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Iron in PDB 3hcr: Human Ferrochelatase with Deuteroporphyrin and Ni Bound

Enzymatic activity of Human Ferrochelatase with Deuteroporphyrin and Ni Bound

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

Protein crystallography data

The structure of Human Ferrochelatase with Deuteroporphyrin and Ni Bound, PDB code: 3hcr 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) 47.32 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.423, 92.935, 109.973, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 25

Other elements in 3hcr:

The structure of Human Ferrochelatase with Deuteroporphyrin and Ni Bound also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Iron Binding Sites:

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

Iron binding site 1 out of 6 in 3hcr

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

b:28.8
occ:1.00
 FE1 A:FES501 0.0 28.8 1.0
S2 A:FES501 2.2 27.6 1.0
S1 A:FES501 2.2 26.4 1.0
SG A:CYS411 2.3 25.6 1.0
SG A:CYS406 2.4 26.1 1.0
FE2 A:FES501 2.7 29.1 1.0
CB A:CYS411 3.3 26.6 1.0
CB A:CYS406 3.4 26.4 1.0
CB A:ASN408 4.3 33.2 1.0
CA A:CYS406 4.3 28.4 1.0
O A:HOH481 4.3 25.0 1.0
O A:HOH452 4.3 28.8 1.0
SG A:CYS196 4.4 28.9 1.0
O A:ASN408 4.6 32.9 1.0
O A:HOH534 4.7 59.2 1.0
CA A:CYS411 4.7 28.5 1.0
SG A:CYS403 4.7 25.0 1.0
N A:ASN408 4.9 31.6 1.0
CB A:CYS196 4.9 27.5 1.0
CB A:CYS403 4.9 24.4 1.0
N A:CYS403 5.0 22.9 1.0
O A:HOH482 5.0 27.8 1.0

Iron binding site 2 out of 6 in 3hcr

Go back to Iron Binding Sites List in 3hcr
Iron binding site 2 out of 6 in the Human Ferrochelatase with Deuteroporphyrin and Ni 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 Deuteroporphyrin and Ni Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:29.1
occ:1.00
 FE2 A:FES501 0.0 29.1 1.0
S1 A:FES501 2.2 26.4 1.0
S2 A:FES501 2.2 27.6 1.0
SG A:CYS196 2.3 28.9 1.0
SG A:CYS403 2.3 25.0 1.0
FE1 A:FES501 2.7 28.8 1.0
CB A:CYS403 3.3 24.4 1.0
CB A:CYS196 3.5 27.5 1.0
O A:HOH8 3.5 26.1 1.0
N A:CYS403 3.9 22.9 1.0
CA A:CYS403 4.2 22.9 1.0
O A:HOH447 4.4 25.6 1.0
SG A:CYS411 4.5 25.6 1.0
SG A:CYS406 4.5 26.1 1.0
CB A:CYS406 4.6 26.4 1.0
CA A:CYS196 4.8 22.8 1.0
NH2 B:ARG798 4.9 28.3 1.0
NE A:ARG272 5.0 39.3 1.0

Iron binding site 3 out of 6 in 3hcr

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Iron binding site 3 out of 6 in the Human Ferrochelatase with Deuteroporphyrin and Ni 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 Deuteroporphyrin and Ni Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe426

b:23.5
occ:1.00
 FE A:FDE426 0.0 23.5 1.0
NA A:FDE426 1.9 21.7 1.0
N1 A:IMD2 2.0 28.9 1.0
NC A:FDE426 2.1 26.8 1.0
NB A:FDE426 2.1 23.8 1.0
ND A:FDE426 2.1 26.9 1.0
C4A A:FDE426 2.9 23.6 1.0
C1A A:FDE426 2.9 24.4 1.0
C2 A:IMD2 2.9 27.2 1.0
C4C A:FDE426 3.1 27.8 1.0
O1 A:OXY425 3.1 46.8 1.0
C4B A:FDE426 3.1 24.5 1.0
CHB A:FDE426 3.1 21.1 1.0
C1B A:FDE426 3.1 22.3 1.0
C1C A:FDE426 3.1 28.2 1.0
CHD A:FDE426 3.1 27.7 1.0
C4D A:FDE426 3.1 25.8 1.0
C1D A:FDE426 3.1 27.5 1.0
C5 A:IMD2 3.3 27.6 1.0
CHA A:FDE426 3.4 24.1 1.0
CHC A:FDE426 3.6 25.5 1.0
C3A A:FDE426 4.2 23.6 1.0
N3 A:IMD2 4.2 28.6 1.0
C2A A:FDE426 4.2 25.0 1.0
O2 A:OXY425 4.2 45.0 1.0
C3C A:FDE426 4.3 28.9 1.0
C3B A:FDE426 4.3 22.9 1.0
C2C A:FDE426 4.3 28.1 1.0
C2B A:FDE426 4.4 23.2 1.0
C2D A:FDE426 4.4 28.6 1.0
C3D A:FDE426 4.5 29.1 1.0
C4 A:IMD2 4.5 26.0 1.0
CD2 A:HIS263 4.9 24.1 1.0

Iron binding site 4 out of 6 in 3hcr

Go back to Iron Binding Sites List in 3hcr
Iron binding site 4 out of 6 in the Human Ferrochelatase with Deuteroporphyrin and Ni 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 Deuteroporphyrin and Ni Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:28.9
occ:1.00
 FE1 B:FES502 0.0 28.9 1.0
S2 B:FES502 2.2 26.6 1.0
S1 B:FES502 2.2 27.5 1.0
SG B:CYS911 2.3 26.4 1.0
SG B:CYS906 2.3 28.6 1.0
FE2 B:FES502 2.7 28.9 1.0
CB B:CYS911 3.2 28.4 1.0
CB B:CYS906 3.4 28.4 1.0
O B:HOH104 4.2 40.8 1.0
CB B:ASN908 4.2 36.8 1.0
O B:HOH254 4.3 32.6 1.0
CA B:CYS906 4.4 29.6 1.0
SG B:CYS696 4.4 29.4 1.0
O B:ASN908 4.6 37.6 1.0
CA B:CYS911 4.7 30.5 1.0
SG B:CYS903 4.8 25.4 1.0
CB B:CYS696 4.8 27.6 1.0
N B:ASN908 4.9 36.7 1.0
N B:CYS903 5.0 24.2 1.0
CB B:CYS903 5.0 25.9 1.0

Iron binding site 5 out of 6 in 3hcr

Go back to Iron Binding Sites List in 3hcr
Iron binding site 5 out of 6 in the Human Ferrochelatase with Deuteroporphyrin and Ni 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 Deuteroporphyrin and Ni Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:28.9
occ:1.00
 FE2 B:FES502 0.0 28.9 1.0
S1 B:FES502 2.2 27.5 1.0
S2 B:FES502 2.3 26.6 1.0
SG B:CYS696 2.3 29.4 1.0
SG B:CYS903 2.3 25.4 1.0
FE1 B:FES502 2.7 28.9 1.0
CB B:CYS903 3.4 25.9 1.0
CB B:CYS696 3.4 27.6 1.0
O B:HOH22 3.6 28.5 1.0
N B:CYS903 3.9 24.2 1.0
O B:HOH99 4.2 37.0 1.0
CA B:CYS903 4.3 24.6 1.0
SG B:CYS906 4.5 28.6 1.0
CB B:CYS906 4.6 28.4 1.0
SG B:CYS911 4.6 26.4 1.0
CA B:CYS696 4.8 24.9 1.0
NE B:ARG772 4.9 35.5 1.0

Iron binding site 6 out of 6 in 3hcr

Go back to Iron Binding Sites List in 3hcr
Iron binding site 6 out of 6 in the Human Ferrochelatase with Deuteroporphyrin and Ni 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 Deuteroporphyrin and Ni Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe927

b:24.4
occ:1.00
 FE B:FDE927 0.0 24.4 1.0
N1 B:IMD1 1.9 31.1 1.0
NA B:FDE927 1.9 23.7 1.0
NC B:FDE927 2.1 25.4 1.0
ND B:FDE927 2.1 28.1 1.0
NB B:FDE927 2.1 23.6 1.0
C5 B:IMD1 2.8 29.2 1.0
C4A B:FDE927 2.9 25.7 1.0
O1 B:OXY926 2.9 44.8 1.0
C1A B:FDE927 3.0 27.0 1.0
CHB B:FDE927 3.0 22.7 1.0
C2 B:IMD1 3.0 30.7 1.0
C4C B:FDE927 3.1 26.4 1.0
C1B B:FDE927 3.1 22.3 1.0
C4D B:FDE927 3.1 28.0 1.0
CHD B:FDE927 3.1 26.9 1.0
C1D B:FDE927 3.1 28.7 1.0
C4B B:FDE927 3.1 23.6 1.0
C1C B:FDE927 3.1 25.3 1.0
CHA B:FDE927 3.4 27.0 1.0
CHC B:FDE927 3.6 24.6 1.0
C4 B:IMD1 4.0 29.6 1.0
O2 B:OXY926 4.1 44.3 1.0
N3 B:IMD1 4.1 28.8 1.0
C3A B:FDE927 4.2 24.7 1.0
C2A B:FDE927 4.3 26.3 1.0
C3C B:FDE927 4.3 25.6 1.0
C2C B:FDE927 4.3 24.4 1.0
C2B B:FDE927 4.3 21.3 1.0
C3B B:FDE927 4.4 21.8 1.0
C2D B:FDE927 4.4 29.8 1.0
C3D B:FDE927 4.4 30.9 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 11:26:11 2024

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