Iron in PDB 1kea: Structure of A Thermostable Thymine-Dna Glycosylase

The structure of Structure of A Thermostable Thymine-Dna Glycosylase, PDB code: 1kea was solved by C.D.Mol, A.S.Arvai, T.J.Begley, R.P.Cunningham, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.77 / 2.00
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	68.215, 68.215, 98.944, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 24.8

The structure of Structure of A Thermostable Thymine-Dna Glycosylase also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Zinc	(Zn)	1 atom

The binding sites of Iron atom in the Structure of A Thermostable Thymine-Dna Glycosylase (pdb code 1kea). 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 A Thermostable Thymine-Dna Glycosylase, PDB code: 1kea:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of A Thermostable Thymine-Dna Glycosylase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of A Thermostable Thymine-Dna Glycosylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe300 b:28.6 occ:1.00 FE1 A:SF4300 0.0 28.6 1.0 S3 A:SF4300 2.2 28.2 1.0 S4 A:SF4300 2.3 28.3 1.0 SG A:CYS207 2.4 30.3 1.0 S2 A:SF4300 2.4 29.2 1.0 FE4 A:SF4300 2.7 29.3 1.0 FE2 A:SF4300 2.7 27.3 1.0 FE3 A:SF4300 2.8 29.1 1.0 CB A:CYS207 3.1 31.1 1.0 S1 A:SF4300 3.9 28.4 1.0 CZ A:PHE192 4.2 22.2 1.0 CA A:CYS207 4.6 32.8 1.0 CG A:MET209 4.6 33.0 1.0 SG A:CYS204 4.7 31.4 1.0 SG A:CYS197 4.8 25.6 1.0 CA A:CYS204 4.8 33.9 1.0 CE A:MET209 4.8 33.1 1.0 CE2 A:PHE192 4.8 22.7 1.0 N A:SER210 4.8 33.9 1.0 CA A:SER210 4.9 34.9 1.0 SG A:CYS213 4.9 31.5 1.0 CB A:CYS213 4.9 34.3 1.0 CG2 A:ILE196 4.9 24.9 1.0 CB A:CYS197 4.9 24.9 1.0

Iron binding site 2 out of 4 in the Structure of A Thermostable Thymine-Dna Glycosylase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of A Thermostable Thymine-Dna Glycosylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe300 b:27.3 occ:1.00 FE2 A:SF4300 0.0 27.3 1.0 S4 A:SF4300 2.2 28.3 1.0 SG A:CYS197 2.3 25.6 1.0 S3 A:SF4300 2.3 28.2 1.0 S1 A:SF4300 2.4 28.4 1.0 FE1 A:SF4300 2.7 28.6 1.0 FE4 A:SF4300 2.8 29.3 1.0 FE3 A:SF4300 2.8 29.1 1.0 CB A:CYS197 3.1 24.9 1.0 CA A:CYS197 3.9 24.8 1.0 S2 A:SF4300 4.0 29.2 1.0 CB A:PRO202 4.3 37.4 1.0 CD A:ARG153 4.5 29.1 1.0 CB A:ARG153 4.7 30.5 1.0 CE2 A:PHE192 4.8 22.7 1.0 N A:CYS197 4.8 24.4 1.0 SG A:CYS207 4.8 30.3 1.0 SG A:CYS204 4.8 31.4 1.0 CZ A:PHE192 4.9 22.2 1.0 NH1 A:ARG153 4.9 27.8 1.0 SG A:CYS213 4.9 31.5 1.0 CG A:PRO202 5.0 37.9 1.0

Iron binding site 3 out of 4 in the Structure of A Thermostable Thymine-Dna Glycosylase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of A Thermostable Thymine-Dna Glycosylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe300 b:29.1 occ:1.00 FE3 A:SF4300 0.0 29.1 1.0 SG A:CYS204 2.2 31.4 1.0 S2 A:SF4300 2.2 29.2 1.0 S1 A:SF4300 2.3 28.4 1.0 S4 A:SF4300 2.3 28.3 1.0 FE4 A:SF4300 2.6 29.3 1.0 FE1 A:SF4300 2.8 28.6 1.0 FE2 A:SF4300 2.8 27.3 1.0 CB A:CYS204 3.3 32.8 1.0 CA A:CYS204 3.7 33.9 1.0 CB A:PRO202 4.0 37.4 1.0 S3 A:SF4300 4.0 28.2 1.0 CG A:PRO202 4.1 37.9 1.0 N A:CYS204 4.2 34.1 1.0 CD2 A:TYR215 4.5 43.9 1.0 SG A:CYS213 4.7 31.5 1.0 CB A:CYS207 4.7 31.1 1.0 SG A:CYS197 4.8 25.6 1.0 CE2 A:TYR215 4.8 44.1 1.0 SG A:CYS207 4.8 30.3 1.0

Iron binding site 4 out of 4 in the Structure of A Thermostable Thymine-Dna Glycosylase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of A Thermostable Thymine-Dna Glycosylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe300 b:29.3 occ:1.00 FE4 A:SF4300 0.0 29.3 1.0 S2 A:SF4300 2.2 29.2 1.0 S1 A:SF4300 2.3 28.4 1.0 S3 A:SF4300 2.4 28.2 1.0 SG A:CYS213 2.4 31.5 1.0 FE3 A:SF4300 2.6 29.1 1.0 FE1 A:SF4300 2.7 28.6 1.0 FE2 A:SF4300 2.8 27.3 1.0 CB A:CYS213 3.2 34.3 1.0 S4 A:SF4300 3.8 28.3 1.0 SG A:CYS204 4.5 31.4 1.0 CA A:CYS213 4.6 36.6 1.0 CB A:TYR216 4.6 48.1 1.0 N A:TYR216 4.7 46.5 1.0 CD2 A:TYR215 4.7 43.9 1.0 CB A:TYR215 4.7 43.8 1.0 SG A:CYS207 4.7 30.3 1.0 SG A:CYS197 4.8 25.6 1.0 CB A:ARG153 4.9 30.5 1.0 CD1 A:TYR154 4.9 31.6 1.0 CA A:TYR154 4.9 32.5 1.0 N A:TYR154 5.0 32.0 1.0

C.D.Mol, A.S.Arvai, T.J.Begley, R.P.Cunningham, J.A.Tainer. Structure and Activity of A Thermostable Thymine-Dna Glycosylase: Evidence For Base Twisting to Remove Mismatched Normal Dna Bases. J.Mol.Biol. V. 315 373 2002.
ISSN: ISSN 0022-2836
PubMed: 11786018
DOI: 10.1006/JMBI.2001.5264