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Iron in PDB 2b3y: Structure of A Monoclinic Crystal Form of Human Cytosolic Aconitase (IRP1)

Enzymatic activity of Structure of A Monoclinic Crystal Form of Human Cytosolic Aconitase (IRP1)

All present enzymatic activity of Structure of A Monoclinic Crystal Form of Human Cytosolic Aconitase (IRP1):
4.2.1.3;

Protein crystallography data

The structure of Structure of A Monoclinic Crystal Form of Human Cytosolic Aconitase (IRP1), PDB code: 2b3y was solved by J.Dupuy, J.C.Fontecilla-Camps, A.Volbeda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.50 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.910, 215.470, 64.010, 90.00, 72.00, 90.00
R / Rfree (%) 21.1 / 26.1

Iron Binding Sites:

The binding sites of Iron atom in the Structure of A Monoclinic Crystal Form of Human Cytosolic Aconitase (IRP1) (pdb code 2b3y). 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 A Monoclinic Crystal Form of Human Cytosolic Aconitase (IRP1), PDB code: 2b3y:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 2b3y

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Iron binding site 1 out of 8 in the Structure of A Monoclinic Crystal Form of Human Cytosolic Aconitase (IRP1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of A Monoclinic Crystal Form of Human Cytosolic Aconitase (IRP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1000

b:25.6
occ:1.00
 FE1 A:SF41000 0.0 25.6 1.0
S3 A:SF41000 2.2 25.3 1.0
S4 A:SF41000 2.3 21.4 1.0
S2 A:SF41000 2.3 21.6 1.0
SG A:CYS437 2.4 26.3 1.0
FE4 A:SF41000 2.7 26.3 1.0
FE2 A:SF41000 2.8 25.1 1.0
FE3 A:SF41000 2.8 22.4 1.0
CB A:CYS437 3.5 22.8 1.0
CG2 A:ILE176 3.7 20.6 1.0
N A:CYS437 3.8 24.8 1.0
S1 A:SF41000 4.0 22.8 1.0
CD2 A:HIS178 4.0 19.9 1.0
CA A:CYS437 4.2 25.5 1.0
O A:HOH1206 4.5 26.4 1.0
OG A:SER436 4.5 22.3 1.0
C A:SER436 4.8 24.4 1.0
SG A:CYS506 4.8 24.0 1.0
SG A:CYS503 4.8 18.2 1.0
N A:THR438 4.9 21.6 1.0
CA A:SER436 4.9 22.4 1.0
NE2 A:HIS178 4.9 19.7 1.0
CG A:HIS178 4.9 18.3 1.0
CB A:ILE176 5.0 17.5 1.0

Iron binding site 2 out of 8 in 2b3y

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Iron binding site 2 out of 8 in the Structure of A Monoclinic Crystal Form of Human Cytosolic Aconitase (IRP1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of A Monoclinic Crystal Form of Human Cytosolic Aconitase (IRP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1000

b:25.1
occ:1.00
 FE2 A:SF41000 0.0 25.1 1.0
S1 A:SF41000 2.3 22.8 1.0
S4 A:SF41000 2.3 21.4 1.0
SG A:CYS506 2.3 24.0 1.0
S3 A:SF41000 2.3 25.3 1.0
FE4 A:SF41000 2.7 26.3 1.0
FE3 A:SF41000 2.7 22.4 1.0
FE1 A:SF41000 2.8 25.6 1.0
CB A:CYS506 3.1 28.9 1.0
O A:HOH1217 3.8 26.1 1.0
OG A:SER436 3.9 22.3 1.0
S2 A:SF41000 3.9 21.6 1.0
CA A:CYS506 4.4 27.8 1.0
CB A:SER436 4.4 24.4 1.0
CA A:SER436 4.4 22.4 1.0
C A:CYS506 4.5 30.0 1.0
CB A:CYS503 4.6 20.4 1.0
O A:HOH1206 4.6 26.4 1.0
OD1 A:ASN535 4.6 26.1 1.0
SG A:CYS437 4.7 26.3 1.0
SG A:CYS503 4.7 18.2 1.0
N A:CYS437 4.8 24.8 1.0
ND2 A:ASN535 4.8 20.6 1.0
N A:ILE507 4.8 26.0 1.0
O A:CYS506 4.9 31.2 1.0

Iron binding site 3 out of 8 in 2b3y

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Iron binding site 3 out of 8 in the Structure of A Monoclinic Crystal Form of Human Cytosolic Aconitase (IRP1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of A Monoclinic Crystal Form of Human Cytosolic Aconitase (IRP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1000

b:22.4
occ:1.00
 FE3 A:SF41000 0.0 22.4 1.0
S2 A:SF41000 2.3 21.6 1.0
S1 A:SF41000 2.3 22.8 1.0
S4 A:SF41000 2.3 21.4 1.0
SG A:CYS503 2.3 18.2 1.0
FE4 A:SF41000 2.6 26.3 1.0
FE2 A:SF41000 2.7 25.1 1.0
FE1 A:SF41000 2.8 25.6 1.0
CB A:CYS503 3.1 20.4 1.0
S3 A:SF41000 3.9 25.3 1.0
CA A:CYS503 3.9 19.0 1.0
NE2 A:HIS126 3.9 25.8 1.0
CE1 A:HIS126 4.0 20.8 1.0
CG2 A:ILE176 4.1 20.6 1.0
O A:HOH1206 4.5 26.4 1.0
N A:CYS503 4.7 19.3 1.0
SG A:CYS506 4.8 24.0 1.0
CD2 A:HIS126 4.8 22.2 1.0
ND1 A:HIS126 4.8 23.8 1.0
CB A:CYS506 4.8 28.9 1.0
O A:HOH1073 5.0 26.8 1.0

Iron binding site 4 out of 8 in 2b3y

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Iron binding site 4 out of 8 in the Structure of A Monoclinic Crystal Form of Human Cytosolic Aconitase (IRP1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of A Monoclinic Crystal Form of Human Cytosolic Aconitase (IRP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1000

b:26.3
occ:1.00
 FE4 A:SF41000 0.0 26.3 1.0
O A:HOH1206 2.1 26.4 1.0
S3 A:SF41000 2.3 25.3 1.0
S2 A:SF41000 2.3 21.6 1.0
S1 A:SF41000 2.3 22.8 1.0
FE3 A:SF41000 2.6 22.4 1.0
FE2 A:SF41000 2.7 25.1 1.0
FE1 A:SF41000 2.7 25.6 1.0
O A:HOH1073 3.8 26.8 1.0
ND1 A:HIS207 3.8 22.3 1.0
S4 A:SF41000 3.8 21.4 1.0
OD1 A:ASP205 4.2 21.7 1.0
OD2 A:ASP205 4.2 26.2 1.0
O A:HOH1217 4.5 26.1 1.0
CE1 A:HIS207 4.6 16.2 1.0
NE2 A:HIS126 4.6 25.8 1.0
CG A:HIS207 4.6 18.0 1.0
CG A:ASP205 4.6 24.8 1.0
CD2 A:HIS178 4.7 19.9 1.0
SG A:CYS506 4.7 24.0 1.0
CB A:HIS207 4.7 18.0 1.0
SG A:CYS437 4.7 26.3 1.0
SG A:CYS503 4.8 18.2 1.0
NE2 A:HIS178 4.9 19.7 1.0
CE1 A:HIS126 5.0 20.8 1.0

Iron binding site 5 out of 8 in 2b3y

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Iron binding site 5 out of 8 in the Structure of A Monoclinic Crystal Form of Human Cytosolic Aconitase (IRP1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of A Monoclinic Crystal Form of Human Cytosolic Aconitase (IRP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1000

b:28.4
occ:1.00
 FE1 B:SF41000 0.0 28.4 1.0
S3 B:SF41000 2.3 30.7 1.0
S4 B:SF41000 2.3 25.2 1.0
S2 B:SF41000 2.3 24.4 1.0
SG B:CYS437 2.4 28.6 1.0
FE4 B:SF41000 2.6 31.2 1.0
FE3 B:SF41000 2.8 22.6 1.0
FE2 B:SF41000 2.8 29.4 1.0
CB B:CYS437 3.6 24.6 1.0
CG2 B:ILE176 3.7 21.1 1.0
N B:CYS437 3.9 27.6 1.0
S1 B:SF41000 3.9 24.4 1.0
CD2 B:HIS178 4.1 18.7 1.0
OXT B:ACT890 4.1 19.9 1.0
CA B:CYS437 4.3 26.4 1.0
O B:HOH1186 4.4 23.6 1.0
OG B:SER436 4.4 25.0 1.0
SG B:CYS503 4.7 20.7 1.0
SG B:CYS506 4.8 28.6 1.0
C B:SER436 4.8 24.8 1.0
N B:THR438 4.9 23.7 1.0
CA B:SER436 4.9 24.6 1.0
NE2 B:HIS178 4.9 19.7 1.0
ND2 B:ASN298 5.0 16.7 1.0
CB B:ILE176 5.0 17.4 1.0

Iron binding site 6 out of 8 in 2b3y

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Iron binding site 6 out of 8 in the Structure of A Monoclinic Crystal Form of Human Cytosolic Aconitase (IRP1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of A Monoclinic Crystal Form of Human Cytosolic Aconitase (IRP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1000

b:29.4
occ:1.00
 FE2 B:SF41000 0.0 29.4 1.0
SG B:CYS506 2.2 28.6 1.0
S1 B:SF41000 2.2 24.4 1.0
S4 B:SF41000 2.3 25.2 1.0
S3 B:SF41000 2.3 30.7 1.0
FE4 B:SF41000 2.6 31.2 1.0
FE3 B:SF41000 2.7 22.6 1.0
FE1 B:SF41000 2.8 28.4 1.0
CB B:CYS506 3.1 26.1 1.0
OG B:SER436 3.6 25.0 1.0
OXT B:ACT890 3.7 19.9 1.0
O B:HOH1180 3.8 29.0 1.0
S2 B:SF41000 3.9 24.4 1.0
CA B:CYS506 4.4 27.8 1.0
CA B:SER436 4.5 24.6 1.0
C B:CYS506 4.5 28.0 1.0
CB B:SER436 4.5 24.6 1.0
CB B:CYS503 4.6 18.9 1.0
OD1 B:ASN535 4.6 28.0 1.0
C B:ACT890 4.6 31.1 1.0
O B:HOH1186 4.6 23.6 1.0
SG B:CYS503 4.7 20.7 1.0
N B:ILE507 4.8 27.2 1.0
NH2 B:ARG541 4.8 37.8 1.0
ND2 B:ASN535 4.8 25.2 1.0
O B:CYS506 4.8 28.9 1.0
SG B:CYS437 4.8 28.6 1.0
O B:ACT890 4.8 33.4 1.0
N B:CYS437 4.9 27.6 1.0

Iron binding site 7 out of 8 in 2b3y

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Iron binding site 7 out of 8 in the Structure of A Monoclinic Crystal Form of Human Cytosolic Aconitase (IRP1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of A Monoclinic Crystal Form of Human Cytosolic Aconitase (IRP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1000

b:22.6
occ:1.00
 FE3 B:SF41000 0.0 22.6 1.0
SG B:CYS503 2.2 20.7 1.0
S4 B:SF41000 2.3 25.2 1.0
S1 B:SF41000 2.3 24.4 1.0
S2 B:SF41000 2.3 24.4 1.0
FE4 B:SF41000 2.7 31.2 1.0
FE2 B:SF41000 2.7 29.4 1.0
FE1 B:SF41000 2.8 28.4 1.0
CB B:CYS503 3.1 18.9 1.0
OXT B:ACT890 3.4 19.9 1.0
CE1 B:HIS126 3.8 21.4 1.0
CA B:CYS503 3.8 18.0 1.0
NE2 B:HIS126 3.9 20.5 1.0
S3 B:SF41000 4.0 30.7 1.0
CG2 B:ILE176 4.0 21.1 1.0
C B:ACT890 4.4 31.1 1.0
ND1 B:HIS126 4.6 21.4 1.0
O B:HOH1186 4.7 23.6 1.0
N B:CYS503 4.7 19.6 1.0
CD2 B:HIS126 4.8 21.0 1.0
SG B:CYS506 4.8 28.6 1.0
CB B:CYS506 4.9 26.1 1.0
C B:CYS503 5.0 19.2 1.0

Iron binding site 8 out of 8 in 2b3y

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Iron binding site 8 out of 8 in the Structure of A Monoclinic Crystal Form of Human Cytosolic Aconitase (IRP1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of A Monoclinic Crystal Form of Human Cytosolic Aconitase (IRP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1000

b:31.2
occ:1.00
 FE4 B:SF41000 0.0 31.2 1.0
OXT B:ACT890 1.6 19.9 1.0
O B:HOH1186 2.2 23.6 1.0
S3 B:SF41000 2.3 30.7 1.0
S2 B:SF41000 2.3 24.4 1.0
S1 B:SF41000 2.3 24.4 1.0
FE1 B:SF41000 2.6 28.4 1.0
FE2 B:SF41000 2.6 29.4 1.0
FE3 B:SF41000 2.7 22.6 1.0
C B:ACT890 2.9 31.1 1.0
O B:ACT890 3.5 33.4 1.0
S4 B:SF41000 3.7 25.2 1.0
ND1 B:HIS207 3.8 22.3 1.0
CH3 B:ACT890 4.0 30.9 1.0
OD1 B:ASP205 4.1 19.5 1.0
OD2 B:ASP205 4.3 25.1 1.0
CE1 B:HIS207 4.5 23.6 1.0
O B:HOH1180 4.5 29.0 1.0
SG B:CYS506 4.6 28.6 1.0
CG B:HIS207 4.6 18.7 1.0
NE2 B:HIS126 4.6 20.5 1.0
CG B:ASP205 4.6 23.8 1.0
SG B:CYS437 4.7 28.6 1.0
CB B:HIS207 4.7 19.9 1.0
SG B:CYS503 4.8 20.7 1.0
CD2 B:HIS178 4.8 18.7 1.0
CE1 B:HIS126 4.9 21.4 1.0
NE2 B:HIS178 4.9 19.7 1.0
ND2 B:ASN535 5.0 25.2 1.0

Reference:

J.Dupuy, A.Volbeda, P.Carpentier, C.Darnault, J.M.Moulis, J.C.Fontecilla-Camps. Crystal Structure of Human Iron Regulatory Protein 1 As Cytosolic Aconitase Structure V. 14 129 2006.
ISSN: ISSN 0969-2126
PubMed: 16407072
DOI: 10.1016/J.STR.2005.09.009
Page generated: Wed Jul 16 23:47:33 2025

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