Iron in PDB 4zbx: Family 4 Uracil-Dna Glycosylase From Sulfolobus Tokodaii (Free Form, X-Ray Wavelength=0.9000)

All present enzymatic activity of Family 4 Uracil-Dna Glycosylase From Sulfolobus Tokodaii (Free Form, X-Ray Wavelength=0.9000):
3.2.2.27;

The structure of Family 4 Uracil-Dna Glycosylase From Sulfolobus Tokodaii (Free Form, X-Ray Wavelength=0.9000), PDB code: 4zbx 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)	36.93 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.189, 52.250, 74.453, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 21.6

The binding sites of Iron atom in the Family 4 Uracil-Dna Glycosylase From Sulfolobus Tokodaii (Free Form, X-Ray Wavelength=0.9000) (pdb code 4zbx). 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=0.9000), PDB code: 4zbx:
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=0.9000)


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=0.9000) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:23.8 occ:1.00 FE1 A:SF4201 0.0 23.8 1.0 S3 A:SF4201 2.2 23.6 1.0 S4 A:SF4201 2.3 25.0 1.0 S2 A:SF4201 2.3 22.1 1.0 SG A:CYS17 2.3 25.9 1.0 FE2 A:SF4201 2.7 22.6 1.0 FE4 A:SF4201 2.7 20.9 1.0 FE3 A:SF4201 2.7 23.1 1.0 CB A:CYS17 3.4 30.3 1.0 N A:CYS17 3.6 29.3 1.0 S1 A:SF4201 3.9 20.4 1.0 CA A:CYS17 3.9 30.1 1.0 O A:CYS17 4.3 26.8 1.0 C A:CYS17 4.3 26.9 1.0 CB A:LEU19 4.4 23.1 1.0 C A:LYS16 4.6 36.3 1.0 CB A:CYS102 4.7 21.0 1.0 SG A:CYS102 4.8 20.6 1.0 N A:LEU19 4.8 26.7 1.0 SG A:CYS14 4.8 22.6 1.0 CB A:ALA101 4.9 30.9 1.0 CG A:LEU19 4.9 21.9 1.0 N A:TRP20 4.9 25.9 1.0 N A:LYS16 4.9 24.9 1.0 CD1 A:LEU19 5.0 21.2 1.0

Iron binding site 2 out of 4 in the Family 4 Uracil-Dna Glycosylase From Sulfolobus Tokodaii (Free Form, X-Ray Wavelength=0.9000)


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=0.9000) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:22.6 occ:1.00 FE2 A:SF4201 0.0 22.6 1.0 S3 A:SF4201 2.2 23.6 1.0 S4 A:SF4201 2.3 25.0 1.0 S1 A:SF4201 2.3 20.4 1.0 SG A:CYS14 2.4 22.6 1.0 FE1 A:SF4201 2.7 23.8 1.0 FE4 A:SF4201 2.7 20.9 1.0 FE3 A:SF4201 2.7 23.1 1.0 CB A:CYS14 3.1 23.8 1.0 S2 A:SF4201 3.9 22.1 1.0 N A:LYS16 4.0 24.9 1.0 CE1 A:TYR105 4.1 20.6 1.0 C A:CYS14 4.2 25.0 1.0 CB A:LYS16 4.2 27.6 1.0 CA A:CYS14 4.3 24.9 1.0 O A:CYS14 4.4 24.7 1.0 N A:CYS17 4.4 29.3 1.0 CA A:LYS16 4.6 29.1 1.0 N A:LYS15 4.6 24.0 1.0 OH A:TYR105 4.8 22.5 1.0 SG A:CYS102 4.8 20.6 1.0 NH1 A:ARG23 4.9 24.3 1.0 C A:LYS16 4.9 36.3 1.0 SG A:CYS17 4.9 25.9 1.0 CZ A:TYR105 5.0 21.7 1.0 CG A:LYS16 5.0 29.9 1.0 C A:LYS15 5.0 27.4 1.0

Iron binding site 3 out of 4 in the Family 4 Uracil-Dna Glycosylase From Sulfolobus Tokodaii (Free Form, X-Ray Wavelength=0.9000)


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=0.9000) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:23.1 occ:1.00 FE3 A:SF4201 0.0 23.1 1.0 S2 A:SF4201 2.3 22.1 1.0 S1 A:SF4201 2.3 20.4 1.0 S4 A:SF4201 2.3 25.0 1.0 SG A:CYS86 2.5 25.2 1.0 FE4 A:SF4201 2.7 20.9 1.0 FE2 A:SF4201 2.7 22.6 1.0 FE1 A:SF4201 2.7 23.8 1.0 CB A:CYS86 3.4 20.6 1.0 NH1 A:ARG23 3.9 24.3 1.0 S3 A:SF4201 3.9 23.6 1.0 N A:CYS86 4.2 18.8 1.0 CA A:CYS86 4.4 19.2 1.0 C A:LYS85 4.6 18.0 1.0 CB A:LEU19 4.7 23.1 1.0 SG A:CYS17 4.7 25.9 1.0 CB A:CYS14 4.8 23.8 1.0 N A:TRP20 4.8 25.9 1.0 SG A:CYS14 4.8 22.6 1.0 SG A:CYS102 4.9 20.6 1.0 CA A:TRP20 4.9 26.6 1.0 O A:CYS14 4.9 24.7 1.0 O A:LYS85 5.0 17.4 1.0

Iron binding site 4 out of 4 in the Family 4 Uracil-Dna Glycosylase From Sulfolobus Tokodaii (Free Form, X-Ray Wavelength=0.9000)


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=0.9000) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:20.9 occ:1.00 FE4 A:SF4201 0.0 20.9 1.0 S1 A:SF4201 2.2 20.4 1.0 S2 A:SF4201 2.3 22.1 1.0 S3 A:SF4201 2.3 23.6 1.0 SG A:CYS102 2.4 20.6 1.0 FE2 A:SF4201 2.7 22.6 1.0 FE3 A:SF4201 2.7 23.1 1.0 FE1 A:SF4201 2.7 23.8 1.0 CB A:CYS102 3.1 21.0 1.0 CA A:CYS102 3.8 19.7 1.0 S4 A:SF4201 3.9 25.0 1.0 N A:LYS85 4.2 16.7 1.0 CE1 A:TYR105 4.3 20.6 1.0 CB A:LYS85 4.4 18.0 1.0 CD1 A:TYR105 4.4 19.8 1.0 N A:CYS102 4.6 22.0 1.0 CA A:LYS85 4.7 15.9 1.0 SG A:CYS86 4.7 25.2 1.0 SG A:CYS17 4.8 25.9 1.0 SG A:CYS14 4.8 22.6 1.0 N A:CYS86 4.8 18.8 1.0 C A:LYS85 4.9 18.0 1.0 C A:CYS102 5.0 21.3 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