Iron in PDB 4zbz: Family 4 Uracil-Dna Glycosylase From Sulfolobus Tokodaii (Free Form, X-Ray Wavelength=1.5418)

All present enzymatic activity of Family 4 Uracil-Dna Glycosylase From Sulfolobus Tokodaii (Free Form, X-Ray Wavelength=1.5418):
3.2.2.27;

The structure of Family 4 Uracil-Dna Glycosylase From Sulfolobus Tokodaii (Free Form, X-Ray Wavelength=1.5418), PDB code: 4zbz 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)	26.17 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.030, 52.345, 74.689, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 20.6

The binding sites of Iron atom in the Family 4 Uracil-Dna Glycosylase From Sulfolobus Tokodaii (Free Form, X-Ray Wavelength=1.5418) (pdb code 4zbz). 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 (Free Form, X-Ray Wavelength=1.5418), PDB code: 4zbz:
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 (Free Form, X-Ray Wavelength=1.5418)


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 (Free Form, X-Ray Wavelength=1.5418) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:23.2 occ:1.00 FE1 A:SF4201 0.0 23.2 1.0 S4 A:SF4201 2.3 22.9 1.0 S3 A:SF4201 2.3 20.5 1.0 S2 A:SF4201 2.3 19.6 1.0 SG A:CYS17 2.4 24.0 1.0 FE2 A:SF4201 2.7 23.4 1.0 FE3 A:SF4201 2.7 22.8 1.0 FE4 A:SF4201 2.7 20.8 1.0 CB A:CYS17 3.5 28.5 1.0 N A:CYS17 3.7 27.6 1.0 S1 A:SF4201 3.9 20.3 1.0 CA A:CYS17 4.0 26.9 1.0 O A:CYS17 4.4 25.1 1.0 C A:CYS17 4.4 27.9 1.0 CB A:LEU19 4.4 20.2 1.0 C A:LYS16 4.6 32.1 1.0 CB A:CYS102 4.7 20.9 1.0 N A:LEU19 4.8 25.6 1.0 SG A:CYS102 4.9 20.1 1.0 SG A:CYS14 4.9 22.0 1.0 SG A:CYS86 4.9 20.8 1.0 N A:TRP20 4.9 21.8 1.0 CG A:LEU19 4.9 20.4 1.0 N A:LYS16 4.9 28.3 1.0 CB A:ALA101 5.0 29.5 1.0

Iron binding site 2 out of 4 in the Family 4 Uracil-Dna Glycosylase From Sulfolobus Tokodaii (Free Form, X-Ray Wavelength=1.5418)


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 (Free Form, X-Ray Wavelength=1.5418) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:23.4 occ:1.00 FE2 A:SF4201 0.0 23.4 1.0 S3 A:SF4201 2.2 20.5 1.0 S4 A:SF4201 2.3 22.9 1.0 S1 A:SF4201 2.3 20.3 1.0 SG A:CYS14 2.4 22.0 1.0 FE1 A:SF4201 2.7 23.2 1.0 FE4 A:SF4201 2.7 20.8 1.0 FE3 A:SF4201 2.7 22.8 1.0 CB A:CYS14 3.2 24.1 1.0 S2 A:SF4201 3.9 19.6 1.0 N A:LYS16 4.1 28.3 1.0 CE1 A:TYR105 4.2 16.6 1.0 C A:CYS14 4.2 26.3 1.0 O A:CYS14 4.2 24.4 1.0 CB A:LYS16 4.3 31.7 1.0 CA A:CYS14 4.3 23.6 1.0 N A:CYS17 4.5 27.6 1.0 CA A:LYS16 4.6 29.2 1.0 N A:LYS15 4.7 23.2 1.0 OH A:TYR105 4.7 21.5 1.0 NH1 A:ARG23 4.8 21.5 1.0 SG A:CYS102 4.9 20.1 1.0 C A:LYS16 4.9 32.1 1.0 SG A:CYS86 4.9 20.8 1.0 CZ A:TYR105 5.0 19.3 1.0

Iron binding site 3 out of 4 in the Family 4 Uracil-Dna Glycosylase From Sulfolobus Tokodaii (Free Form, X-Ray Wavelength=1.5418)


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 (Free Form, X-Ray Wavelength=1.5418) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:22.8 occ:1.00 FE3 A:SF4201 0.0 22.8 1.0 S2 A:SF4201 2.3 19.6 1.0 S4 A:SF4201 2.3 22.9 1.0 S1 A:SF4201 2.3 20.3 1.0 SG A:CYS86 2.4 20.8 1.0 FE4 A:SF4201 2.7 20.8 1.0 FE1 A:SF4201 2.7 23.2 1.0 FE2 A:SF4201 2.7 23.4 1.0 CB A:CYS86 3.2 20.3 1.0 NH1 A:ARG23 3.8 21.5 1.0 S3 A:SF4201 3.9 20.5 1.0 N A:CYS86 4.0 15.0 1.0 CA A:CYS86 4.2 15.5 1.0 C A:LYS85 4.4 14.3 1.0 CB A:LEU19 4.7 20.2 1.0 SG A:CYS17 4.8 24.0 1.0 N A:TRP20 4.8 21.8 1.0 O A:LYS85 4.8 14.2 1.0 SG A:CYS102 4.9 20.1 1.0 SG A:CYS14 4.9 22.0 1.0 CB A:CYS14 4.9 24.1 1.0 O A:CYS14 4.9 24.4 1.0 CA A:TRP20 5.0 24.8 1.0 N A:LYS85 5.0 13.2 1.0

Iron binding site 4 out of 4 in the Family 4 Uracil-Dna Glycosylase From Sulfolobus Tokodaii (Free Form, X-Ray Wavelength=1.5418)


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 (Free Form, X-Ray Wavelength=1.5418) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:20.8 occ:1.00 FE4 A:SF4201 0.0 20.8 1.0 S1 A:SF4201 2.3 20.3 1.0 S2 A:SF4201 2.3 19.6 1.0 S3 A:SF4201 2.3 20.5 1.0 SG A:CYS102 2.4 20.1 1.0 FE2 A:SF4201 2.7 23.4 1.0 FE3 A:SF4201 2.7 22.8 1.0 FE1 A:SF4201 2.7 23.2 1.0 CB A:CYS102 3.1 20.9 1.0 CA A:CYS102 3.8 17.2 1.0 S4 A:SF4201 3.9 22.9 1.0 N A:LYS85 4.1 13.2 1.0 CE1 A:TYR105 4.3 16.6 1.0 CD1 A:TYR105 4.4 15.7 1.0 CB A:LYS85 4.4 16.9 1.0 N A:CYS102 4.7 18.4 1.0 CA A:LYS85 4.7 12.7 1.0 N A:CYS86 4.8 15.0 1.0 SG A:CYS14 4.8 22.0 1.0 SG A:CYS86 4.8 20.8 1.0 SG A:CYS17 4.8 24.0 1.0 C A:LYS85 4.9 14.3 1.0 C A:CYS102 5.0 17.4 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