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Iron in PDB 2b3x: Structure of An Orthorhombic Crystal Form of Human Cytosolic Aconitase (IRP1)

Enzymatic activity of Structure of An Orthorhombic Crystal Form of Human Cytosolic Aconitase (IRP1)

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

Protein crystallography data

The structure of Structure of An Orthorhombic Crystal Form of Human Cytosolic Aconitase (IRP1), PDB code: 2b3x 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) 113.23 / 2.54
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 75.352, 103.307, 225.957, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 22.5

Other elements in 2b3x:

The structure of Structure of An Orthorhombic Crystal Form of Human Cytosolic Aconitase (IRP1) also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Structure of An Orthorhombic Crystal Form of Human Cytosolic Aconitase (IRP1) (pdb code 2b3x). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of An Orthorhombic Crystal Form of Human Cytosolic Aconitase (IRP1), PDB code: 2b3x:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 2b3x

Go back to Iron Binding Sites List in 2b3x
Iron binding site 1 out of 4 in the Structure of An Orthorhombic 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 An Orthorhombic Crystal Form of Human Cytosolic Aconitase (IRP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1000

b:23.6
occ:1.00
 FE1 A:SF41000 0.0 23.6 1.0
S2 A:SF41000 2.3 23.3 1.0
S3 A:SF41000 2.3 24.8 1.0
SG A:CYS437 2.3 26.3 1.0
S4 A:SF41000 2.3 22.9 1.0
FE2 A:SF41000 2.7 23.7 1.0
FE4 A:SF41000 2.7 21.9 0.8
FE3 A:SF41000 2.8 20.4 1.0
CG2 A:ILE176 3.7 22.0 1.0
CB A:CYS437 3.7 25.2 1.0
N A:CYS437 3.9 23.7 1.0
S1 A:SF41000 3.9 22.2 1.0
CD2 A:HIS178 4.2 18.5 1.0
CA A:CYS437 4.4 25.4 1.0
O A:HOH1149 4.6 18.5 0.8
OG A:SER436 4.6 25.7 1.0
SG A:CYS506 4.7 24.4 1.0
SG A:CYS503 4.8 20.7 1.0
C A:SER436 4.9 23.8 1.0
CA A:SER436 4.9 23.5 1.0
N A:THR438 4.9 25.9 1.0
ND2 A:ASN298 4.9 25.3 1.0

Iron binding site 2 out of 4 in 2b3x

Go back to Iron Binding Sites List in 2b3x
Iron binding site 2 out of 4 in the Structure of An Orthorhombic 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 An Orthorhombic Crystal Form of Human Cytosolic Aconitase (IRP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1000

b:23.7
occ:1.00
 FE2 A:SF41000 0.0 23.7 1.0
S1 A:SF41000 2.3 22.2 1.0
S3 A:SF41000 2.3 24.8 1.0
S4 A:SF41000 2.3 22.9 1.0
SG A:CYS506 2.3 24.4 1.0
FE4 A:SF41000 2.7 21.9 0.8
FE1 A:SF41000 2.7 23.6 1.0
FE3 A:SF41000 2.7 20.4 1.0
CB A:CYS506 3.4 24.3 1.0
S2 A:SF41000 3.8 23.3 1.0
OG A:SER436 4.1 25.7 1.0
C A:CYS506 4.5 25.7 1.0
CA A:CYS506 4.5 24.9 1.0
CA A:SER436 4.5 23.5 1.0
OD1 A:ASN535 4.6 28.3 1.0
ND2 A:ASN535 4.6 28.0 1.0
O A:CYS506 4.6 25.8 1.0
CB A:SER436 4.7 23.4 1.0
O A:HOH1149 4.7 18.5 0.8
CB A:CYS503 4.7 21.0 1.0
SG A:CYS503 4.7 20.7 1.0
SG A:CYS437 4.7 26.3 1.0
N A:ILE507 4.8 26.0 1.0
N A:CYS437 4.9 23.7 1.0

Iron binding site 3 out of 4 in 2b3x

Go back to Iron Binding Sites List in 2b3x
Iron binding site 3 out of 4 in the Structure of An Orthorhombic 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 An Orthorhombic Crystal Form of Human Cytosolic Aconitase (IRP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1000

b:20.4
occ:1.00
 FE3 A:SF41000 0.0 20.4 1.0
SG A:CYS503 2.2 20.7 1.0
S4 A:SF41000 2.3 22.9 1.0
S1 A:SF41000 2.3 22.2 1.0
S2 A:SF41000 2.3 23.3 1.0
FE2 A:SF41000 2.7 23.7 1.0
FE4 A:SF41000 2.7 21.9 0.8
FE1 A:SF41000 2.8 23.6 1.0
CB A:CYS503 3.1 21.0 1.0
CA A:CYS503 3.8 21.2 1.0
CG2 A:ILE176 3.8 22.0 1.0
S3 A:SF41000 3.9 24.8 1.0
CE1 A:HIS126 4.1 23.3 1.0
NE2 A:HIS126 4.3 22.0 1.0
N A:CYS503 4.6 20.7 1.0
O A:HOH1149 4.6 18.5 0.8
SG A:CYS506 4.7 24.4 1.0
SG A:CYS437 4.9 26.3 1.0
ND1 A:HIS126 4.9 23.1 1.0
C A:CYS503 4.9 21.8 1.0

Iron binding site 4 out of 4 in 2b3x

Go back to Iron Binding Sites List in 2b3x
Iron binding site 4 out of 4 in the Structure of An Orthorhombic 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 An Orthorhombic Crystal Form of Human Cytosolic Aconitase (IRP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1000

b:21.9
occ:0.80
 FE4 A:SF41000 0.0 21.9 0.8
O A:HOH1149 2.2 18.5 0.8
S3 A:SF41000 2.3 24.8 1.0
S2 A:SF41000 2.3 23.3 1.0
S1 A:SF41000 2.3 22.2 1.0
FE2 A:SF41000 2.7 23.7 1.0
FE3 A:SF41000 2.7 20.4 1.0
FE1 A:SF41000 2.7 23.6 1.0
ND1 A:HIS207 3.8 21.7 1.0
S4 A:SF41000 3.9 22.9 1.0
OD1 A:ASP205 4.0 25.4 1.0
OD2 A:ASP205 4.2 24.1 1.0
CG A:ASP205 4.5 23.5 1.0
CE1 A:HIS207 4.6 21.0 1.0
CG A:HIS207 4.6 21.2 1.0
SG A:CYS503 4.7 20.7 1.0
CB A:HIS207 4.7 21.3 1.0
SG A:CYS506 4.8 24.4 1.0
SG A:CYS437 4.8 26.3 1.0
NE2 A:HIS126 4.8 22.0 1.0
CD2 A:HIS178 4.9 18.5 1.0
NE2 A:HIS178 5.0 19.4 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: Sat Aug 3 19:30:42 2024

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