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Iron in PDB 1ui0: Crystal Structure of Uracil-Dna Glycosylase From Thermus Thermophilus HB8

Protein crystallography data

The structure of Crystal Structure of Uracil-Dna Glycosylase From Thermus Thermophilus HB8, PDB code: 1ui0 was solved by J.Hoseki, A.Okamoto, R.Masui, T.Shibata, Y.Inoue, S.Yokoyama, S.Kuramitsu, Riken Structural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.429, 59.512, 80.971, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 20.1

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Uracil-Dna Glycosylase From Thermus Thermophilus HB8 (pdb code 1ui0). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Uracil-Dna Glycosylase From Thermus Thermophilus HB8, PDB code: 1ui0:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1ui0

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Iron binding site 1 out of 4 in the Crystal Structure of Uracil-Dna Glycosylase From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Uracil-Dna Glycosylase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe210

b:5.4
occ:1.00
 FE1 A:SF4210 0.0 5.4 1.0
S2 A:SF4210 2.3 4.7 1.0
S3 A:SF4210 2.3 5.8 1.0
S4 A:SF4210 2.3 5.8 1.0
SG A:CYS13 2.3 5.3 1.0
FE3 A:SF4210 2.7 5.1 1.0
FE4 A:SF4210 2.7 5.1 1.0
FE2 A:SF4210 2.7 5.9 1.0
CB A:CYS13 3.3 4.7 1.0
S1 A:SF4210 3.9 5.1 1.0
NE1 A:TRP104 3.9 6.7 1.0
N A:ALA15 4.0 7.8 1.0
CB A:ALA15 4.1 8.7 1.0
C A:CYS13 4.2 6.2 1.0
CA A:CYS13 4.4 5.7 1.0
O A:CYS13 4.4 6.5 1.0
N A:CYS16 4.5 6.6 1.0
CA A:ALA15 4.5 8.2 1.0
N A:THR14 4.5 8.0 1.0
CD1 A:TRP104 4.6 5.2 1.0
NH1 A:ARG22 4.8 7.0 1.0
SG A:CYS84 4.8 4.9 1.0
SG A:CYS100 4.8 4.4 1.0
SG A:CYS16 4.9 6.7 1.0
C A:ALA15 4.9 7.8 1.0
C A:THR14 4.9 8.6 1.0

Iron binding site 2 out of 4 in 1ui0

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Iron binding site 2 out of 4 in the Crystal Structure of Uracil-Dna Glycosylase From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Uracil-Dna Glycosylase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe210

b:5.9
occ:1.00
 FE2 A:SF4210 0.0 5.9 1.0
S3 A:SF4210 2.3 5.8 1.0
S4 A:SF4210 2.3 5.8 1.0
S1 A:SF4210 2.3 5.1 1.0
SG A:CYS16 2.3 6.7 1.0
FE4 A:SF4210 2.7 5.1 1.0
FE3 A:SF4210 2.7 5.1 1.0
FE1 A:SF4210 2.7 5.4 1.0
CB A:CYS16 3.3 5.9 1.0
N A:CYS16 3.7 6.6 1.0
S2 A:SF4210 3.8 4.7 1.0
CA A:CYS16 3.9 5.6 1.0
CB A:LEU18 4.3 7.1 1.0
O A:CYS16 4.3 7.1 1.0
C A:CYS16 4.3 7.1 1.0
C A:ALA15 4.6 7.8 1.0
CB A:CYS100 4.7 4.7 1.0
SG A:CYS100 4.7 4.4 1.0
SG A:CYS84 4.8 4.9 1.0
N A:LEU18 4.8 6.7 1.0
CD1 A:LEU18 4.8 7.9 1.0
CG A:LEU18 4.9 6.1 1.0
SG A:CYS13 4.9 5.3 1.0
N A:MET19 4.9 8.8 1.0
CA A:LEU18 5.0 6.6 1.0

Iron binding site 3 out of 4 in 1ui0

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Iron binding site 3 out of 4 in the Crystal Structure of Uracil-Dna Glycosylase From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Uracil-Dna Glycosylase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe210

b:5.1
occ:1.00
 FE3 A:SF4210 0.0 5.1 1.0
S4 A:SF4210 2.3 5.8 1.0
S1 A:SF4210 2.3 5.1 1.0
S2 A:SF4210 2.3 4.7 1.0
SG A:CYS100 2.3 4.4 1.0
FE4 A:SF4210 2.7 5.1 1.0
FE1 A:SF4210 2.7 5.4 1.0
FE2 A:SF4210 2.7 5.9 1.0
CB A:CYS100 3.1 4.7 1.0
S3 A:SF4210 3.8 5.8 1.0
CA A:CYS100 3.9 6.2 1.0
N A:LYS83 4.0 3.4 1.0
CD1 A:TRP104 4.1 5.2 1.0
CG A:LYS83 4.2 4.0 1.0
NE1 A:TRP104 4.3 6.7 1.0
CB A:LYS83 4.3 4.3 1.0
SG A:CYS13 4.7 5.3 1.0
SG A:CYS16 4.7 6.7 1.0
CA A:LYS83 4.7 4.1 1.0
SG A:CYS84 4.7 4.9 1.0
N A:CYS100 4.7 7.0 1.0
CA A:VAL82 4.9 3.8 1.0
N A:CYS84 5.0 4.2 1.0
C A:VAL82 5.0 3.8 1.0
C A:CYS100 5.0 5.8 1.0

Iron binding site 4 out of 4 in 1ui0

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Iron binding site 4 out of 4 in the Crystal Structure of Uracil-Dna Glycosylase From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Uracil-Dna Glycosylase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe210

b:5.1
occ:1.00
 FE4 A:SF4210 0.0 5.1 1.0
S1 A:SF4210 2.3 5.1 1.0
S2 A:SF4210 2.3 4.7 1.0
S3 A:SF4210 2.3 5.8 1.0
SG A:CYS84 2.3 4.9 1.0
FE2 A:SF4210 2.7 5.9 1.0
FE3 A:SF4210 2.7 5.1 1.0
FE1 A:SF4210 2.7 5.4 1.0
CB A:CYS84 3.4 5.0 1.0
S4 A:SF4210 3.8 5.8 1.0
NH1 A:ARG22 3.9 7.0 1.0
N A:CYS84 4.0 4.2 1.0
CA A:CYS84 4.3 4.3 1.0
C A:LYS83 4.4 4.3 1.0
CB A:LYS83 4.5 4.3 1.0
SG A:CYS16 4.7 6.7 1.0
N A:LYS83 4.7 3.4 1.0
CB A:LEU18 4.7 7.1 1.0
CA A:LYS83 4.7 4.1 1.0
SG A:CYS13 4.8 5.3 1.0
SG A:CYS100 4.8 4.4 1.0
N A:MET19 4.9 8.8 1.0
CB A:CYS13 5.0 4.7 1.0

Reference:

J.Hoseki, A.Okamoto, R.Masui, T.Shibata, Y.Inoue, S.Yokoyama, S.Kuramitsu. Crystal Structure of A Family 4 Uracil-Dna Glycosylase From Thermus Thermophilus HB8 J.Mol.Biol. V. 333 515 2003.
ISSN: ISSN 0022-2836
PubMed: 14556741
DOI: 10.1016/J.JMB.2003.08.030
Page generated: Wed Jul 16 21:23:44 2025

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