 1.0 CHA E:HEM301 3.5 81.1 1.0 OG1 E:THR172 4.2 81.6 1.0 C2B E:HEM301 4.2 79.0 1.0 C3B E:HEM301 4.2 78.4 1.0 ND1 E:HIS158 4.2 77.9 1.0 C2C E:HEM301 4.2 78.0 1.0 C3C E:HEM301 4.2 78.5 1.0 C2D E:HEM301 4.3 77.9 1.0 C3A E:HEM301 4.3 91.4 1.0 C3D E:HEM301 4.3 80.3 1.0 C2A E:HEM301 4.3 91.2 1.0 CG E:HIS158 4.4 75.4 1.0

G.Patil, D.J.Alonso De Armino, Y.Guo, P.G.Furtmuller, D.Borek, D.A.Estrin, S.Hofbauer. Insights Into the Flexibility of the Domain-Linking Loop in Actinobacterial Coproheme Decarboxylase Through Structures and Molecular Dynamics Simulations. Protein Sci. V. 34 70027 2025.
ISSN: ESSN 1469-896X
PubMed: 39865384
DOI: 10.1002/PRO.70027