Iron in PDB 7q4g: Structure of Coproheme Decarboxylase From Corynebacterium Dipththeriae Y135A Mutant in Complex with Coproheme

The structure of Structure of Coproheme Decarboxylase From Corynebacterium Dipththeriae Y135A Mutant in Complex with Coproheme, PDB code: 7q4g was solved by H.Michlits, N.Valente, G.Mlynek, S.Hofbauer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.31 / 1.82
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.117, 123.517, 78.3, 90, 98.02, 90
R / Rfree (%)	17.3 / 21.9

The binding sites of Iron atom in the Structure of Coproheme Decarboxylase From Corynebacterium Dipththeriae Y135A Mutant in Complex with Coproheme (pdb code 7q4g). 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 Corynebacterium Dipththeriae Y135A Mutant in Complex with Coproheme, PDB code: 7q4g:
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 Corynebacterium Dipththeriae Y135A Mutant in Complex with Coproheme


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 Corynebacterium Dipththeriae Y135A Mutant in Complex with Coproheme within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:23.5 occ:1.00 FE A:FEC401 0.0 23.5 1.0 ND A:FEC401 2.0 24.8 1.0 NA A:FEC401 2.0 26.9 1.0 NC A:FEC401 2.0 25.8 1.0 NB A:FEC401 2.0 24.8 1.0 NE2 A:HIS158 2.2 26.5 1.0 C4D A:FEC401 3.0 24.4 1.0 C4A A:FEC401 3.0 27.9 1.0 C4C A:FEC401 3.0 26.3 1.0 C4B A:FEC401 3.0 28.2 1.0 C1C A:FEC401 3.0 26.5 1.0 C1D A:FEC401 3.1 25.3 1.0 C1A A:FEC401 3.1 20.4 1.0 CE1 A:HIS158 3.1 28.0 1.0 C1B A:FEC401 3.1 26.1 1.0 HE1 A:HIS158 3.2 33.6 1.0 HG21 A:THR172 3.2 27.7 1.0 CD2 A:HIS158 3.2 25.5 1.0 CHA A:FEC401 3.4 22.1 1.0 CHC A:FEC401 3.4 31.4 1.0 HD2 A:HIS158 3.4 30.6 1.0 CHD A:FEC401 3.4 27.5 1.0 CHB A:FEC401 3.4 24.9 1.0 CG2 A:THR172 4.1 23.0 1.0 C3D A:FEC401 4.2 26.5 1.0 C3C A:FEC401 4.2 30.6 1.0 C3B A:FEC401 4.2 26.5 1.0 C2C A:FEC401 4.2 28.6 1.0 ND1 A:HIS158 4.2 25.8 1.0 HHA A:FEC401 4.2 26.5 1.0 C3A A:FEC401 4.2 24.8 1.0 C2D A:FEC401 4.3 25.9 1.0 HHC A:FEC401 4.3 37.7 1.0 C2A A:FEC401 4.3 26.6 1.0 HE2 A:MET202 4.3 36.9 1.0 C2B A:FEC401 4.3 26.2 1.0 CG A:HIS158 4.3 23.5 1.0 HHD A:FEC401 4.3 33.0 1.0 HG23 A:THR172 4.3 27.7 1.0 HHB A:FEC401 4.4 29.9 1.0 HE1 A:HIS118 4.4 30.9 1.0 HG22 A:THR172 4.5 27.7 1.0 HE1 A:PHE187 4.7 29.8 1.0 HE1 A:MET202 4.7 36.9 1.0 HZ A:PHE187 4.8 24.2 1.0 CE A:MET202 4.8 30.8 1.0 CE1 A:HIS118 4.9 25.7 1.0 HE3 A:MET202 4.9 36.9 1.0

Iron binding site 2 out of 5 in the Structure of Coproheme Decarboxylase From Corynebacterium Dipththeriae Y135A Mutant in Complex with Coproheme


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 Corynebacterium Dipththeriae Y135A Mutant in Complex with Coproheme within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:24.3 occ:1.00 FE B:FEC401 0.0 24.3 1.0 NC B:FEC401 2.0 33.7 1.0 NA B:FEC401 2.0 28.1 1.0 NB B:FEC401 2.0 27.8 1.0 ND B:FEC401 2.0 29.5 1.0 NE2 B:HIS158 2.2 25.6 1.0 C4C B:FEC401 3.0 31.0 1.0 C4A B:FEC401 3.0 28.7 1.0 C4B B:FEC401 3.0 29.8 1.0 C4D B:FEC401 3.0 26.3 1.0 C1C B:FEC401 3.0 33.9 1.0 C1D B:FEC401 3.1 32.8 1.0 C1B B:FEC401 3.1 27.1 1.0 C1A B:FEC401 3.1 26.8 1.0 CD2 B:HIS158 3.1 28.6 1.0 CE1 B:HIS158 3.2 32.2 1.0 HD2 B:HIS158 3.3 34.3 1.0 HG21 B:THR172 3.3 39.5 1.0 CHC B:FEC401 3.4 32.4 1.0 HE1 B:HIS158 3.4 38.7 1.0 CHD B:FEC401 3.4 28.7 1.0 CHA B:FEC401 3.4 27.0 1.0 CHB B:FEC401 3.4 29.6 1.0 CG2 B:THR172 4.2 32.9 1.0 C3B B:FEC401 4.2 32.9 1.0 C3C B:FEC401 4.2 36.8 1.0 HE1 B:HIS118 4.2 41.1 1.0 C2C B:FEC401 4.2 35.3 1.0 C3D B:FEC401 4.2 29.3 1.0 C3A B:FEC401 4.2 26.7 1.0 C2D B:FEC401 4.3 29.5 1.0 HHC B:FEC401 4.3 38.9 1.0 C2B B:FEC401 4.3 27.5 1.0 HHA B:FEC401 4.3 32.4 1.0 HG23 B:THR172 4.3 39.5 1.0 CG B:HIS158 4.3 32.6 1.0 C2A B:FEC401 4.3 31.9 1.0 ND1 B:HIS158 4.3 27.1 1.0 HHB B:FEC401 4.3 35.6 1.0 HHD B:FEC401 4.3 34.5 1.0 HE2 B:MET202 4.3 42.4 1.0 HE1 B:MET202 4.4 42.4 1.0 HG22 B:THR172 4.5 39.5 1.0 HE1 B:PHE187 4.6 37.5 1.0 CE B:MET202 4.7 35.3 1.0 HE3 B:MET202 4.7 42.4 1.0 CE1 B:HIS118 4.7 34.2 1.0 HG1 B:THR172 4.9 36.8 1.0 HB1 B:ALA170 4.9 41.4 1.0

Iron binding site 3 out of 5 in the Structure of Coproheme Decarboxylase From Corynebacterium Dipththeriae Y135A Mutant in Complex with Coproheme


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 Corynebacterium Dipththeriae Y135A Mutant in Complex with Coproheme within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:26.5 occ:1.00 FE C:FEC401 0.0 26.5 1.0 NC C:FEC401 1.9 29.6 1.0 NA C:FEC401 2.0 24.6 1.0 ND C:FEC401 2.0 25.5 1.0 NB C:FEC401 2.0 26.1 1.0 NE2 C:HIS158 2.1 26.0 1.0 C4C C:FEC401 3.0 27.5 1.0 C4A C:FEC401 3.0 28.4 1.0 C4D C:FEC401 3.0 29.4 1.0 C4B C:FEC401 3.0 31.2 1.0 C1C C:FEC401 3.0 29.8 1.0 CE1 C:HIS158 3.1 32.1 1.0 C1A C:FEC401 3.1 26.8 1.0 C1D C:FEC401 3.1 27.4 1.0 C1B C:FEC401 3.1 30.8 1.0 CD2 C:HIS158 3.1 26.7 1.0 HE1 C:HIS158 3.2 38.6 1.0 HG21 C:THR172 3.2 36.3 1.0 HD2 C:HIS158 3.3 32.1 1.0 CHC C:FEC401 3.3 30.5 1.0 CHA C:FEC401 3.4 26.6 1.0 CHB C:FEC401 3.4 24.8 1.0 CHD C:FEC401 3.4 23.2 1.0 CG2 C:THR172 4.1 30.2 1.0 HE2 C:MET202 4.2 40.0 1.0 ND1 C:HIS158 4.2 30.8 1.0 C3C C:FEC401 4.2 27.5 1.0 C2C C:FEC401 4.2 28.7 1.0 HHC C:FEC401 4.2 36.6 1.0 HE1 C:HIS118 4.2 38.4 1.0 C3D C:FEC401 4.2 24.5 1.0 C3A C:FEC401 4.2 25.5 1.0 C3B C:FEC401 4.2 29.2 1.0 C2D C:FEC401 4.3 28.7 1.0 CG C:HIS158 4.3 30.2 1.0 HHA C:FEC401 4.3 32.0 1.0 C2A C:FEC401 4.3 29.6 1.0 C2B C:FEC401 4.3 30.8 1.0 HG22 C:THR172 4.3 36.3 1.0 HHB C:FEC401 4.4 29.8 1.0 HHD C:FEC401 4.4 27.9 1.0 HG23 C:THR172 4.4 36.3 1.0 HE1 C:MET202 4.4 40.0 1.0 HE1 C:PHE187 4.6 35.1 1.0 CE C:MET202 4.6 33.3 1.0 HE3 C:MET202 4.7 40.0 1.0 CE1 C:HIS118 4.8 31.9 1.0 HD1 C:HIS158 5.0 37.0 1.0 HZ C:PHE187 5.0 29.9 1.0

Iron binding site 4 out of 5 in the Structure of Coproheme Decarboxylase From Corynebacterium Dipththeriae Y135A Mutant in Complex with Coproheme


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 Corynebacterium Dipththeriae Y135A Mutant in Complex with Coproheme within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:28.4 occ:1.00 FE D:FEC401 0.0 28.4 1.0 NC D:FEC401 2.0 31.9 1.0 ND D:FEC401 2.0 26.2 1.0 NA D:FEC401 2.0 26.0 1.0 NB D:FEC401 2.0 30.1 1.0 NE2 D:HIS158 2.1 26.5 1.0 C4D D:FEC401 2.9 26.7 1.0 C4C D:FEC401 3.0 32.2 1.0 C4B D:FEC401 3.0 28.2 1.0 C4A D:FEC401 3.0 35.2 1.0 C1C D:FEC401 3.0 32.4 1.0 C1D D:FEC401 3.0 31.5 1.0 CE1 D:HIS158 3.1 29.8 1.0 C1A D:FEC401 3.1 29.7 1.0 C1B D:FEC401 3.1 31.3 1.0 CD2 D:HIS158 3.2 32.4 1.0 HE1 D:HIS158 3.2 35.8 1.0 HG21 D:THR172 3.3 39.9 1.0 CHA D:FEC401 3.4 28.5 1.0 CHC D:FEC401 3.4 31.2 1.0 HD2 D:HIS158 3.4 38.9 1.0 CHD D:FEC401 3.4 31.9 1.0 CHB D:FEC401 3.5 29.1 1.0 CG2 D:THR172 4.2 33.2 1.0 C3D D:FEC401 4.2 27.5 1.0 C3C D:FEC401 4.2 34.8 1.0 ND1 D:HIS158 4.2 32.7 1.0 C2C D:FEC401 4.2 37.0 1.0 C2D D:FEC401 4.2 27.6 1.0 HHA D:FEC401 4.2 34.2 1.0 C3B D:FEC401 4.2 32.6 1.0 C3A D:FEC401 4.2 30.6 1.0 HHC D:FEC401 4.3 37.5 1.0 CG D:HIS158 4.3 26.0 1.0 C2A D:FEC401 4.3 32.4 1.0 HHD D:FEC401 4.3 38.3 1.0 HG23 D:THR172 4.3 39.9 1.0 C2B D:FEC401 4.3 35.0 1.0 HHB D:FEC401 4.4 35.0 1.0 HE1 D:HIS118 4.4 41.3 1.0 HE2 D:MET202 4.4 39.9 1.0 HG22 D:THR172 4.5 39.9 1.0 HE1 D:PHE187 4.7 38.9 1.0 HZ D:PHE187 4.8 34.4 1.0 CE1 D:HIS118 4.9 34.4 1.0 HD1 D:HIS158 5.0 39.2 1.0

Iron binding site 5 out of 5 in the Structure of Coproheme Decarboxylase From Corynebacterium Dipththeriae Y135A Mutant in Complex with Coproheme


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 Corynebacterium Dipththeriae Y135A Mutant in Complex with Coproheme within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe401 b:31.6 occ:1.00 FE E:FEC401 0.0 31.6 1.0 NC E:FEC401 2.0 39.1 1.0 NB E:FEC401 2.0 42.8 1.0 ND E:FEC401 2.0 33.7 1.0 NA E:FEC401 2.0 30.1 1.0 NE2 E:HIS158 2.2 40.9 1.0 C4B E:FEC401 3.0 46.1 1.0 C4C E:FEC401 3.0 40.5 1.0 C4D E:FEC401 3.0 37.5 1.0 C4A E:FEC401 3.0 37.8 1.0 C1C E:FEC401 3.0 47.5 1.0 C1D E:FEC401 3.1 36.7 1.0 C1A E:FEC401 3.1 34.9 1.0 C1B E:FEC401 3.1 43.7 1.0 CD2 E:HIS158 3.1 38.1 1.0 CE1 E:HIS158 3.2 37.0 1.0 HD2 E:HIS158 3.2 45.7 1.0 HG21 E:THR172 3.3 38.6 1.0 CHC E:FEC401 3.3 47.5 1.0 CHA E:FEC401 3.4 34.2 1.0 CHD E:FEC401 3.4 35.2 1.0 CHB E:FEC401 3.4 41.5 1.0 HE1 E:HIS158 3.4 44.4 1.0 C3C E:FEC401 4.2 45.7 1.0 C3D E:FEC401 4.2 37.8 1.0 C2C E:FEC401 4.2 47.0 1.0 C3B E:FEC401 4.2 51.1 1.0 HHC E:FEC401 4.2 57.0 1.0 CG2 E:THR172 4.2 32.1 1.0 HHA E:FEC401 4.2 41.1 1.0 C2D E:FEC401 4.3 39.4 1.0 HE2 E:MET202 4.3 43.3 1.0 C3A E:FEC401 4.3 36.2 1.0 CG E:HIS158 4.3 33.4 1.0 ND1 E:HIS158 4.3 35.0 1.0 C2B E:FEC401 4.3 52.8 1.0 HHB E:FEC401 4.3 49.8 1.0 HHD E:FEC401 4.3 42.3 1.0 C2A E:FEC401 4.3 34.2 1.0 HG23 E:THR172 4.4 38.6 1.0 HE1 E:HIS118 4.5 71.5 1.0 HG22 E:THR172 4.6 38.6 1.0 HE1 E:MET202 4.8 43.3 1.0 HE1 E:PHE187 4.8 46.6 1.0 HE3 E:MET202 4.8 43.3 1.0 CE E:MET202 4.8 36.1 1.0 CE1 E:HIS118 5.0 59.6 1.0 HD22 E:LEU155 5.0 46.3 1.0

H.Michlits, N.Valente, G.Mlynek, S.Hofbauer. Initial Steps to Engineer Coproheme Decarboxylase to Obtain Stereospecific Monovinyl, Monopropionyl Deuterohemes. Front Bioeng Biotechnol V. 9 07678 2021.
ISSN: ISSN 2296-4185
PubMed: 35141216
DOI: 10.3389/FBIOE.2021.807678