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Iron in PDB 2qd2: F110A Variant of Human Ferrochelatase with Protoheme Bound

Enzymatic activity of F110A Variant of Human Ferrochelatase with Protoheme Bound

All present enzymatic activity of F110A Variant of Human Ferrochelatase with Protoheme Bound:
4.99.1.1;

Protein crystallography data

The structure of F110A Variant of Human Ferrochelatase with Protoheme Bound, PDB code: 2qd2 was solved by A.E.Medlock, T.A.Dailey, T.A.Ross, H.A.Dailey, W.N.Lanzilota, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.99 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.203, 92.644, 109.030, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 26.1

Iron Binding Sites:

The binding sites of Iron atom in the F110A Variant of Human Ferrochelatase with Protoheme Bound (pdb code 2qd2). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the F110A Variant of Human Ferrochelatase with Protoheme Bound, PDB code: 2qd2:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 2qd2

Go back to Iron Binding Sites List in 2qd2
Iron binding site 1 out of 6 in the F110A Variant of Human Ferrochelatase with Protoheme Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of F110A Variant of Human Ferrochelatase with Protoheme Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe424

b:24.6
occ:1.00
 FE1 A:FES424 0.0 24.6 1.0
S2 A:FES424 2.2 25.2 1.0
S1 A:FES424 2.2 26.2 1.0
SG A:CYS411 2.3 25.5 1.0
SG A:CYS406 2.3 26.7 1.0
FE2 A:FES424 2.7 24.8 1.0
CB A:CYS411 3.2 26.3 1.0
CB A:CYS406 3.4 26.4 1.0
O A:HOH713 3.8 36.8 1.0
CA A:CYS406 4.3 27.0 1.0
O A:HOH644 4.3 23.6 1.0
O A:HOH630 4.3 20.8 1.0
CB A:ASN408 4.4 29.7 1.0
SG A:CYS196 4.4 25.6 1.0
O A:ASN408 4.4 30.3 1.0
SG A:CYS403 4.6 25.2 1.0
CA A:CYS411 4.7 27.3 1.0
CB A:CYS403 4.8 24.0 1.0
N A:CYS403 4.8 24.1 1.0
N A:ASN408 4.9 30.0 1.0
CB A:CYS196 4.9 23.2 1.0
CB A:SER402 4.9 26.2 1.0
OG A:SER402 5.0 28.6 1.0
C A:CYS406 5.0 27.5 1.0

Iron binding site 2 out of 6 in 2qd2

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Iron binding site 2 out of 6 in the F110A Variant of Human Ferrochelatase with Protoheme Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of F110A Variant of Human Ferrochelatase with Protoheme Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe424

b:24.8
occ:1.00
 FE2 A:FES424 0.0 24.8 1.0
S1 A:FES424 2.2 26.2 1.0
S2 A:FES424 2.3 25.2 1.0
SG A:CYS196 2.3 25.6 1.0
SG A:CYS403 2.3 25.2 1.0
FE1 A:FES424 2.7 24.6 1.0
CB A:CYS196 3.4 23.2 1.0
CB A:CYS403 3.4 24.0 1.0
O A:HOH713 3.6 36.8 1.0
O A:HOH616 3.7 22.2 1.0
N A:CYS403 3.9 24.1 1.0
CA A:CYS403 4.2 24.1 1.0
O A:HOH797 4.2 47.1 1.0
SG A:CYS411 4.4 25.5 1.0
SG A:CYS406 4.5 26.7 1.0
CB A:CYS406 4.5 26.4 1.0
CA A:CYS196 4.8 22.1 1.0
C A:SER402 5.0 25.1 1.0

Iron binding site 3 out of 6 in 2qd2

Go back to Iron Binding Sites List in 2qd2
Iron binding site 3 out of 6 in the F110A Variant of Human Ferrochelatase with Protoheme Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of F110A Variant of Human Ferrochelatase with Protoheme Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:26.2
occ:1.00
 FE A:HEM602 0.0 26.2 1.0
NA A:HEM602 2.0 28.6 1.0
NC A:HEM602 2.0 27.5 1.0
ND A:HEM602 2.0 27.9 1.0
NB A:HEM602 2.0 27.3 1.0
N3 A:IMD425 2.4 34.5 1.0
O1 A:BCT1 2.6 50.9 1.0
C1D A:HEM602 3.0 28.5 1.0
C4C A:HEM602 3.0 26.6 1.0
C4A A:HEM602 3.0 28.3 1.0
C1C A:HEM602 3.0 26.1 1.0
C1B A:HEM602 3.0 27.1 1.0
C4D A:HEM602 3.0 28.9 1.0
C1A A:HEM602 3.1 28.4 1.0
C4B A:HEM602 3.1 26.8 1.0
C2 A:IMD425 3.3 34.1 1.0
CHD A:HEM602 3.3 27.7 1.0
CHB A:HEM602 3.3 27.7 1.0
C4 A:IMD425 3.4 34.5 1.0
CHA A:HEM602 3.4 28.6 1.0
CHC A:HEM602 3.4 26.5 1.0
C A:BCT1 3.6 51.3 1.0
O3 A:BCT1 4.0 51.1 1.0
C3A A:HEM602 4.2 29.0 1.0
C2A A:HEM602 4.3 29.6 1.0
C2D A:HEM602 4.3 29.3 1.0
C2C A:HEM602 4.3 25.9 1.0
C3B A:HEM602 4.3 26.2 1.0
C3D A:HEM602 4.3 29.6 1.0
C2B A:HEM602 4.3 26.7 1.0
C3C A:HEM602 4.3 26.7 1.0
N1 A:IMD425 4.5 34.6 1.0
C5 A:IMD425 4.5 34.1 1.0
O2 A:BCT1 4.7 51.3 1.0

Iron binding site 4 out of 6 in 2qd2

Go back to Iron Binding Sites List in 2qd2
Iron binding site 4 out of 6 in the F110A Variant of Human Ferrochelatase with Protoheme Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of F110A Variant of Human Ferrochelatase with Protoheme Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe424

b:23.9
occ:1.00
 FE1 B:FES424 0.0 23.9 1.0
S2 B:FES424 2.2 25.6 1.0
S1 B:FES424 2.2 25.0 1.0
SG B:CYS411 2.3 24.7 1.0
SG B:CYS406 2.3 26.5 1.0
FE2 B:FES424 2.7 24.1 1.0
CB B:CYS411 3.2 25.4 1.0
CB B:CYS406 3.4 26.6 1.0
O B:HOH665 4.3 25.9 1.0
CA B:CYS406 4.3 28.3 1.0
O B:HOH620 4.3 22.0 1.0
CB B:ASN408 4.3 29.5 1.0
SG B:CYS196 4.4 24.3 1.0
O B:HOH713 4.4 34.4 1.0
O B:ASN408 4.5 29.2 1.0
SG B:CYS403 4.6 25.4 1.0
CA B:CYS411 4.7 26.6 1.0
CB B:CYS403 4.8 24.8 1.0
N B:CYS403 4.8 25.1 1.0
CB B:CYS196 4.8 21.7 1.0
N B:ASN408 4.9 30.0 1.0
OG B:SER402 5.0 29.6 1.0
CB B:SER402 5.0 27.5 1.0

Iron binding site 5 out of 6 in 2qd2

Go back to Iron Binding Sites List in 2qd2
Iron binding site 5 out of 6 in the F110A Variant of Human Ferrochelatase with Protoheme Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of F110A Variant of Human Ferrochelatase with Protoheme Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe424

b:24.1
occ:1.00
 FE2 B:FES424 0.0 24.1 1.0
S1 B:FES424 2.2 25.0 1.0
S2 B:FES424 2.3 25.6 1.0
SG B:CYS196 2.3 24.3 1.0
SG B:CYS403 2.3 25.4 1.0
FE1 B:FES424 2.7 23.9 1.0
CB B:CYS196 3.4 21.7 1.0
CB B:CYS403 3.4 24.8 1.0
O B:HOH612 3.7 20.2 1.0
N B:CYS403 3.9 25.1 1.0
O B:HOH713 4.0 34.4 1.0
CA B:CYS403 4.2 24.8 1.0
SG B:CYS411 4.5 24.7 1.0
SG B:CYS406 4.5 26.5 1.0
CB B:CYS406 4.6 26.6 1.0
CA B:CYS196 4.8 20.5 1.0
CD B:ARG272 4.8 30.9 1.0
NH1 B:ARG272 4.9 33.2 1.0

Iron binding site 6 out of 6 in 2qd2

Go back to Iron Binding Sites List in 2qd2
Iron binding site 6 out of 6 in the F110A Variant of Human Ferrochelatase with Protoheme Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of F110A Variant of Human Ferrochelatase with Protoheme Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:26.1
occ:1.00
 FE B:HEM601 0.0 26.1 1.0
NA B:HEM601 2.0 28.0 1.0
NC B:HEM601 2.0 27.3 1.0
ND B:HEM601 2.0 27.2 1.0
NB B:HEM601 2.0 27.4 1.0
N3 B:IMD425 2.4 27.8 1.0
O1 B:BCT2 2.8 30.3 1.0
C1D B:HEM601 3.0 27.5 1.0
C4C B:HEM601 3.0 26.6 1.0
C1C B:HEM601 3.0 26.6 1.0
C4A B:HEM601 3.0 28.1 1.0
C1B B:HEM601 3.0 27.4 1.0
C4D B:HEM601 3.0 27.7 1.0
C1A B:HEM601 3.1 28.1 1.0
C4B B:HEM601 3.1 27.4 1.0
CHD B:HEM601 3.3 27.0 1.0
CHB B:HEM601 3.4 27.6 1.0
C4 B:IMD425 3.4 28.2 1.0
C2 B:IMD425 3.4 27.9 1.0
CHA B:HEM601 3.4 28.2 1.0
CHC B:HEM601 3.4 27.4 1.0
C B:BCT2 4.1 31.2 1.0
C3A B:HEM601 4.2 28.6 1.0
C2A B:HEM601 4.3 29.6 1.0
C2C B:HEM601 4.3 26.7 1.0
C2D B:HEM601 4.3 28.0 1.0
C3D B:HEM601 4.3 28.5 1.0
C3B B:HEM601 4.3 27.5 1.0
C2B B:HEM601 4.3 27.6 1.0
C3C B:HEM601 4.3 26.8 1.0
C5 B:IMD425 4.5 28.1 1.0
N1 B:IMD425 4.5 28.7 1.0
O3 B:BCT2 4.9 32.3 1.0
O2 B:BCT2 4.9 32.2 1.0

Reference:

A.E.Medlock, T.A.Dailey, T.A.Ross, H.A.Dailey, W.N.Lanzilotta. A Pi-Helix Switch Selective For Porphyrin Deprotonation and Product Release in Human Ferrochelatase. J.Mol.Biol. V. 373 1006 2007.
ISSN: ISSN 0022-2836
PubMed: 17884090
DOI: 10.1016/J.JMB.2007.08.040
Page generated: Sun Aug 4 01:41:15 2024

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