Iron in PDB 3hco: Human Ferrochelatase with Cd and Protoporphyrin IX Bound

All present enzymatic activity of Human Ferrochelatase with Cd and Protoporphyrin IX Bound:
4.99.1.1;

The structure of Human Ferrochelatase with Cd and Protoporphyrin IX Bound, PDB code: 3hco was solved by A.E.Medlock, H.A.Dailey, W.N.Lanzilotta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.19 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.266, 92.827, 109.555, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 25.2

The binding sites of Iron atom in the Human Ferrochelatase with Cd and Protoporphyrin IX Bound (pdb code 3hco). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Human Ferrochelatase with Cd and Protoporphyrin IX Bound, PDB code: 3hco:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Human Ferrochelatase with Cd and Protoporphyrin IX Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Human Ferrochelatase with Cd and Protoporphyrin IX Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:18.7 occ:1.00 FE1 A:FES501 0.0 18.7 1.0 S2 A:FES501 2.2 22.1 1.0 S1 A:FES501 2.3 18.7 1.0 SG A:CYS411 2.3 19.9 1.0 SG A:CYS406 2.3 19.7 1.0 FE2 A:FES501 2.8 16.4 1.0 CB A:CYS411 3.1 18.3 1.0 CB A:CYS406 3.2 19.0 1.0 CA A:CYS406 4.1 20.1 1.0 O A:HOH54 4.2 40.2 1.0 O A:HOH52 4.2 26.2 1.0 O A:HOH24 4.3 24.0 1.0 CB A:ASN408 4.3 23.6 1.0 O A:ASN408 4.4 22.2 1.0 SG A:CYS196 4.5 18.1 1.0 CA A:CYS411 4.6 19.8 1.0 SG A:CYS403 4.8 17.2 1.0 N A:ASN408 4.8 22.8 1.0 CB A:CYS403 4.8 15.7 1.0 O A:HOH571 4.8 42.7 1.0 N A:CYS403 4.9 16.6 1.0 CB A:SER402 4.9 21.1 1.0 C A:CYS406 4.9 20.9 1.0 CB A:CYS196 5.0 13.8 1.0

Iron binding site 2 out of 6 in the Human Ferrochelatase with Cd and Protoporphyrin IX Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Human Ferrochelatase with Cd and Protoporphyrin IX Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:16.4 occ:1.00 FE2 A:FES501 0.0 16.4 1.0 S1 A:FES501 2.2 18.7 1.0 S2 A:FES501 2.2 22.1 1.0 SG A:CYS196 2.3 18.1 1.0 SG A:CYS403 2.3 17.2 1.0 FE1 A:FES501 2.8 18.7 1.0 CB A:CYS403 3.3 15.7 1.0 CB A:CYS196 3.4 13.8 1.0 O A:HOH53 3.5 17.9 1.0 N A:CYS403 3.9 16.6 1.0 CA A:CYS403 4.2 15.3 1.0 O A:HOH54 4.4 40.2 1.0 CB A:CYS406 4.5 19.0 1.0 O A:HOH55 4.5 36.5 1.0 SG A:CYS411 4.5 19.9 1.0 SG A:CYS406 4.6 19.7 1.0 CA A:CYS196 4.7 13.8 1.0 NH2 B:ARG798 4.9 22.2 1.0 NE A:ARG272 4.9 24.2 1.0 NH2 A:ARG272 5.0 23.3 1.0

Iron binding site 3 out of 6 in the Human Ferrochelatase with Cd and Protoporphyrin IX Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Human Ferrochelatase with Cd and Protoporphyrin IX Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe426 b:15.8 occ:1.00 FE A:HEM426 0.0 15.8 1.0 N1 A:IMD424 1.9 25.2 1.0 NB A:HEM426 2.0 16.9 1.0 ND A:HEM426 2.0 17.3 1.0 NC A:HEM426 2.1 13.9 1.0 NA A:HEM426 2.1 16.7 1.0 O3 A:BCT425 2.5 42.2 1.0 C2 A:IMD424 2.9 22.7 1.0 C5 A:IMD424 3.0 20.8 1.0 C1D A:HEM426 3.0 16.9 1.0 C1B A:HEM426 3.0 16.9 1.0 C4B A:HEM426 3.0 17.1 1.0 C4C A:HEM426 3.0 14.3 1.0 C4D A:HEM426 3.1 15.2 1.0 C1C A:HEM426 3.1 16.9 1.0 C4A A:HEM426 3.1 18.1 1.0 C1A A:HEM426 3.1 16.7 1.0 CHD A:HEM426 3.4 16.6 1.0 CHB A:HEM426 3.4 19.4 1.0 CHC A:HEM426 3.4 16.6 1.0 CHA A:HEM426 3.5 17.2 1.0 C A:BCT425 3.7 41.5 1.0 N3 A:IMD424 4.1 22.6 1.0 C4 A:IMD424 4.1 21.6 1.0 O2 A:BCT425 4.2 42.5 1.0 C2B A:HEM426 4.2 19.9 1.0 C3B A:HEM426 4.2 17.4 1.0 C2D A:HEM426 4.3 16.8 1.0 C3D A:HEM426 4.3 17.5 1.0 C3C A:HEM426 4.3 11.5 1.0 C2A A:HEM426 4.3 20.1 1.0 C3A A:HEM426 4.3 18.5 1.0 C2C A:HEM426 4.3 12.5 1.0 O1 A:BCT425 4.7 39.8 1.0 CD2 A:HIS263 5.0 18.3 1.0

Iron binding site 4 out of 6 in the Human Ferrochelatase with Cd and Protoporphyrin IX Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Human Ferrochelatase with Cd and Protoporphyrin IX Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:19.1 occ:1.00 FE1 B:FES501 0.0 19.1 1.0 S2 B:FES501 2.2 21.4 1.0 S1 B:FES501 2.3 19.4 1.0 SG B:CYS906 2.3 19.7 1.0 SG B:CYS911 2.3 20.7 1.0 FE2 B:FES501 2.8 17.8 1.0 CB B:CYS911 3.1 20.2 1.0 CB B:CYS906 3.2 19.4 1.0 CA B:CYS906 4.1 20.5 1.0 O B:HOH151 4.2 24.7 1.0 O B:HOH130 4.2 25.9 1.0 O B:HOH153 4.3 40.1 1.0 CB B:ASN908 4.3 25.2 1.0 O B:ASN908 4.4 25.9 1.0 SG B:CYS696 4.5 19.9 1.0 CA B:CYS911 4.6 21.3 1.0 SG B:CYS903 4.8 17.4 1.0 N B:ASN908 4.8 24.8 1.0 CB B:SER902 4.9 22.4 1.0 N B:CYS903 4.9 18.6 1.0 C B:CYS906 4.9 21.5 1.0 CB B:CYS903 4.9 17.6 1.0 CB B:CYS696 5.0 17.1 1.0 OG B:SER902 5.0 24.7 1.0

Iron binding site 5 out of 6 in the Human Ferrochelatase with Cd and Protoporphyrin IX Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Human Ferrochelatase with Cd and Protoporphyrin IX Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:17.8 occ:1.00 FE2 B:FES501 0.0 17.8 1.0 S1 B:FES501 2.2 19.4 1.0 S2 B:FES501 2.2 21.4 1.0 SG B:CYS696 2.3 19.9 1.0 SG B:CYS903 2.3 17.4 1.0 FE1 B:FES501 2.8 19.1 1.0 CB B:CYS903 3.4 17.6 1.0 CB B:CYS696 3.4 17.1 1.0 O B:HOH152 3.6 20.3 1.0 N B:CYS903 3.9 18.6 1.0 CA B:CYS903 4.2 17.6 1.0 O A:HOH537 4.3 35.5 1.0 O B:HOH154 4.4 34.0 1.0 CB B:CYS906 4.4 19.4 1.0 O B:HOH153 4.6 40.1 1.0 SG B:CYS911 4.6 20.7 1.0 SG B:CYS906 4.6 19.7 1.0 CA B:CYS696 4.8 15.4 1.0 NE B:ARG772 4.9 25.2 1.0 NH2 A:ARG298 4.9 23.3 1.0

Iron binding site 6 out of 6 in the Human Ferrochelatase with Cd and Protoporphyrin IX Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Human Ferrochelatase with Cd and Protoporphyrin IX Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe926 b:16.9 occ:1.00 FE B:HEM926 0.0 16.9 1.0 N1 B:IMD2 1.9 24.5 1.0 N1 B:IMD3 1.9 28.6 1.0 ND B:HEM926 2.0 16.2 1.0 NB B:HEM926 2.0 18.1 1.0 NC B:HEM926 2.1 14.5 1.0 NA B:HEM926 2.1 17.1 1.0 C5 B:IMD3 2.9 29.8 1.0 C5 B:IMD2 2.9 22.7 1.0 C2 B:IMD2 2.9 22.7 1.0 C2 B:IMD3 3.0 30.4 1.0 C4D B:HEM926 3.0 16.8 1.0 C1D B:HEM926 3.0 16.5 1.0 C4B B:HEM926 3.0 17.7 1.0 C4C B:HEM926 3.1 13.2 1.0 C1B B:HEM926 3.1 18.5 1.0 C1C B:HEM926 3.1 17.0 1.0 C4A B:HEM926 3.1 19.6 1.0 C1A B:HEM926 3.1 18.3 1.0 CHC B:HEM926 3.4 17.1 1.0 CHD B:HEM926 3.4 14.9 1.0 CHB B:HEM926 3.4 18.3 1.0 CHA B:HEM926 3.4 16.8 1.0 C4 B:IMD3 4.0 29.3 1.0 C4 B:IMD2 4.1 22.2 1.0 N3 B:IMD2 4.1 22.3 1.0 N3 B:IMD3 4.1 31.8 1.0 C3B B:HEM926 4.3 18.6 1.0 C3D B:HEM926 4.3 17.4 1.0 C2D B:HEM926 4.3 17.3 1.0 C2B B:HEM926 4.3 20.3 1.0 C3C B:HEM926 4.3 11.8 1.0 C2C B:HEM926 4.3 11.5 1.0 C2A B:HEM926 4.3 21.9 1.0 C3A B:HEM926 4.4 19.3 1.0 CD2 B:HIS763 4.9 18.5 1.0

A.E.Medlock, M.Carter, T.A.Dailey, H.A.Dailey, W.N.Lanzilotta. Product Release Rather Than Chelation Determines Metal Specificity For Ferrochelatase. J.Mol.Biol. V. 393 308 2009.
ISSN: ISSN 0022-2836
PubMed: 19703464
DOI: 10.1016/J.JMB.2009.08.042