Iron in PDB 5kn8: Muty N-Terminal Domain in Complex with Undamaged Dna

The structure of Muty N-Terminal Domain in Complex with Undamaged Dna, PDB code: 5kn8 was solved by L.Wang, S.Chakravarthy, G.L.Verdine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.35 / 1.81
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.200, 38.618, 83.796, 90.00, 104.00, 90.00
R / Rfree (%)	16.7 / 22

The structure of Muty N-Terminal Domain in Complex with Undamaged Dna also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Iron atom in the Muty N-Terminal Domain in Complex with Undamaged Dna (pdb code 5kn8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Muty N-Terminal Domain in Complex with Undamaged Dna, PDB code: 5kn8:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Muty N-Terminal Domain in Complex with Undamaged Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Muty N-Terminal Domain in Complex with Undamaged Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:17.0 occ:1.00 FE1 A:SF4301 0.0 17.0 1.0 S3 A:SF4301 2.2 17.6 1.0 S2 A:SF4301 2.2 17.6 1.0 S4 A:SF4301 2.2 17.5 1.0 SG A:CYS205 2.3 18.8 1.0 FE2 A:SF4301 2.7 16.9 1.0 FE4 A:SF4301 2.7 17.9 1.0 FE3 A:SF4301 2.8 16.8 1.0 CB A:CYS205 3.3 17.0 1.0 CA A:CYS205 3.5 14.9 1.0 S1 A:SF4301 3.8 17.5 1.0 N A:CYS205 4.1 19.7 1.0 CB A:PRO203 4.2 15.8 1.0 CG A:PRO203 4.6 18.2 1.0 CB A:CYS208 4.7 15.2 1.0 CB A:PHE217 4.7 25.6 1.0 SG A:CYS214 4.8 17.5 1.0 CB A:ALA222 4.8 15.9 1.0 C A:CYS205 4.8 15.3 1.0 SG A:CYS208 4.8 17.3 1.0 SG A:CYS198 4.9 17.1 1.0 C A:SER204 4.9 16.9 1.0 CD1 A:PHE217 5.0 25.4 1.0

Iron binding site 2 out of 4 in the Muty N-Terminal Domain in Complex with Undamaged Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Muty N-Terminal Domain in Complex with Undamaged Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:16.9 occ:1.00 FE2 A:SF4301 0.0 16.9 1.0 S3 A:SF4301 2.2 17.6 1.0 S1 A:SF4301 2.2 17.5 1.0 S4 A:SF4301 2.2 17.5 1.0 SG A:CYS198 2.4 17.1 1.0 FE1 A:SF4301 2.7 17.0 1.0 FE3 A:SF4301 2.7 16.8 1.0 FE4 A:SF4301 2.8 17.9 1.0 CB A:CYS198 3.2 17.1 1.0 S2 A:SF4301 3.8 17.6 1.0 CA A:CYS198 3.9 13.5 1.0 CD A:ARG153 4.0 12.8 1.0 NH1 A:ARG153 4.4 12.7 1.0 CB A:ARG153 4.5 15.4 1.0 CB A:PRO203 4.6 15.8 1.0 SG A:CYS208 4.8 17.3 1.0 N A:CYS198 4.8 14.9 1.0 CG A:ARG153 4.9 16.9 1.0 SG A:CYS214 4.9 17.5 1.0 SG A:CYS205 4.9 18.8 1.0 C A:CYS198 5.0 17.0 1.0

Iron binding site 3 out of 4 in the Muty N-Terminal Domain in Complex with Undamaged Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Muty N-Terminal Domain in Complex with Undamaged Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:16.8 occ:1.00 FE3 A:SF4301 0.0 16.8 1.0 S2 A:SF4301 2.2 17.6 1.0 S4 A:SF4301 2.2 17.5 1.0 S1 A:SF4301 2.2 17.5 1.0 SG A:CYS208 2.3 17.3 1.0 FE4 A:SF4301 2.7 17.9 1.0 FE2 A:SF4301 2.7 16.9 1.0 FE1 A:SF4301 2.8 17.0 1.0 CB A:CYS208 3.1 15.2 1.0 S3 A:SF4301 3.8 17.6 1.0 CG2 A:VAL210 4.3 15.8 1.0 CA A:CYS208 4.5 19.5 1.0 CA A:CYS205 4.7 14.9 1.0 CA A:GLN211 4.7 26.4 1.0 N A:GLN211 4.7 22.5 1.0 SG A:CYS198 4.8 17.1 1.0 C A:VAL210 4.9 24.5 1.0 CG1 A:VAL197 4.9 14.1 1.0 CB A:CYS198 4.9 17.1 1.0 SG A:CYS205 4.9 18.8 1.0 SG A:CYS214 4.9 17.5 1.0 CB A:CYS214 5.0 14.9 1.0 O A:VAL210 5.0 19.8 1.0

Iron binding site 4 out of 4 in the Muty N-Terminal Domain in Complex with Undamaged Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Muty N-Terminal Domain in Complex with Undamaged Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:17.9 occ:1.00 FE4 A:SF4301 0.0 17.9 1.0 S1 A:SF4301 2.2 17.5 1.0 S3 A:SF4301 2.2 17.6 1.0 S2 A:SF4301 2.2 17.6 1.0 SG A:CYS214 2.4 17.5 1.0 FE3 A:SF4301 2.7 16.8 1.0 FE1 A:SF4301 2.7 17.0 1.0 FE2 A:SF4301 2.8 16.9 1.0 CB A:CYS214 3.1 14.9 1.0 S4 A:SF4301 3.8 17.5 1.0 CB A:PHE217 4.4 25.6 1.0 CB A:ARG153 4.4 15.4 1.0 CA A:CYS214 4.5 15.2 1.0 CD2 A:LEU154 4.6 16.2 1.0 N A:PHE217 4.7 20.1 1.0 SG A:CYS205 4.8 18.8 1.0 SG A:CYS208 4.9 17.3 1.0 SG A:CYS198 4.9 17.1 1.0

L.Wang, S.Chakravarthy, G.L.Verdine. Structural Basis For the Lesion-Scanning Mechanism of the Muty Dna Glycosylase. J. Biol. Chem. V. 292 5007 2017.
ISSN: ESSN 1083-351X
PubMed: 28130451
DOI: 10.1074/JBC.M116.757039