Iron in PDB 8a5f: Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 R61Q Variant

The structure of Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 R61Q Variant, PDB code: 8a5f 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)	44.82 / 1.38
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	179.318, 38.04, 36.353, 90, 90.96, 90
R / Rfree (%)	15.1 / 18

The structure of Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 R61Q 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 R61Q Variant (pdb code 8a5f). 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 R61Q Variant, PDB code: 8a5f:
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 R61Q 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 R61Q Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe303 b:23.0 occ:1.00 FE1 A:SF4303 0.0 23.0 1.0 S2 A:SF4303 2.2 22.9 1.0 S3 A:SF4303 2.3 22.4 1.0 S4 A:SF4303 2.3 23.3 1.0 SG A:CYS224 2.3 21.4 1.0 FE2 A:SF4303 2.7 23.8 1.0 FE4 A:SF4303 2.7 23.2 1.0 FE3 A:SF4303 2.7 24.4 1.0 CB A:CYS224 3.2 21.5 1.0 S1 A:SF4303 3.9 23.3 1.0 CA A:CYS224 3.9 24.1 1.0 CD A:ARG182 4.2 21.7 1.0 CB A:PRO229 4.4 25.4 1.0 NH1 A:ARG182 4.5 22.4 1.0 SG A:CYS234 4.7 23.6 1.0 CB A:ARG182 4.7 20.5 1.0 SG A:CYS240 4.8 22.2 1.0 SG A:CYS231 4.8 24.5 1.0 N A:CYS224 4.9 22.4 1.0 C A:CYS224 4.9 21.2 1.0 CG A:PRO229 5.0 24.8 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 R61Q 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 R61Q Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe303 b:23.8 occ:1.00 FE2 A:SF4303 0.0 23.8 1.0 S1 A:SF4303 2.3 23.3 1.0 SG A:CYS234 2.3 23.6 1.0 S3 A:SF4303 2.3 22.4 1.0 S4 A:SF4303 2.3 23.3 1.0 FE4 A:SF4303 2.7 23.2 1.0 FE1 A:SF4303 2.7 23.0 1.0 FE3 A:SF4303 2.7 24.4 1.0 CB A:CYS234 3.0 23.5 1.0 S2 A:SF4303 3.8 22.9 1.0 NE2 A:HIS219 4.3 23.0 1.0 CB A:LEU236 4.5 22.6 1.0 CA A:CYS234 4.5 24.6 1.0 CA A:CYS231 4.7 27.6 1.0 SG A:CYS231 4.7 24.5 1.0 SG A:CYS224 4.7 21.4 1.0 N A:ARG237 4.7 24.2 1.0 CA A:ARG237 4.8 24.9 1.0 SG A:CYS240 4.8 22.2 1.0 CB A:CYS224 4.8 21.5 1.0 C A:LEU236 4.9 22.6 1.0 CB A:CYS240 4.9 22.2 1.0 CB A:CYS231 5.0 30.4 1.0 N A:LEU236 5.0 24.0 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 R61Q 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 R61Q Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe303 b:24.4 occ:1.00 FE3 A:SF4303 0.0 24.4 1.0 SG A:CYS231 2.2 24.5 1.0 S4 A:SF4303 2.3 23.3 1.0 S1 A:SF4303 2.3 23.3 1.0 S2 A:SF4303 2.3 22.9 1.0 FE2 A:SF4303 2.7 23.8 1.0 FE4 A:SF4303 2.7 23.2 1.0 FE1 A:SF4303 2.7 23.0 1.0 CB A:CYS231 3.3 30.4 1.0 CA A:CYS231 3.6 27.6 1.0 S3 A:SF4303 3.9 22.4 1.0 CB A:PRO229 4.2 25.4 1.0 N A:CYS231 4.2 26.5 1.0 CG A:PRO229 4.4 24.8 1.0 CB A:CYS234 4.7 23.5 1.0 SG A:CYS240 4.7 22.2 1.0 SG A:CYS234 4.7 23.6 1.0 CG2 A:VAL250 4.7 26.2 1.0 SG A:CYS224 4.8 21.4 1.0 C A:CYS231 4.9 27.0 1.0 CB A:TYR243 4.9 23.5 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 R61Q 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 R61Q Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe303 b:23.2 occ:1.00 FE4 A:SF4303 0.0 23.2 1.0 S3 A:SF4303 2.2 22.4 1.0 S1 A:SF4303 2.3 23.3 1.0 SG A:CYS240 2.3 22.2 1.0 S2 A:SF4303 2.3 22.9 1.0 FE2 A:SF4303 2.7 23.8 1.0 FE1 A:SF4303 2.7 23.0 1.0 FE3 A:SF4303 2.7 24.4 1.0 CB A:CYS240 3.1 22.2 1.0 S4 A:SF4303 3.9 23.3 1.0 CA A:CYS240 4.6 22.8 1.0 CB A:TYR243 4.6 23.5 1.0 N A:TYR243 4.6 22.9 1.0 CB A:ARG182 4.7 20.5 1.0 CG2 A:VAL183 4.7 22.9 1.0 SG A:CYS231 4.7 24.5 1.0 CB A:ALA242 4.7 23.2 1.0 SG A:CYS234 4.8 23.6 1.0 SG A:CYS224 4.8 21.4 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