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Iron in PDB 3hcp: Human Ferrochelatase with Mn and Deuteroporphyrin Bound

Enzymatic activity of Human Ferrochelatase with Mn and Deuteroporphyrin Bound

All present enzymatic activity of Human Ferrochelatase with Mn and Deuteroporphyrin Bound:
4.99.1.1;

Protein crystallography data

The structure of Human Ferrochelatase with Mn and Deuteroporphyrin Bound, PDB code: 3hcp 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) 46.83 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.574, 93.687, 109.483, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20.1

Iron Binding Sites:

The binding sites of Iron atom in the Human Ferrochelatase with Mn and Deuteroporphyrin Bound (pdb code 3hcp). 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 Mn and Deuteroporphyrin Bound, PDB code: 3hcp:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 3hcp

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Iron binding site 1 out of 6 in the Human Ferrochelatase with Mn and Deuteroporphyrin 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 Mn and Deuteroporphyrin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:12.7
occ:1.00
 FE1 A:FES501 0.0 12.7 1.0
S2 A:FES501 2.2 13.5 1.0
S1 A:FES501 2.2 8.8 1.0
SG A:CYS411 2.3 13.4 1.0
SG A:CYS406 2.3 10.6 1.0
FE2 A:FES501 2.8 11.0 1.0
CB A:CYS411 3.1 10.6 1.0
CB A:CYS406 3.2 10.3 1.0
O A:HOH43 4.2 16.2 1.0
CA A:CYS406 4.2 10.8 1.0
O A:HOH482 4.2 10.3 1.0
O A:HOH560 4.2 28.6 1.0
CB A:ASN408 4.4 13.6 1.0
O A:ASN408 4.5 15.3 1.0
SG A:CYS196 4.6 13.5 1.0
CA A:CYS411 4.6 11.6 1.0
SG A:CYS403 4.8 9.4 1.0
N A:ASN408 4.8 13.9 1.0
N A:CYS403 4.9 11.0 1.0
CB A:CYS403 4.9 10.4 1.0
CB A:CYS196 5.0 9.7 1.0

Iron binding site 2 out of 6 in 3hcp

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Iron binding site 2 out of 6 in the Human Ferrochelatase with Mn and Deuteroporphyrin 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 Mn and Deuteroporphyrin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:11.0
occ:1.00
 FE2 A:FES501 0.0 11.0 1.0
S1 A:FES501 2.2 8.8 1.0
S2 A:FES501 2.2 13.5 1.0
SG A:CYS403 2.3 9.4 1.0
SG A:CYS196 2.3 13.5 1.0
FE1 A:FES501 2.8 12.7 1.0
CB A:CYS403 3.3 10.4 1.0
CB A:CYS196 3.4 9.7 1.0
O A:HOH29 3.7 15.3 1.0
N A:CYS403 3.9 11.0 1.0
CA A:CYS403 4.2 10.0 1.0
O A:HOH56 4.3 19.2 1.0
CB A:CYS406 4.4 10.3 1.0
O A:HOH560 4.5 28.6 1.0
SG A:CYS406 4.6 10.6 1.0
SG A:CYS411 4.6 13.4 1.0
NE A:ARG272 4.8 18.6 1.0
CA A:CYS196 4.8 9.4 1.0
NH2 B:ARG798 5.0 11.3 1.0
NH2 A:ARG272 5.0 16.8 1.0

Iron binding site 3 out of 6 in 3hcp

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Iron binding site 3 out of 6 in the Human Ferrochelatase with Mn and Deuteroporphyrin 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 Mn and Deuteroporphyrin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe425

b:14.0
occ:1.00
 FE A:FDE425 0.0 14.0 1.0
N1 A:IMD424 1.9 17.2 1.0
NC A:FDE425 2.1 13.9 1.0
NA A:FDE425 2.1 14.5 1.0
ND A:FDE425 2.1 15.5 1.0
NB A:FDE425 2.1 12.2 1.0
C2 A:IMD424 3.0 15.6 1.0
C5 A:IMD424 3.0 15.7 1.0
C1A A:FDE425 3.1 16.9 1.0
C4C A:FDE425 3.1 14.6 1.0
C4A A:FDE425 3.1 13.8 1.0
C1C A:FDE425 3.1 14.5 1.0
C4B A:FDE425 3.1 11.6 1.0
C1B A:FDE425 3.1 12.1 1.0
C4D A:FDE425 3.1 16.7 1.0
C1D A:FDE425 3.1 17.3 1.0
CHB A:FDE425 3.1 13.2 1.0
CHD A:FDE425 3.2 13.2 1.0
CHA A:FDE425 3.4 14.3 1.0
CHC A:FDE425 3.5 13.3 1.0
N3 A:IMD424 4.1 17.2 1.0
C4 A:IMD424 4.2 16.9 1.0
O A:HOH468 4.3 35.2 1.0
C3C A:FDE425 4.3 14.8 1.0
C2C A:FDE425 4.3 14.4 1.0
C3D A:FDE425 4.3 14.5 1.0
C3B A:FDE425 4.4 11.3 1.0
C2D A:FDE425 4.4 15.9 1.0
C2A A:FDE425 4.4 14.3 1.0
C2B A:FDE425 4.4 11.2 1.0
C3A A:FDE425 4.4 14.4 1.0

Iron binding site 4 out of 6 in 3hcp

Go back to Iron Binding Sites List in 3hcp
Iron binding site 4 out of 6 in the Human Ferrochelatase with Mn and Deuteroporphyrin 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 Mn and Deuteroporphyrin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:14.1
occ:1.00
 FE1 B:FES501 0.0 14.1 1.0
S2 B:FES501 2.2 15.9 1.0
S1 B:FES501 2.3 10.2 1.0
SG B:CYS906 2.3 11.9 1.0
SG B:CYS911 2.3 14.6 1.0
FE2 B:FES501 2.8 11.7 1.0
CB B:CYS911 3.2 13.2 1.0
CB B:CYS906 3.3 11.5 1.0
O B:HOH206 4.1 25.8 1.0
O B:HOH28 4.2 10.7 1.0
CA B:CYS906 4.2 12.3 1.0
O B:HOH138 4.2 20.5 1.0
CB B:ASN908 4.4 14.5 1.0
O B:ASN908 4.5 15.4 1.0
SG B:CYS696 4.6 14.2 1.0
CA B:CYS911 4.6 13.9 1.0
SG B:CYS903 4.8 10.3 1.0
N B:ASN908 4.8 15.9 1.0
N B:CYS903 4.9 12.6 1.0
CB B:CYS903 4.9 11.2 1.0
CB B:SER902 5.0 14.8 1.0

Iron binding site 5 out of 6 in 3hcp

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Iron binding site 5 out of 6 in the Human Ferrochelatase with Mn and Deuteroporphyrin 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 Mn and Deuteroporphyrin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:11.7
occ:1.00
 FE2 B:FES501 0.0 11.7 1.0
S2 B:FES501 2.2 15.9 1.0
S1 B:FES501 2.2 10.2 1.0
SG B:CYS696 2.3 14.2 1.0
SG B:CYS903 2.3 10.3 1.0
FE1 B:FES501 2.8 14.1 1.0
CB B:CYS903 3.3 11.2 1.0
CB B:CYS696 3.5 10.0 1.0
O B:HOH32 3.7 14.8 1.0
N B:CYS903 3.9 12.6 1.0
CA B:CYS903 4.2 11.9 1.0
O B:HOH213 4.4 20.6 1.0
O B:HOH206 4.4 25.8 1.0
CB B:CYS906 4.5 11.5 1.0
SG B:CYS906 4.6 11.9 1.0
SG B:CYS911 4.6 14.6 1.0
CA B:CYS696 4.8 10.7 1.0
NE B:ARG772 4.8 21.2 1.0
NH2 A:ARG298 4.9 11.1 1.0

Iron binding site 6 out of 6 in 3hcp

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Iron binding site 6 out of 6 in the Human Ferrochelatase with Mn and Deuteroporphyrin 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 Mn and Deuteroporphyrin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe925

b:22.8
occ:1.00
 FE B:FDE925 0.0 22.8 1.0
N1 B:IMD924 1.9 29.7 1.0
NA B:FDE925 2.1 22.3 1.0
NC B:FDE925 2.1 22.4 1.0
NB B:FDE925 2.1 20.9 1.0
ND B:FDE925 2.1 23.8 1.0
C2 B:IMD924 2.9 28.6 1.0
C5 B:IMD924 2.9 28.2 1.0
C4A B:FDE925 3.0 24.1 1.0
CHB B:FDE925 3.1 21.9 1.0
C4C B:FDE925 3.1 22.5 1.0
C1A B:FDE925 3.1 26.2 1.0
C1B B:FDE925 3.1 21.2 1.0
C1D B:FDE925 3.1 23.8 1.0
C1C B:FDE925 3.1 23.7 1.0
CHD B:FDE925 3.1 23.4 1.0
C4B B:FDE925 3.1 21.4 1.0
C4D B:FDE925 3.2 24.9 1.0
CHA B:FDE925 3.5 23.3 1.0
CHC B:FDE925 3.5 22.1 1.0
N3 B:IMD924 4.1 29.8 1.0
C4 B:IMD924 4.1 29.6 1.0
O B:HOH225 4.1 41.6 1.0
C3C B:FDE925 4.3 22.7 1.0
C2C B:FDE925 4.3 22.6 1.0
C2D B:FDE925 4.4 24.4 1.0
C3D B:FDE925 4.4 23.1 1.0
C3B B:FDE925 4.4 21.0 1.0
C3A B:FDE925 4.4 24.3 1.0
C2A B:FDE925 4.4 24.6 1.0
C2B B:FDE925 4.4 20.2 1.0
O B:HOH523 4.7 61.5 1.0
ND1 B:HIS763 5.0 24.9 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: Sun Aug 4 11:25:53 2024

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