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Iron in PDB 3hcn: Hg and Protoporphyrin Bound Human Ferrochelatase

Enzymatic activity of Hg and Protoporphyrin Bound Human Ferrochelatase

All present enzymatic activity of Hg and Protoporphyrin Bound Human Ferrochelatase:
4.99.1.1;

Protein crystallography data

The structure of Hg and Protoporphyrin Bound Human Ferrochelatase, PDB code: 3hcn 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) 47.13 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.479, 92.964, 109.360, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 23.6

Iron Binding Sites:

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

Iron binding site 1 out of 6 in 3hcn

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Iron binding site 1 out of 6 in the Hg and Protoporphyrin Bound Human Ferrochelatase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Hg and Protoporphyrin Bound Human Ferrochelatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:15.0
occ:1.00
 FE1 A:FES501 0.0 15.0 1.0
S1 A:FES501 2.2 15.0 1.0
S2 A:FES501 2.2 17.3 1.0
SG A:CYS406 2.3 16.4 1.0
SG A:CYS411 2.3 17.1 1.0
FE2 A:FES501 2.7 14.1 1.0
CB A:CYS411 3.2 16.4 1.0
CB A:CYS406 3.3 15.1 1.0
O A:HOH667 4.1 31.0 1.0
O A:HOH53 4.2 18.5 1.0
CA A:CYS406 4.2 16.7 1.0
CB A:ASN408 4.3 18.4 1.0
O A:HOH453 4.4 20.6 1.0
O A:ASN408 4.5 19.7 1.0
SG A:CYS196 4.5 15.7 1.0
CA A:CYS411 4.7 17.0 1.0
SG A:CYS403 4.7 14.2 1.0
N A:ASN408 4.8 18.3 1.0
N A:CYS403 4.9 14.4 1.0
CB A:CYS403 4.9 13.4 1.0
O A:HOH704 4.9 37.0 1.0
CB A:CYS196 4.9 12.4 1.0
C A:CYS406 5.0 17.4 1.0
CB A:SER402 5.0 22.9 1.0

Iron binding site 2 out of 6 in 3hcn

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Iron binding site 2 out of 6 in the Hg and Protoporphyrin Bound Human Ferrochelatase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Hg and Protoporphyrin Bound Human Ferrochelatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:14.1
occ:1.00
 FE2 A:FES501 0.0 14.1 1.0
S2 A:FES501 2.2 17.3 1.0
S1 A:FES501 2.2 15.0 1.0
SG A:CYS196 2.3 15.7 1.0
SG A:CYS403 2.3 14.2 1.0
FE1 A:FES501 2.7 15.0 1.0
CB A:CYS403 3.4 13.4 1.0
CB A:CYS196 3.4 12.4 1.0
O A:HOH11 3.5 18.2 1.0
N A:CYS403 3.9 14.4 1.0
CA A:CYS403 4.3 13.6 1.0
O B:HOH358 4.3 39.5 1.0
O A:HOH667 4.4 31.0 1.0
CB A:CYS406 4.5 15.1 1.0
SG A:CYS411 4.5 17.1 1.0
SG A:CYS406 4.6 16.4 1.0
CA A:CYS196 4.7 12.7 1.0
NE A:ARG272 4.9 24.6 1.0
NH2 B:ARG798 5.0 20.5 1.0

Iron binding site 3 out of 6 in 3hcn

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Iron binding site 3 out of 6 in the Hg and Protoporphyrin Bound Human Ferrochelatase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Hg and Protoporphyrin Bound Human Ferrochelatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe424

b:14.6
occ:1.00
 FE A:HEM424 0.0 14.6 1.0
ND A:HEM424 2.0 17.0 1.0
NB A:HEM424 2.0 16.3 1.0
NC A:HEM424 2.0 12.4 1.0
NA A:HEM424 2.0 14.7 1.0
N1 A:IMD2 2.2 27.7 1.0
O2 A:BCT1 2.6 44.7 1.0
C1D A:HEM424 3.0 15.5 1.0
C4C A:HEM424 3.0 15.5 1.0
C1B A:HEM424 3.0 15.9 1.0
C4A A:HEM424 3.1 17.8 1.0
C1C A:HEM424 3.1 14.0 1.0
C4D A:HEM424 3.1 15.5 1.0
C4B A:HEM424 3.1 13.8 1.0
C1A A:HEM424 3.1 18.2 1.0
C2 A:IMD2 3.1 26.0 1.0
C5 A:IMD2 3.2 25.8 1.0
CHB A:HEM424 3.4 17.9 1.0
CHD A:HEM424 3.4 16.8 1.0
CHA A:HEM424 3.4 18.1 1.0
CHC A:HEM424 3.5 13.6 1.0
C A:BCT1 3.8 45.3 1.0
N3 A:IMD2 4.2 26.2 1.0
C3A A:HEM424 4.3 18.6 1.0
C4 A:IMD2 4.3 26.1 1.0
C2B A:HEM424 4.3 15.7 1.0
C3D A:HEM424 4.3 17.7 1.0
C2D A:HEM424 4.3 16.1 1.0
C2C A:HEM424 4.3 13.4 1.0
C3B A:HEM424 4.3 15.3 1.0
C2A A:HEM424 4.3 18.9 1.0
C3C A:HEM424 4.3 14.3 1.0
O3 A:BCT1 4.6 46.2 1.0
O1 A:BCT1 4.6 45.7 1.0

Iron binding site 4 out of 6 in 3hcn

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Iron binding site 4 out of 6 in the Hg and Protoporphyrin Bound Human Ferrochelatase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Hg and Protoporphyrin Bound Human Ferrochelatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:15.3
occ:1.00
 FE1 B:FES502 0.0 15.3 1.0
S2 B:FES502 2.2 17.2 1.0
S1 B:FES502 2.2 15.7 1.0
SG B:CYS906 2.3 16.2 1.0
SG B:CYS911 2.3 17.2 1.0
FE2 B:FES502 2.7 15.3 1.0
CB B:CYS911 3.2 16.3 1.0
CB B:CYS906 3.3 14.7 1.0
O B:HOH161 4.1 24.4 1.0
CA B:CYS906 4.2 16.4 1.0
O B:HOH64 4.2 18.3 1.0
CB B:ASN908 4.3 19.2 1.0
O B:HOH67 4.4 21.8 1.0
O B:HOH469 4.4 32.1 1.0
SG B:CYS696 4.5 17.2 1.0
O B:ASN908 4.5 20.6 1.0
CA B:CYS911 4.7 15.6 1.0
SG B:CYS903 4.7 14.7 1.0
N B:ASN908 4.8 20.2 1.0
N B:CYS903 4.9 14.4 1.0
CB B:CYS903 4.9 12.5 1.0
CB B:CYS696 4.9 13.9 1.0
CB B:SER902 4.9 22.1 1.0
C B:CYS906 5.0 17.4 1.0

Iron binding site 5 out of 6 in 3hcn

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Iron binding site 5 out of 6 in the Hg and Protoporphyrin Bound Human Ferrochelatase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Hg and Protoporphyrin Bound Human Ferrochelatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:15.3
occ:1.00
 FE2 B:FES502 0.0 15.3 1.0
S2 B:FES502 2.2 17.2 1.0
S1 B:FES502 2.2 15.7 1.0
SG B:CYS696 2.3 17.2 1.0
SG B:CYS903 2.3 14.7 1.0
FE1 B:FES502 2.7 15.3 1.0
CB B:CYS903 3.4 12.5 1.0
CB B:CYS696 3.4 13.9 1.0
O B:HOH16 3.5 19.1 1.0
N B:CYS903 3.9 14.4 1.0
O A:HOH783 4.2 30.7 1.0
CA B:CYS903 4.2 14.2 1.0
O B:HOH161 4.3 24.4 1.0
CB B:CYS906 4.5 14.7 1.0
SG B:CYS911 4.5 17.2 1.0
SG B:CYS906 4.5 16.2 1.0
CA B:CYS696 4.8 13.7 1.0
NE B:ARG772 4.9 24.9 1.0

Iron binding site 6 out of 6 in 3hcn

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Iron binding site 6 out of 6 in the Hg and Protoporphyrin Bound Human Ferrochelatase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Hg and Protoporphyrin Bound Human Ferrochelatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe926

b:15.0
occ:1.00
 FE B:HEM926 0.0 15.0 1.0
ND B:HEM926 2.0 16.8 1.0
NA B:HEM926 2.0 16.6 1.0
NB B:HEM926 2.0 17.8 1.0
NC B:HEM926 2.0 13.4 1.0
N1 B:IMD925 2.3 20.9 1.0
N1 B:IMD3 2.3 20.8 1.0
C1D B:HEM926 3.0 15.9 1.0
C4C B:HEM926 3.0 16.8 1.0
C4D B:HEM926 3.0 16.6 1.0
C1B B:HEM926 3.0 17.2 1.0
C4A B:HEM926 3.0 18.9 1.0
C1C B:HEM926 3.0 15.4 1.0
C1A B:HEM926 3.1 19.2 1.0
C4B B:HEM926 3.1 14.8 1.0
C5 B:IMD925 3.2 19.0 1.0
C5 B:IMD3 3.2 21.2 1.0
C2 B:IMD925 3.3 19.8 1.0
C2 B:IMD3 3.3 21.3 1.0
CHB B:HEM926 3.4 19.2 1.0
CHD B:HEM926 3.4 16.6 1.0
CHA B:HEM926 3.4 17.9 1.0
CHC B:HEM926 3.4 14.4 1.0
C3A B:HEM926 4.2 18.7 1.0
C3D B:HEM926 4.3 16.9 1.0
C2A B:HEM926 4.3 18.9 1.0
C2D B:HEM926 4.3 17.6 1.0
C2B B:HEM926 4.3 17.8 1.0
C2C B:HEM926 4.3 14.0 1.0
C3B B:HEM926 4.3 16.3 1.0
C4 B:IMD925 4.3 20.3 1.0
C3C B:HEM926 4.3 15.1 1.0
N3 B:IMD925 4.3 21.0 1.0
C4 B:IMD3 4.4 22.1 1.0
N3 B:IMD3 4.4 22.4 1.0
CD2 B:HIS763 4.9 17.7 1.0

Reference:

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
Page generated: Tue Aug 5 01:54:41 2025

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