Iron in PDB 7rdt: Structure of Human NTHL1 - Linker 1 Chimera

All present enzymatic activity of Structure of Human NTHL1 - Linker 1 Chimera:
4.2.99.18;

The structure of Structure of Human NTHL1 - Linker 1 Chimera, PDB code: 7rdt was solved by B.L.Carroll, S.Doublie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.05 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.37, 71.68, 86.52, 90, 90, 90
R / Rfree (%)	18.1 / 23.1

The binding sites of Iron atom in the Structure of Human NTHL1 - Linker 1 Chimera (pdb code 7rdt). 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 Human NTHL1 - Linker 1 Chimera, PDB code: 7rdt:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of Human NTHL1 - Linker 1 Chimera


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Human NTHL1 - Linker 1 Chimera within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:30.5 occ:1.00 FE1 A:SF4401 0.0 30.5 1.0 SG A:CYS293 2.3 31.0 1.0 S3 A:SF4401 2.3 28.1 1.0 S4 A:SF4401 2.3 32.8 1.0 S2 A:SF4401 2.3 29.4 1.0 FE2 A:SF4401 2.7 21.9 1.0 FE3 A:SF4401 2.7 28.5 1.0 FE4 A:SF4401 2.7 26.9 1.0 CB A:CYS293 3.1 39.4 1.0 S1 A:SF4401 3.9 26.1 1.0 CZ A:PHE278 3.9 32.1 1.0 CB A:ASN295 4.2 31.8 1.0 CA A:CYS293 4.6 47.3 1.0 CA A:CYS290 4.6 36.3 1.0 CE2 A:PHE278 4.7 26.3 1.0 SG A:CYS290 4.8 36.0 1.0 C A:ASN295 4.8 31.5 1.0 CE1 A:PHE278 4.8 36.1 1.0 N A:ASN295 4.9 45.2 1.0 CA A:ASN295 4.9 41.4 1.0 N A:GLN296 4.9 35.4 1.0 CG2 A:THR282 4.9 36.9 1.0 CB A:CYS290 4.9 37.0 1.0 SG A:CYS299 4.9 27.0 1.0 CB A:CYS299 5.0 28.8 1.0 SG A:CYS283 5.0 24.7 1.0

Iron binding site 2 out of 4 in the Structure of Human NTHL1 - Linker 1 Chimera


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Human NTHL1 - Linker 1 Chimera within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:21.9 occ:1.00 FE2 A:SF4401 0.0 21.9 1.0 S3 A:SF4401 2.3 28.1 1.0 S4 A:SF4401 2.3 32.8 1.0 S1 A:SF4401 2.3 26.1 1.0 SG A:CYS283 2.5 24.7 1.0 FE1 A:SF4401 2.7 30.5 1.0 FE3 A:SF4401 2.7 28.5 1.0 FE4 A:SF4401 2.7 26.9 1.0 CB A:CYS283 3.3 25.6 1.0 S2 A:SF4401 3.9 29.4 1.0 CA A:CYS283 3.9 28.2 1.0 CE2 A:PHE278 4.3 26.3 1.0 CZ A:PHE278 4.3 32.1 1.0 CD A:ARG241 4.5 17.1 1.0 CB A:PRO288 4.5 32.1 1.0 NH1 A:ARG241 4.6 21.6 1.0 SG A:CYS299 4.7 27.0 1.0 SG A:CYS293 4.8 31.0 1.0 N A:CYS283 4.8 32.8 1.0 SG A:CYS290 4.9 36.0 1.0

Iron binding site 3 out of 4 in the Structure of Human NTHL1 - Linker 1 Chimera


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Human NTHL1 - Linker 1 Chimera within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:28.5 occ:1.00 FE3 A:SF4401 0.0 28.5 1.0 S1 A:SF4401 2.3 26.1 1.0 S4 A:SF4401 2.3 32.8 1.0 S2 A:SF4401 2.3 29.4 1.0 SG A:CYS290 2.3 36.0 1.0 FE4 A:SF4401 2.7 26.9 1.0 FE2 A:SF4401 2.7 21.9 1.0 FE1 A:SF4401 2.7 30.5 1.0 CB A:CYS290 3.2 37.0 1.0 CA A:CYS290 3.6 36.3 1.0 S3 A:SF4401 3.9 28.1 1.0 N A:CYS290 4.0 36.2 1.0 CB A:PRO288 4.0 32.1 1.0 CG A:PRO288 4.3 31.0 1.0 CB A:ALA302 4.5 21.3 1.0 SG A:CYS299 4.7 27.0 1.0 CB A:CYS293 4.7 39.4 1.0 SG A:CYS293 4.8 31.0 1.0 C A:ARG289 4.8 36.9 1.0 SG A:CYS283 4.9 24.7 1.0 C A:CYS290 4.9 39.1 1.0 C A:PRO288 4.9 39.8 1.0

Iron binding site 4 out of 4 in the Structure of Human NTHL1 - Linker 1 Chimera


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Human NTHL1 - Linker 1 Chimera within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:26.9 occ:1.00 FE4 A:SF4401 0.0 26.9 1.0 SG A:CYS299 2.3 27.0 1.0 S1 A:SF4401 2.3 26.1 1.0 S3 A:SF4401 2.3 28.1 1.0 S2 A:SF4401 2.3 29.4 1.0 FE3 A:SF4401 2.7 28.5 1.0 FE1 A:SF4401 2.7 30.5 1.0 FE2 A:SF4401 2.7 21.9 1.0 CB A:CYS299 3.0 28.8 1.0 S4 A:SF4401 3.9 32.8 1.0 CD2 A:LEU242 4.3 27.8 1.0 CB A:ALA302 4.3 21.3 1.0 CA A:CYS299 4.4 26.9 1.0 N A:ALA302 4.6 28.2 1.0 SG A:CYS290 4.7 36.0 1.0 SG A:CYS293 4.8 31.0 1.0 O A:ASN295 4.8 32.2 1.0 CB A:ASN295 4.9 31.8 1.0 CB A:ALA301 4.9 26.2 1.0 SG A:CYS283 5.0 24.7 1.0

B.L.Carroll, K.E.Zahn, J.P.Hanley, S.S.Wallace, J.A.Dragon, S.Doublie. Caught in Motion: Human NTHL1 Undergoes Interdomain Rearrangement Necessary For Catalysis. Nucleic Acids Res. V. 49 13165 2021.
ISSN: ESSN 1362-4962
PubMed: 34871433
DOI: 10.1093/NAR/GKAB1162