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Iron in PDB 2hre: Structure of Human Ferrochelatase Variant E343K with Protoporphyrin IX Bound

Enzymatic activity of Structure of Human Ferrochelatase Variant E343K with Protoporphyrin IX Bound

All present enzymatic activity of Structure of Human Ferrochelatase Variant E343K with Protoporphyrin IX Bound:
4.99.1.1;

Protein crystallography data

The structure of Structure of Human Ferrochelatase Variant E343K with Protoporphyrin IX Bound, PDB code: 2hre was solved by A.Medlock, L.Swartz, T.A.Dailey, 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) 43.66 / 2.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 61.952, 88.388, 93.253, 102.41, 109.34, 105.58
R / Rfree (%) 21.6 / 27.9

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Human Ferrochelatase Variant E343K with Protoporphyrin IX Bound (pdb code 2hre). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Structure of Human Ferrochelatase Variant E343K with Protoporphyrin IX Bound, PDB code: 2hre:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 2hre

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Iron binding site 1 out of 8 in the Structure of Human Ferrochelatase Variant E343K with 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 Structure of Human Ferrochelatase Variant E343K with Protoporphyrin IX Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:53.4
occ:1.00
 FE1 A:FES501 0.0 53.4 1.0
S1 A:FES501 2.3 53.3 1.0
S2 A:FES501 2.3 52.2 1.0
SG A:CYS411 2.4 57.0 1.0
SG A:CYS406 2.4 52.8 1.0
FE2 A:FES501 2.7 52.0 1.0
CB A:CYS411 3.1 58.7 1.0
CB A:CYS406 3.4 51.7 1.0
CB A:ASN408 4.2 55.2 1.0
SG A:CYS196 4.3 27.6 1.0
CA A:CYS406 4.4 51.8 1.0
O A:ASN408 4.5 56.2 1.0
CA A:CYS411 4.5 58.6 1.0
CB A:CYS403 4.6 48.2 1.0
N A:CYS403 4.7 46.9 1.0
N A:ASN408 4.7 54.0 1.0
CB A:SER402 4.7 45.6 1.0
SG A:CYS403 4.7 49.0 1.0
CA A:ASN408 4.9 55.0 1.0
N A:VAL407 5.0 52.1 1.0

Iron binding site 2 out of 8 in 2hre

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Iron binding site 2 out of 8 in the Structure of Human Ferrochelatase Variant E343K with 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 Structure of Human Ferrochelatase Variant E343K with Protoporphyrin IX Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:52.0
occ:1.00
 FE2 A:FES501 0.0 52.0 1.0
SG A:CYS196 2.2 27.6 1.0
S2 A:FES501 2.2 52.2 1.0
S1 A:FES501 2.3 53.3 1.0
SG A:CYS403 2.4 49.0 1.0
FE1 A:FES501 2.7 53.4 1.0
CB A:CYS403 3.2 48.2 1.0
CB A:CYS196 3.4 24.1 1.0
N A:CYS403 3.7 46.9 1.0
O A:HOH625 3.9 17.2 1.0
CA A:CYS403 4.1 47.8 1.0
SG A:CYS411 4.5 57.0 1.0
CB A:CYS406 4.6 51.7 1.0
SG A:CYS406 4.6 52.8 1.0
CA A:CYS196 4.7 22.3 1.0
C A:SER402 4.9 46.0 1.0

Iron binding site 3 out of 8 in 2hre

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Iron binding site 3 out of 8 in the Structure of Human Ferrochelatase Variant E343K with 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 Structure of Human Ferrochelatase Variant E343K with Protoporphyrin IX Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:51.0
occ:1.00
 FE1 B:FES502 0.0 51.0 1.0
S2 B:FES502 2.2 50.0 1.0
S1 B:FES502 2.3 49.3 1.0
SG B:CYS411 2.4 61.4 1.0
SG B:CYS406 2.5 41.1 1.0
FE2 B:FES502 2.7 51.4 1.0
CB B:CYS411 3.2 60.0 1.0
NH2 B:ARG272 3.2 44.9 1.0
CB B:CYS406 3.5 43.9 1.0
CZ B:ARG272 3.8 43.8 1.0
CB B:ASN408 4.1 50.2 1.0
NE B:ARG272 4.4 41.3 1.0
CA B:CYS406 4.4 44.9 1.0
NH1 B:ARG272 4.4 46.4 1.0
SG B:CYS196 4.5 21.2 1.0
O B:ASN408 4.6 51.3 1.0
CA B:CYS411 4.6 59.8 1.0
O B:HOH735 4.6 25.4 1.0
CB B:SER402 4.6 39.9 1.0
N B:CYS403 4.6 40.5 1.0
CB B:CYS403 4.7 41.5 1.0
N B:ASN408 4.7 48.6 1.0
OG B:SER402 4.8 40.8 1.0
SG B:CYS403 4.8 41.5 1.0
O B:HOH719 4.9 25.1 1.0
CA B:ASN408 4.9 50.1 1.0

Iron binding site 4 out of 8 in 2hre

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Iron binding site 4 out of 8 in the Structure of Human Ferrochelatase Variant E343K with 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 Structure of Human Ferrochelatase Variant E343K with Protoporphyrin IX Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:51.4
occ:1.00
 FE2 B:FES502 0.0 51.4 1.0
S1 B:FES502 2.2 49.3 1.0
S2 B:FES502 2.3 50.0 1.0
SG B:CYS196 2.3 21.2 1.0
SG B:CYS403 2.6 41.5 1.0
FE1 B:FES502 2.7 51.0 1.0
CB B:CYS403 3.4 41.5 1.0
CB B:CYS196 3.6 16.6 1.0
N B:CYS403 3.8 40.5 1.0
O B:HOH761 3.8 19.5 1.0
CA B:CYS403 4.2 41.6 1.0
SG B:CYS411 4.5 61.4 1.0
CB B:CYS406 4.7 43.9 1.0
SG B:CYS406 4.7 41.1 1.0
O B:HOH735 4.7 25.4 1.0
NE B:ARG272 4.7 41.3 1.0
CZ B:ARG272 4.7 43.8 1.0
NH2 B:ARG272 4.9 44.9 1.0
CA B:CYS196 4.9 17.2 1.0
C B:SER402 4.9 39.9 1.0

Iron binding site 5 out of 8 in 2hre

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Iron binding site 5 out of 8 in the Structure of Human Ferrochelatase Variant E343K with 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 Structure of Human Ferrochelatase Variant E343K with Protoporphyrin IX Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe503

b:47.4
occ:1.00
 FE1 C:FES503 0.0 47.4 1.0
S1 C:FES503 2.2 47.1 1.0
S2 C:FES503 2.3 46.4 1.0
SG C:CYS406 2.5 44.4 1.0
SG C:CYS411 2.5 63.4 1.0
FE2 C:FES503 2.7 47.3 1.0
CB C:CYS411 3.2 63.3 1.0
CB C:CYS406 3.4 45.0 1.0
CA C:CYS406 4.2 44.7 1.0
CB C:ASN408 4.4 47.9 1.0
O C:ASN408 4.4 51.7 1.0
SG C:CYS196 4.4 24.1 1.0
CA C:CYS411 4.6 62.6 1.0
N C:CYS403 4.6 41.4 1.0
CB C:CYS403 4.6 42.1 1.0
N C:ASN408 4.7 48.5 1.0
CB C:SER402 4.8 41.0 1.0
SG C:CYS403 4.8 42.6 1.0
O C:HOH678 4.8 42.6 1.0
C C:CYS406 4.9 44.8 1.0
N C:CYS411 4.9 60.8 1.0

Iron binding site 6 out of 8 in 2hre

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Iron binding site 6 out of 8 in the Structure of Human Ferrochelatase Variant E343K with 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 Structure of Human Ferrochelatase Variant E343K with Protoporphyrin IX Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe503

b:47.3
occ:1.00
 FE2 C:FES503 0.0 47.3 1.0
S2 C:FES503 2.2 46.4 1.0
S1 C:FES503 2.3 47.1 1.0
SG C:CYS403 2.4 42.6 1.0
SG C:CYS196 2.4 24.1 1.0
FE1 C:FES503 2.7 47.4 1.0
CB C:CYS403 3.1 42.1 1.0
N C:CYS403 3.6 41.4 1.0
O C:HOH695 3.6 39.1 1.0
CB C:CYS196 3.7 20.8 1.0
CA C:CYS403 3.9 42.4 1.0
O C:HOH650 3.9 36.6 1.0
CB C:CYS406 4.4 45.0 1.0
SG C:CYS406 4.6 44.4 1.0
C C:SER402 4.7 40.8 1.0
SG C:CYS411 4.7 63.4 1.0
CA C:CYS196 5.0 19.4 1.0
CB C:CYS411 5.0 63.3 1.0

Iron binding site 7 out of 8 in 2hre

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Iron binding site 7 out of 8 in the Structure of Human Ferrochelatase Variant E343K with Protoporphyrin IX Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of Human Ferrochelatase Variant E343K with Protoporphyrin IX Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe504

b:50.7
occ:1.00
 FE1 D:FES504 0.0 50.7 1.0
S1 D:FES504 2.3 50.9 1.0
S2 D:FES504 2.3 50.0 1.0
SG D:CYS411 2.4 60.3 1.0
SG D:CYS406 2.4 48.7 1.0
FE2 D:FES504 2.7 50.6 1.0
CB D:CYS411 3.3 60.5 1.0
CB D:CYS406 3.3 50.4 1.0
CB D:ASN408 4.0 53.8 1.0
CA D:CYS406 4.2 50.7 1.0
O D:ASN408 4.5 56.2 1.0
N D:ASN408 4.6 54.1 1.0
SG D:CYS196 4.6 24.3 1.0
CB D:CYS403 4.6 44.0 1.0
N D:CYS403 4.7 42.4 1.0
CB D:SER402 4.7 39.1 1.0
CA D:CYS411 4.7 60.7 1.0
CA D:ASN408 4.8 54.8 1.0
N D:VAL407 4.9 51.9 1.0
C D:CYS406 4.9 51.4 1.0
SG D:CYS403 5.0 44.9 1.0
CG D:ASN408 5.0 53.7 1.0

Iron binding site 8 out of 8 in 2hre

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Iron binding site 8 out of 8 in the Structure of Human Ferrochelatase Variant E343K with Protoporphyrin IX Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of Human Ferrochelatase Variant E343K with Protoporphyrin IX Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe504

b:50.6
occ:1.00
 FE2 D:FES504 0.0 50.6 1.0
SG D:CYS196 2.3 24.3 1.0
S2 D:FES504 2.3 50.0 1.0
S1 D:FES504 2.3 50.9 1.0
FE1 D:FES504 2.7 50.7 1.0
SG D:CYS403 2.8 44.9 1.0
CB D:CYS403 3.4 44.0 1.0
CB D:CYS196 3.5 20.1 1.0
N D:CYS403 3.8 42.4 1.0
NH1 D:ARG272 4.1 42.0 1.0
CA D:CYS403 4.2 43.8 1.0
SG D:CYS411 4.4 60.3 1.0
CB D:CYS406 4.7 50.4 1.0
CA D:CYS196 4.8 18.8 1.0
SG D:CYS406 4.8 48.7 1.0
C D:SER402 4.9 40.6 1.0

Reference:

A.Medlock, L.Swartz, T.A.Dailey, H.A.Dailey, W.N.Lanzilotta. Substrate Interactions with Human Ferrochelatase Proc.Natl.Acad.Sci.Usa V. 104 1789 2007.
ISSN: ISSN 0027-8424
PubMed: 17261801
DOI: 10.1073/PNAS.0606144104
Page generated: Sun Dec 13 14:46:29 2020

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