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Iron in PDB 2qd1: 2.2 Angstrom Structure of the Human Ferrochelatase Variant E343K with Substrate Bound

Enzymatic activity of 2.2 Angstrom Structure of the Human Ferrochelatase Variant E343K with Substrate Bound

All present enzymatic activity of 2.2 Angstrom Structure of the Human Ferrochelatase Variant E343K with Substrate Bound:
4.99.1.1;

Protein crystallography data

The structure of 2.2 Angstrom Structure of the Human Ferrochelatase Variant E343K with Substrate Bound, PDB code: 2qd1 was solved by A.E.Medlock, T.A.Dailey, T.A.Ross, 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) 42.08 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 61.893, 88.454, 93.100, 102.49, 108.99, 105.55
R / Rfree (%) 22.2 / 26.1

Iron Binding Sites:

The binding sites of Iron atom in the 2.2 Angstrom Structure of the Human Ferrochelatase Variant E343K with Substrate Bound (pdb code 2qd1). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the 2.2 Angstrom Structure of the Human Ferrochelatase Variant E343K with Substrate Bound, PDB code: 2qd1:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 2qd1

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Iron binding site 1 out of 8 in the 2.2 Angstrom Structure of the Human Ferrochelatase Variant E343K with Substrate Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 2.2 Angstrom Structure of the Human Ferrochelatase Variant E343K with Substrate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1001

b:31.0
occ:1.00
 FE1 A:FES1001 0.0 31.0 1.0
S2 A:FES1001 2.2 31.9 1.0
S1 A:FES1001 2.2 31.5 1.0
SG A:CYS411 2.3 32.7 1.0
SG A:CYS406 2.3 31.6 1.0
FE2 A:FES1001 2.7 30.5 1.0
CB A:CYS411 3.2 34.5 1.0
CB A:CYS406 3.4 32.2 1.0
O A:HOH1043 4.0 39.9 1.0
O A:HOH1048 4.2 26.4 1.0
CB A:ASN408 4.2 33.5 1.0
CA A:CYS406 4.2 32.1 1.0
SG A:CYS196 4.4 26.9 1.0
SG A:CYS403 4.5 32.2 1.0
O A:ASN408 4.6 34.0 1.0
CA A:CYS411 4.7 35.5 1.0
CB A:CYS403 4.7 30.7 1.0
N A:CYS403 4.7 30.8 1.0
CB A:SER402 4.8 30.6 1.0
N A:ASN408 4.9 34.2 1.0

Iron binding site 2 out of 8 in 2qd1

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Iron binding site 2 out of 8 in the 2.2 Angstrom Structure of the Human Ferrochelatase Variant E343K with Substrate Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 2.2 Angstrom Structure of the Human Ferrochelatase Variant E343K with Substrate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1001

b:30.5
occ:1.00
 FE2 A:FES1001 0.0 30.5 1.0
S2 A:FES1001 2.2 31.9 1.0
S1 A:FES1001 2.2 31.5 1.0
SG A:CYS196 2.3 26.9 1.0
SG A:CYS403 2.3 32.2 1.0
FE1 A:FES1001 2.7 31.0 1.0
CB A:CYS196 3.4 22.3 1.0
CB A:CYS403 3.4 30.7 1.0
O A:HOH1047 3.7 23.2 1.0
N A:CYS403 3.8 30.8 1.0
CA A:CYS403 4.2 30.6 1.0
SG A:CYS406 4.5 31.6 1.0
SG A:CYS411 4.5 32.7 1.0
CB A:CYS406 4.5 32.2 1.0
CD A:ARG272 4.6 27.4 1.0
CA A:CYS196 4.7 19.8 1.0
C A:SER402 5.0 30.7 1.0

Iron binding site 3 out of 8 in 2qd1

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Iron binding site 3 out of 8 in the 2.2 Angstrom Structure of the Human Ferrochelatase Variant E343K with Substrate Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of 2.2 Angstrom Structure of the Human Ferrochelatase Variant E343K with Substrate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:31.6
occ:1.00
 FE1 B:FES1002 0.0 31.6 1.0
S1 B:FES1002 2.2 31.9 1.0
S2 B:FES1002 2.2 31.9 1.0
SG B:CYS411 2.3 33.1 1.0
SG B:CYS406 2.3 32.1 1.0
FE2 B:FES1002 2.7 31.1 1.0
CB B:CYS411 3.2 34.8 1.0
CB B:CYS406 3.4 31.6 1.0
O B:HOH1119 4.0 32.6 1.0
O B:HOH1123 4.2 33.8 1.0
O B:HOH1166 4.2 49.1 1.0
CA B:CYS406 4.2 31.5 1.0
CB B:ASN408 4.4 33.5 1.0
SG B:CYS196 4.4 27.8 1.0
SG B:CYS403 4.5 30.6 1.0
O B:ASN408 4.6 34.7 1.0
N B:CYS403 4.6 29.9 1.0
CB B:CYS403 4.6 30.1 1.0
CA B:CYS411 4.6 36.0 1.0
CB B:SER402 4.8 30.5 1.0
N B:ASN408 4.9 34.3 1.0

Iron binding site 4 out of 8 in 2qd1

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Iron binding site 4 out of 8 in the 2.2 Angstrom Structure of the Human Ferrochelatase Variant E343K with Substrate Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of 2.2 Angstrom Structure of the Human Ferrochelatase Variant E343K with Substrate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:31.1
occ:1.00
 FE2 B:FES1002 0.0 31.1 1.0
S1 B:FES1002 2.2 31.9 1.0
S2 B:FES1002 2.2 31.9 1.0
SG B:CYS196 2.3 27.8 1.0
SG B:CYS403 2.3 30.6 1.0
FE1 B:FES1002 2.7 31.6 1.0
CB B:CYS403 3.4 30.1 1.0
CB B:CYS196 3.4 23.1 1.0
O B:HOH1166 3.6 49.1 1.0
O B:HOH1056 3.7 31.9 1.0
N B:CYS403 3.8 29.9 1.0
O D:HOH1072 4.0 31.9 1.0
CA B:CYS403 4.2 29.9 1.0
SG B:CYS411 4.5 33.1 1.0
SG B:CYS406 4.5 32.1 1.0
CB B:CYS406 4.6 31.6 1.0
CD B:ARG272 4.7 27.3 1.0
CA B:CYS196 4.7 20.5 1.0
O B:HOH1119 4.9 32.6 1.0
C B:SER402 4.9 30.0 1.0

Iron binding site 5 out of 8 in 2qd1

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Iron binding site 5 out of 8 in the 2.2 Angstrom Structure of the Human Ferrochelatase Variant E343K with Substrate Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of 2.2 Angstrom Structure of the Human Ferrochelatase Variant E343K with Substrate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1003

b:28.2
occ:1.00
 FE1 C:FES1003 0.0 28.2 1.0
S1 C:FES1003 2.2 28.7 1.0
S2 C:FES1003 2.3 29.2 1.0
SG C:CYS411 2.3 32.2 1.0
SG C:CYS406 2.3 28.4 1.0
FE2 C:FES1003 2.7 28.0 1.0
CB C:CYS411 3.3 33.7 1.0
CB C:CYS406 3.4 29.5 1.0
O C:HOH1078 4.2 32.7 1.0
CA C:CYS406 4.3 30.5 1.0
CB C:ASN408 4.3 35.1 1.0
O C:HOH1079 4.4 34.6 1.0
SG C:CYS196 4.5 24.7 1.0
SG C:CYS403 4.6 30.1 1.0
O C:ASN408 4.6 34.7 1.0
N C:CYS403 4.7 29.4 1.0
CA C:CYS411 4.7 34.9 1.0
CB C:CYS403 4.7 29.3 1.0
O C:HOH1026 4.8 26.8 1.0
CB C:SER402 4.8 30.1 1.0
N C:ASN408 4.9 34.0 1.0
CB C:CYS196 5.0 19.3 1.0

Iron binding site 6 out of 8 in 2qd1

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Iron binding site 6 out of 8 in the 2.2 Angstrom Structure of the Human Ferrochelatase Variant E343K with Substrate Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of 2.2 Angstrom Structure of the Human Ferrochelatase Variant E343K with Substrate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1003

b:28.0
occ:1.00
 FE2 C:FES1003 0.0 28.0 1.0
S1 C:FES1003 2.2 28.7 1.0
S2 C:FES1003 2.2 29.2 1.0
SG C:CYS196 2.3 24.7 1.0
SG C:CYS403 2.3 30.1 1.0
FE1 C:FES1003 2.7 28.2 1.0
CB C:CYS196 3.4 19.3 1.0
CB C:CYS403 3.4 29.3 1.0
O C:HOH1031 3.7 21.2 1.0
N C:CYS403 3.8 29.4 1.0
CA C:CYS403 4.2 29.5 1.0
SG C:CYS411 4.5 32.2 1.0
SG C:CYS406 4.5 28.4 1.0
O C:HOH1078 4.5 32.7 1.0
CB C:CYS406 4.6 29.5 1.0
CD C:ARG272 4.6 27.9 1.0
NH1 C:ARG272 4.7 30.1 1.0
CA C:CYS196 4.7 16.4 1.0
C C:SER402 4.9 29.7 1.0

Iron binding site 7 out of 8 in 2qd1

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Iron binding site 7 out of 8 in the 2.2 Angstrom Structure of the Human Ferrochelatase Variant E343K with Substrate Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of 2.2 Angstrom Structure of the Human Ferrochelatase Variant E343K with Substrate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1004

b:28.5
occ:1.00
 FE1 D:FES1004 0.0 28.5 1.0
S2 D:FES1004 2.2 28.1 1.0
S1 D:FES1004 2.2 29.0 1.0
SG D:CYS411 2.3 32.0 1.0
SG D:CYS406 2.3 29.9 1.0
FE2 D:FES1004 2.7 27.3 1.0
CB D:CYS411 3.3 33.2 1.0
CB D:CYS406 3.4 29.8 1.0
CB D:ASN408 4.2 31.9 1.0
CA D:CYS406 4.2 30.1 1.0
O D:HOH1073 4.4 29.1 1.0
O D:HOH1042 4.4 29.3 1.0
O D:ASN408 4.5 33.2 1.0
SG D:CYS196 4.5 23.6 1.0
SG D:CYS403 4.6 28.7 1.0
CA D:CYS411 4.7 34.5 1.0
N D:ASN408 4.7 31.9 1.0
CB D:CYS403 4.7 28.8 1.0
N D:CYS403 4.8 28.7 1.0
CB D:SER402 4.8 29.8 1.0
CA D:ASN408 4.9 32.1 1.0
C D:CYS406 5.0 30.3 1.0

Iron binding site 8 out of 8 in 2qd1

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Iron binding site 8 out of 8 in the 2.2 Angstrom Structure of the Human Ferrochelatase Variant E343K with Substrate Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of 2.2 Angstrom Structure of the Human Ferrochelatase Variant E343K with Substrate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1004

b:27.3
occ:1.00
 FE2 D:FES1004 0.0 27.3 1.0
S2 D:FES1004 2.2 28.1 1.0
S1 D:FES1004 2.2 29.0 1.0
SG D:CYS196 2.3 23.6 1.0
SG D:CYS403 2.3 28.7 1.0
FE1 D:FES1004 2.7 28.5 1.0
CB D:CYS403 3.4 28.8 1.0
CB D:CYS196 3.4 20.3 1.0
O D:HOH1052 3.7 17.6 1.0
N D:CYS403 3.8 28.7 1.0
CA D:CYS403 4.2 28.5 1.0
CD D:ARG272 4.4 19.5 0.5
SG D:CYS411 4.5 32.0 1.0
CD D:ARG272 4.5 23.8 0.5
SG D:CYS406 4.5 29.9 1.0
CB D:CYS406 4.5 29.8 1.0
CA D:CYS196 4.8 17.9 1.0
NH1 D:ARG272 4.9 18.0 0.5
C D:SER402 5.0 29.0 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: Thu Jul 17 03:38:22 2025

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