Iron in PDB 8a5c: Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 Y100L Variant

The structure of Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 Y100L Variant, PDB code: 8a5c was solved by P.T.Borges, F.Rollo, E.Moe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.63 / 1.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	178.526, 37.827, 36.55, 90, 90.61, 90
R / Rfree (%)	19.4 / 24.7

The structure of Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 Y100L Variant also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Iron atom in the Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 Y100L Variant (pdb code 8a5c). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 Y100L Variant, PDB code: 8a5c:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 Y100L Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 Y100L Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:43.6 occ:1.00 FE1 A:SF4301 0.0 43.6 1.0 S3 A:SF4301 2.2 46.6 1.0 S2 A:SF4301 2.2 49.2 1.0 S4 A:SF4301 2.3 49.0 1.0 SG A:CYS224 2.3 49.5 1.0 FE4 A:SF4301 2.6 48.4 1.0 FE2 A:SF4301 2.7 48.5 1.0 FE3 A:SF4301 2.8 50.0 1.0 CB A:CYS224 3.2 45.3 1.0 S1 A:SF4301 3.9 48.8 1.0 CA A:CYS224 3.9 57.2 1.0 CD A:ARG182 4.3 47.2 1.0 CB A:PRO229 4.5 45.6 1.0 SG A:CYS240 4.6 48.6 1.0 NH1 A:ARG182 4.6 50.2 1.0 SG A:CYS234 4.6 50.5 1.0 CB A:ARG182 4.8 39.8 1.0 N A:CYS224 4.9 57.3 1.0 SG A:CYS231 4.9 52.5 1.0 C A:CYS224 5.0 60.2 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 Y100L Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 Y100L Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:48.5 occ:1.00 FE2 A:SF4301 0.0 48.5 1.0 SG A:CYS234 2.2 50.5 1.0 S4 A:SF4301 2.2 49.0 1.0 S3 A:SF4301 2.3 46.6 1.0 S1 A:SF4301 2.3 48.8 1.0 FE1 A:SF4301 2.7 43.6 1.0 FE4 A:SF4301 2.7 48.4 1.0 FE3 A:SF4301 2.7 50.0 1.0 CB A:CYS234 3.0 42.5 1.0 S2 A:SF4301 3.8 49.2 1.0 NE2 A:HIS219 4.2 58.1 1.0 CA A:CYS234 4.4 53.8 1.0 CA A:CYS231 4.6 60.3 1.0 SG A:CYS240 4.6 48.6 1.0 CB A:LEU236 4.7 53.8 1.0 N A:ARG237 4.7 55.9 1.0 SG A:CYS224 4.7 49.5 1.0 CA A:ARG237 4.7 46.0 1.0 SG A:CYS231 4.8 52.5 1.0 CB A:CYS224 4.8 45.3 1.0 CB A:CYS231 4.9 55.5 1.0 CG1 A:VAL223 4.9 52.4 1.0 CB A:CYS240 4.9 44.7 1.0 C A:LEU236 5.0 53.5 1.0 CG A:LEU236 5.0 46.4 1.0 CD1 A:LEU236 5.0 40.0 1.0 N A:LEU236 5.0 51.3 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 Y100L Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 Y100L Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:50.0 occ:1.00 FE3 A:SF4301 0.0 50.0 1.0 S1 A:SF4301 2.3 48.8 1.0 S4 A:SF4301 2.3 49.0 1.0 SG A:CYS231 2.3 52.5 1.0 S2 A:SF4301 2.3 49.2 1.0 FE2 A:SF4301 2.7 48.5 1.0 FE4 A:SF4301 2.7 48.4 1.0 FE1 A:SF4301 2.8 43.6 1.0 CB A:CYS231 3.2 55.5 1.0 CA A:CYS231 3.6 60.3 1.0 S3 A:SF4301 3.9 46.6 1.0 N A:CYS231 4.1 58.3 1.0 CB A:PRO229 4.1 45.6 1.0 CG A:PRO229 4.4 54.4 1.0 SG A:CYS240 4.6 48.6 1.0 CB A:CYS234 4.6 42.5 1.0 SG A:CYS234 4.6 50.5 1.0 CG2 A:VAL250 4.7 50.8 1.0 SG A:CYS224 4.9 49.5 1.0 C A:CYS231 4.9 55.8 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 Y100L Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 Y100L Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:48.4 occ:1.00 FE4 A:SF4301 0.0 48.4 1.0 SG A:CYS240 2.1 48.6 1.0 S3 A:SF4301 2.2 46.6 1.0 S2 A:SF4301 2.2 49.2 1.0 S1 A:SF4301 2.3 48.8 1.0 FE1 A:SF4301 2.6 43.6 1.0 FE2 A:SF4301 2.7 48.5 1.0 FE3 A:SF4301 2.7 50.0 1.0 CB A:CYS240 3.2 44.7 1.0 S4 A:SF4301 3.8 49.0 1.0 CG2 A:VAL183 4.6 48.0 1.0 CA A:CYS240 4.6 51.6 1.0 CB A:ALA242 4.6 44.3 1.0 N A:TYR243 4.6 54.4 1.0 SG A:CYS234 4.7 50.5 1.0 CB A:ARG182 4.7 39.8 1.0 SG A:CYS224 4.8 49.5 1.0 SG A:CYS231 4.8 52.5 1.0 CB A:TYR243 4.8 52.1 1.0

F.Rollo, P.T.Borges, C.M.Silveira, M.T.G.Rosa, S.Todorovic, E.Moe. Disentangling Unusual Catalytic Properties and the Role of the [4FE-4S] Cluster of Three Endonuclease III From the Extremophile D. Radiodurans. Molecules V. 27 2022.
ISSN: ESSN 1420-3049
PubMed: 35807515
DOI: 10.3390/MOLECULES27134270