Iron in PDB 4zby: Family 4 Uracil-Dna Glycosylase From Sulfolobus Tokodaii (Uracil Complex Form)

All present enzymatic activity of Family 4 Uracil-Dna Glycosylase From Sulfolobus Tokodaii (Uracil Complex Form):
3.2.2.27;

The structure of Family 4 Uracil-Dna Glycosylase From Sulfolobus Tokodaii (Uracil Complex Form), PDB code: 4zby was solved by A.Kawai, S.Miyamoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.68 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.056, 52.222, 74.062, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 20.7

The binding sites of Iron atom in the Family 4 Uracil-Dna Glycosylase From Sulfolobus Tokodaii (Uracil Complex Form) (pdb code 4zby). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Family 4 Uracil-Dna Glycosylase From Sulfolobus Tokodaii (Uracil Complex Form), PDB code: 4zby:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Family 4 Uracil-Dna Glycosylase From Sulfolobus Tokodaii (Uracil Complex Form)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Family 4 Uracil-Dna Glycosylase From Sulfolobus Tokodaii (Uracil Complex Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:23.1 occ:1.00 FE1 A:SF4201 0.0 23.1 1.0 S4 A:SF4201 2.2 20.9 1.0 S3 A:SF4201 2.2 22.0 1.0 S2 A:SF4201 2.3 19.2 1.0 SG A:CYS17 2.3 24.3 1.0 FE2 A:SF4201 2.7 22.5 1.0 FE4 A:SF4201 2.7 21.0 1.0 FE3 A:SF4201 2.7 20.7 1.0 CB A:CYS17 3.4 28.0 1.0 N A:CYS17 3.6 27.5 1.0 S1 A:SF4201 3.9 17.6 1.0 CA A:CYS17 3.9 28.0 1.0 O A:CYS17 4.3 23.4 1.0 C A:CYS17 4.3 29.1 1.0 CB A:LEU19 4.4 22.7 1.0 C A:LYS16 4.5 31.8 1.0 CB A:CYS102 4.6 21.5 1.0 SG A:CYS102 4.8 19.0 1.0 SG A:CYS86 4.8 21.2 1.0 N A:LEU19 4.8 23.2 1.0 CG A:LEU19 4.8 21.5 1.0 SG A:CYS14 4.9 23.2 1.0 N A:LYS16 4.9 24.6 1.0 CD1 A:LEU19 4.9 18.8 1.0

Iron binding site 2 out of 4 in the Family 4 Uracil-Dna Glycosylase From Sulfolobus Tokodaii (Uracil Complex Form)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Family 4 Uracil-Dna Glycosylase From Sulfolobus Tokodaii (Uracil Complex Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:22.5 occ:1.00 FE2 A:SF4201 0.0 22.5 1.0 S3 A:SF4201 2.2 22.0 1.0 S4 A:SF4201 2.3 20.9 1.0 S1 A:SF4201 2.3 17.6 1.0 SG A:CYS14 2.4 23.2 1.0 FE1 A:SF4201 2.7 23.1 1.0 FE4 A:SF4201 2.7 21.0 1.0 FE3 A:SF4201 2.7 20.7 1.0 CB A:CYS14 3.1 19.4 1.0 S2 A:SF4201 3.8 19.2 1.0 N A:LYS16 4.0 24.6 1.0 CE2 A:TYR105 4.1 21.2 1.0 C A:CYS14 4.2 25.8 1.0 O A:CYS14 4.3 24.6 1.0 CA A:CYS14 4.3 22.8 1.0 CB A:LYS16 4.3 25.8 1.0 N A:CYS17 4.4 27.5 1.0 CA A:LYS16 4.6 28.1 1.0 N A:LYS15 4.6 25.7 1.0 NH1 A:ARG23 4.8 22.2 1.0 SG A:CYS102 4.8 19.0 1.0 SG A:CYS17 4.8 24.3 1.0 C A:LYS16 4.8 31.8 1.0 OH A:TYR105 4.8 25.3 1.0 SG A:CYS86 4.9 21.2 1.0 C A:LYS15 4.9 27.1 1.0 CA A:LYS15 5.0 26.6 1.0 CD2 A:TYR105 5.0 20.1 1.0

Iron binding site 3 out of 4 in the Family 4 Uracil-Dna Glycosylase From Sulfolobus Tokodaii (Uracil Complex Form)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Family 4 Uracil-Dna Glycosylase From Sulfolobus Tokodaii (Uracil Complex Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:20.7 occ:1.00 FE3 A:SF4201 0.0 20.7 1.0 S1 A:SF4201 2.2 17.6 1.0 S2 A:SF4201 2.3 19.2 1.0 S4 A:SF4201 2.3 20.9 1.0 SG A:CYS86 2.3 21.2 1.0 FE4 A:SF4201 2.7 21.0 1.0 FE1 A:SF4201 2.7 23.1 1.0 FE2 A:SF4201 2.7 22.5 1.0 CB A:CYS86 3.3 18.6 1.0 NH1 A:ARG23 3.8 22.2 1.0 S3 A:SF4201 3.8 22.0 1.0 N A:CYS86 3.9 15.1 1.0 CA A:CYS86 4.2 19.1 1.0 C A:LYS85 4.3 15.9 1.0 SG A:CYS17 4.7 24.3 1.0 CB A:LEU19 4.7 22.7 1.0 SG A:CYS102 4.8 19.0 1.0 CB A:CYS14 4.8 19.4 1.0 O A:LYS85 4.8 19.4 1.0 SG A:CYS14 4.9 23.2 1.0 O A:CYS14 4.9 24.6 1.0 CA A:LYS85 4.9 15.2 1.0 N A:LYS85 5.0 15.0 1.0 CB A:LYS85 5.0 17.9 1.0 N A:TRP20 5.0 22.8 1.0

Iron binding site 4 out of 4 in the Family 4 Uracil-Dna Glycosylase From Sulfolobus Tokodaii (Uracil Complex Form)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Family 4 Uracil-Dna Glycosylase From Sulfolobus Tokodaii (Uracil Complex Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:21.0 occ:1.00 FE4 A:SF4201 0.0 21.0 1.0 S2 A:SF4201 2.2 19.2 1.0 S1 A:SF4201 2.3 17.6 1.0 S3 A:SF4201 2.3 22.0 1.0 SG A:CYS102 2.3 19.0 1.0 FE3 A:SF4201 2.7 20.7 1.0 FE2 A:SF4201 2.7 22.5 1.0 FE1 A:SF4201 2.7 23.1 1.0 CB A:CYS102 3.0 21.5 1.0 S4 A:SF4201 3.8 20.9 1.0 CA A:CYS102 3.8 21.9 1.0 N A:LYS85 4.1 15.0 1.0 CE2 A:TYR105 4.4 21.2 1.0 CB A:LYS85 4.4 17.9 1.0 CD2 A:TYR105 4.4 20.1 1.0 CA A:LYS85 4.6 15.2 1.0 N A:CYS102 4.7 21.4 1.0 SG A:CYS86 4.7 21.2 1.0 SG A:CYS17 4.7 24.3 1.0 N A:CYS86 4.7 15.1 1.0 SG A:CYS14 4.8 23.2 1.0 C A:LYS85 4.9 15.9 1.0 C A:CYS102 5.0 20.6 1.0

A.Kawai, S.Higuchi, M.Tsunoda, K.T.Nakamura, Y.Yamagata, S.Miyamoto. Crystal Structure of Family 4 Uracil-Dna Glycosylase From Sulfolobus Tokodaii and A Function of Tyrosine 170 in Dna Binding Febs Lett. V. 589 2675 2015.
ISSN: ISSN 0014-5793
PubMed: 26318717
DOI: 10.1016/J.FEBSLET.2015.08.019