Iron in PDB 6xub: Structure of Coproheme Decarboxylase From Corynebacterium Diphteriae in Complex with Monovinyl Monopropionyl Deuteroheme

The structure of Structure of Coproheme Decarboxylase From Corynebacterium Diphteriae in Complex with Monovinyl Monopropionyl Deuteroheme, PDB code: 6xub was solved by H.Michlits, B.Lier, V.Pfanzagl, K.Djinovic-Carugo, P.G.Furtmueller, C.Oostenbrink, C.Obinger, S.Hofbauer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.19 / 1.78
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.969, 123.382, 78.009, 90.00, 98.71, 90.00
R / Rfree (%)	17.4 / 22.7

The binding sites of Iron atom in the Structure of Coproheme Decarboxylase From Corynebacterium Diphteriae in Complex with Monovinyl Monopropionyl Deuteroheme (pdb code 6xub). 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 Diphteriae in Complex with Monovinyl Monopropionyl Deuteroheme, PDB code: 6xub:
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 Diphteriae in Complex with Monovinyl Monopropionyl Deuteroheme


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 Diphteriae in Complex with Monovinyl Monopropionyl Deuteroheme within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:0.5 occ:1.00 FE A:VOV301 0.0 0.5 1.0 N05 A:VOV301 2.0 61.5 1.0 N04 A:VOV301 2.0 35.0 1.0 N02 A:VOV301 2.0 40.9 1.0 N03 A:VOV301 2.0 49.8 1.0 NE2 A:HIS158 2.3 27.1 1.0 C18 A:VOV301 3.0 19.9 1.0 C43 A:VOV301 3.0 20.4 1.0 C29 A:VOV301 3.0 23.6 1.0 C10 A:VOV301 3.0 23.7 1.0 C21 A:VOV301 3.0 29.3 1.0 C32 A:VOV301 3.0 27.6 1.0 C40 A:VOV301 3.0 22.1 1.0 C07 A:VOV301 3.0 30.3 1.0 HG21 A:THR172 3.1 42.0 1.0 CE1 A:HIS158 3.2 29.1 1.0 HE1 A:HIS158 3.2 35.0 1.0 C17 A:VOV301 3.3 22.5 1.0 C28 A:VOV301 3.3 27.3 1.0 C06 A:VOV301 3.4 28.0 1.0 CD2 A:HIS158 3.4 25.2 1.0 C39 A:VOV301 3.4 33.7 1.0 HD2 A:HIS158 3.6 30.3 1.0 CG2 A:THR172 4.1 35.0 1.0 C30 A:VOV301 4.2 36.5 1.0 C31 A:VOV301 4.2 31.9 1.0 H171 A:VOV301 4.2 27.0 1.0 C19 A:VOV301 4.2 20.5 1.0 C09 A:VOV301 4.2 29.0 1.0 C08 A:VOV301 4.2 30.8 1.0 H281 A:VOV301 4.2 32.8 1.0 C42 A:VOV301 4.2 22.9 1.0 C20 A:VOV301 4.3 19.4 1.0 C41 A:VOV301 4.3 30.8 1.0 H061 A:VOV301 4.3 33.6 1.0 H391 A:VOV301 4.3 40.5 1.0 HG23 A:THR172 4.3 42.0 1.0 ND1 A:HIS158 4.3 22.1 1.0 HE1 A:HIS118 4.4 46.0 1.0 CG A:HIS158 4.5 23.4 1.0 HE2 A:MET202 4.5 39.3 1.0 HG22 A:THR172 4.5 42.0 1.0 HZ A:PHE187 4.8 30.1 1.0 HE2 A:HIS118 4.8 40.2 1.0 HE1 A:PHE187 4.8 32.6 1.0 CE1 A:HIS118 4.9 38.3 1.0 HE1 A:MET202 4.9 39.3 1.0 HB A:THR172 4.9 42.7 1.0 CB A:THR172 4.9 35.6 1.0

Iron binding site 2 out of 5 in the Structure of Coproheme Decarboxylase From Corynebacterium Diphteriae in Complex with Monovinyl Monopropionyl Deuteroheme


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 Diphteriae in Complex with Monovinyl Monopropionyl Deuteroheme within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:0.5 occ:1.00 FE B:VOV401 0.0 0.5 1.0 N05 B:VOV401 2.0 79.9 1.0 N03 B:VOV401 2.0 70.8 1.0 N04 B:VOV401 2.0 76.1 1.0 N02 B:VOV401 2.0 91.8 1.0 NE2 B:HIS158 2.3 33.5 1.0 C10 B:VOV401 3.0 51.3 1.0 C18 B:VOV401 3.0 34.0 1.0 C43 B:VOV401 3.0 48.1 1.0 C32 B:VOV401 3.0 33.6 1.0 C21 B:VOV401 3.0 30.1 1.0 C40 B:VOV401 3.0 43.7 1.0 C29 B:VOV401 3.0 30.5 1.0 C07 B:VOV401 3.0 67.3 1.0 HG21 B:THR172 3.2 33.3 1.0 CE1 B:HIS158 3.3 29.3 1.0 CD2 B:HIS158 3.3 33.6 1.0 C17 B:VOV401 3.3 32.8 1.0 C06 B:VOV401 3.4 58.3 1.0 C28 B:VOV401 3.4 29.2 1.0 C39 B:VOV401 3.4 39.7 1.0 HE1 B:HIS158 3.4 35.2 1.0 HD2 B:HIS158 3.4 40.4 1.0 CG2 B:THR172 4.1 27.7 1.0 C42 B:VOV401 4.2 39.7 1.0 C19 B:VOV401 4.2 36.2 1.0 H171 B:VOV401 4.2 39.4 1.0 C09 B:VOV401 4.2 47.8 1.0 C31 B:VOV401 4.2 39.9 1.0 C20 B:VOV401 4.2 32.4 1.0 C08 B:VOV401 4.2 58.6 1.0 C41 B:VOV401 4.2 52.5 1.0 C30 B:VOV401 4.3 36.2 1.0 H061 B:VOV401 4.3 70.0 1.0 H391 B:VOV401 4.3 47.7 1.0 HG23 B:THR172 4.3 33.3 1.0 H281 B:VOV401 4.3 35.1 1.0 HE1 B:HIS118 4.4 37.3 1.0 ND1 B:HIS158 4.4 30.1 1.0 CG B:HIS158 4.4 31.7 1.0 HE2 B:MET202 4.5 45.7 1.0 HG22 B:THR172 4.6 33.3 1.0 HE1 B:PHE187 4.6 45.5 1.0 HZ B:PHE187 4.7 38.6 1.0 HE2 B:HIS118 4.7 46.7 1.0 CE1 B:HIS118 4.8 31.1 1.0 HB B:THR172 5.0 38.9 1.0

Iron binding site 3 out of 5 in the Structure of Coproheme Decarboxylase From Corynebacterium Diphteriae in Complex with Monovinyl Monopropionyl Deuteroheme


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 Diphteriae in Complex with Monovinyl Monopropionyl Deuteroheme within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:0.0 occ:1.00 FE C:VOV501 0.0 0.0 1.0 N03 C:VOV501 2.0 0.3 1.0 N05 C:VOV501 2.0 0.7 1.0 N04 C:VOV501 2.0 0.4 1.0 N02 C:VOV501 2.0 0.9 1.0 NE2 C:HIS158 2.2 73.5 1.0 C10 C:VOV501 3.0 100.0 1.0 C18 C:VOV501 3.0 0.9 1.0 C29 C:VOV501 3.0 0.8 1.0 C21 C:VOV501 3.0 0.6 1.0 C43 C:VOV501 3.0 0.0 1.0 C32 C:VOV501 3.0 0.7 1.0 C07 C:VOV501 3.0 0.1 1.0 C40 C:VOV501 3.0 0.1 1.0 CD2 C:HIS158 3.1 33.0 1.0 HG21 C:THR172 3.2 44.1 1.0 HD2 C:HIS158 3.2 39.6 1.0 CE1 C:HIS158 3.3 42.3 1.0 C17 C:VOV501 3.3 76.7 1.0 C28 C:VOV501 3.4 90.9 1.0 C06 C:VOV501 3.4 0.7 1.0 C39 C:VOV501 3.4 0.5 1.0 HE1 C:HIS158 3.5 50.8 1.0 C30 C:VOV501 4.2 66.6 1.0 C42 C:VOV501 4.2 81.6 1.0 CG2 C:THR172 4.2 36.7 1.0 C19 C:VOV501 4.2 65.4 1.0 C20 C:VOV501 4.2 59.4 1.0 C31 C:VOV501 4.2 78.4 1.0 C08 C:VOV501 4.2 64.7 1.0 C09 C:VOV501 4.2 55.2 1.0 H171 C:VOV501 4.2 92.1 1.0 C41 C:VOV501 4.2 78.1 1.0 H281 C:VOV501 4.3 0.1 1.0 H391 C:VOV501 4.3 0.1 1.0 H061 C:VOV501 4.3 0.6 1.0 CG C:HIS158 4.3 35.3 1.0 ND1 C:HIS158 4.3 35.6 1.0 HE1 C:HIS118 4.4 50.1 1.0 HG23 C:THR172 4.5 44.1 1.0 HG22 C:THR172 4.5 44.1 1.0 HE2 C:MET202 4.6 38.9 1.0 HE1 C:PHE187 4.8 46.3 1.0 CE1 C:HIS118 4.9 41.8 1.0 HE1 C:MET202 4.9 38.9 1.0 HZ C:PHE187 4.9 39.2 1.0 HB C:THR172 4.9 35.4 1.0

Iron binding site 4 out of 5 in the Structure of Coproheme Decarboxylase From Corynebacterium Diphteriae in Complex with Monovinyl Monopropionyl Deuteroheme


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 Diphteriae in Complex with Monovinyl Monopropionyl Deuteroheme within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:0.0 occ:1.00 FE D:VOV301 0.0 0.0 1.0 N05 D:VOV301 2.0 0.7 1.0 N03 D:VOV301 2.0 0.5 1.0 N04 D:VOV301 2.0 0.3 1.0 N02 D:VOV301 2.0 0.9 1.0 NE2 D:HIS158 2.4 0.2 1.0 C18 D:VOV301 3.0 1.0 1.0 C43 D:VOV301 3.0 0.3 1.0 C10 D:VOV301 3.0 1.0 1.0 C32 D:VOV301 3.0 0.0 1.0 C21 D:VOV301 3.0 0.6 1.0 C40 D:VOV301 3.0 0.5 1.0 C29 D:VOV301 3.0 0.5 1.0 C07 D:VOV301 3.1 0.3 1.0 HD2 D:HIS158 3.1 0.1 1.0 CD2 D:HIS158 3.1 83.4 1.0 HG21 D:THR172 3.2 45.4 1.0 C17 D:VOV301 3.3 0.1 1.0 C39 D:VOV301 3.4 98.0 1.0 C06 D:VOV301 3.4 0.3 1.0 C28 D:VOV301 3.4 0.0 1.0 CE1 D:HIS158 3.5 86.8 1.0 HE1 D:HIS158 3.8 0.2 1.0 CG2 D:THR172 4.2 37.8 1.0 C19 D:VOV301 4.2 72.1 1.0 C42 D:VOV301 4.2 70.7 1.0 C20 D:VOV301 4.2 68.7 1.0 H171 D:VOV301 4.2 0.9 1.0 C31 D:VOV301 4.2 82.8 1.0 C09 D:VOV301 4.2 72.1 1.0 C41 D:VOV301 4.2 74.9 1.0 C30 D:VOV301 4.2 84.7 1.0 C08 D:VOV301 4.2 74.1 1.0 H391 D:VOV301 4.3 0.7 1.0 H061 D:VOV301 4.3 0.8 1.0 H281 D:VOV301 4.3 0.4 1.0 CG D:HIS158 4.4 72.3 1.0 HG22 D:THR172 4.5 45.4 1.0 ND1 D:HIS158 4.5 84.1 1.0 HG23 D:THR172 4.6 45.4 1.0 HZ D:PHE187 4.8 34.6 1.0 HE1 D:HIS118 4.9 97.4 1.0 HE2 D:MET202 4.9 62.9 1.0 HB D:THR172 4.9 52.5 1.0

Iron binding site 5 out of 5 in the Structure of Coproheme Decarboxylase From Corynebacterium Diphteriae in Complex with Monovinyl Monopropionyl Deuteroheme


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 Diphteriae in Complex with Monovinyl Monopropionyl Deuteroheme within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe401 b:50.0 occ:1.00 FE E:VOV401 0.0 50.0 1.0 N03 E:VOV401 2.0 54.7 1.0 N05 E:VOV401 2.0 50.8 1.0 N04 E:VOV401 2.0 66.8 1.0 N02 E:VOV401 2.0 62.1 1.0 NE2 E:HIS158 2.4 46.6 1.0 C18 E:VOV401 3.0 59.1 1.0 C32 E:VOV401 3.0 67.7 1.0 C40 E:VOV401 3.0 53.8 1.0 C43 E:VOV401 3.1 58.4 1.0 C21 E:VOV401 3.1 63.8 1.0 C10 E:VOV401 3.1 50.5 1.0 C29 E:VOV401 3.1 74.2 1.0 C07 E:VOV401 3.1 66.9 1.0 CD2 E:HIS158 3.3 52.3 1.0 HD2 E:HIS158 3.3 62.8 1.0 C17 E:VOV401 3.4 51.0 1.0 C39 E:VOV401 3.4 58.1 1.0 C28 E:VOV401 3.4 75.7 1.0 C06 E:VOV401 3.4 65.8 1.0 CE1 E:HIS158 3.4 48.8 1.0 HE1 E:HIS158 3.6 58.6 1.0 HG21 E:THR172 4.2 41.6 1.0 C19 E:VOV401 4.2 51.2 1.0 H171 E:VOV401 4.2 61.2 1.0 C20 E:VOV401 4.2 52.6 1.0 C42 E:VOV401 4.2 54.5 1.0 C31 E:VOV401 4.2 76.2 1.0 C41 E:VOV401 4.3 54.8 1.0 H391 E:VOV401 4.3 69.7 1.0 C30 E:VOV401 4.3 78.9 1.0 C09 E:VOV401 4.3 44.9 1.0 C08 E:VOV401 4.3 49.7 1.0 OG1 E:THR172 4.3 42.2 1.0 H281 E:VOV401 4.3 90.9 1.0 H061 E:VOV401 4.3 79.0 1.0 CG E:HIS158 4.5 45.7 1.0 ND1 E:HIS158 4.5 39.5 1.0 HG1 E:THR172 4.6 50.7 1.0 HZ E:PHE187 4.6 59.3 1.0 HD23 E:LEU185 4.7 71.7 1.0 HD21 E:LEU185 4.8 71.7 1.0 HE2 E:MET202 4.8 0.2 1.0 HE1 E:MET202 4.8 0.2 1.0 HD22 E:LEU155 5.0 52.0 1.0 HE2 E:HIS118 5.0 0.6 1.0 CG2 E:THR172 5.0 34.6 1.0

H.Michlits, B.Lier, V.Pfanzagl, K.Djinovic-Carugo, P.G.Furtmueller, C.Oostenbrink, C.Obinger, S.Hofbauer. Actinobacterial Coproheme Decarboxylases Use Histidine As Distal Base to Promote Compound I Formation Acs Catalysis 2020.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.0C00411