Iron in PDB 8a5g: Crystal Structure of Deinococcus Radiodurans Endonuclease III-3 Double Mutant

The structure of Crystal Structure of Deinococcus Radiodurans Endonuclease III-3 Double Mutant, PDB code: 8a5g 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)	44.50 / 1.89
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.345, 38.827, 71.988, 90, 99.71, 90
R / Rfree (%)	23.8 / 28.9

The structure of Crystal Structure of Deinococcus Radiodurans Endonuclease III-3 Double Mutant also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Iron atom in the Crystal Structure of Deinococcus Radiodurans Endonuclease III-3 Double Mutant (pdb code 8a5g). 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-3 Double Mutant, PDB code: 8a5g:
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-3 Double Mutant


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-3 Double Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:38.6 occ:1.00 FE1 A:SF4401 0.0 38.6 1.0 S2 A:SF4401 2.3 19.3 1.0 S4 A:SF4401 2.3 60.9 1.0 S3 A:SF4401 2.3 72.3 1.0 SG A:CYS317 2.4 72.2 1.0 FE4 A:SF4401 2.7 42.0 1.0 FE3 A:SF4401 2.7 45.4 1.0 FE2 A:SF4401 2.8 46.8 1.0 CB A:CYS317 3.2 75.2 1.0 CB A:ARG258 3.8 56.2 1.0 S1 A:SF4401 3.8 41.6 1.0 CB A:SER319 4.2 73.6 1.0 O A:ARG258 4.2 57.2 1.0 C A:ARG258 4.2 54.2 1.0 CG A:LEU259 4.5 49.9 1.0 N A:LEU259 4.5 51.6 1.0 SG A:CYS301 4.5 64.8 1.0 N A:ALA320 4.6 73.8 1.0 CD2 A:LEU259 4.6 51.7 1.0 CA A:CYS317 4.6 71.6 1.0 CA A:ARG258 4.7 57.1 1.0 CG A:ARG258 4.8 52.8 1.0 SG A:CYS311 4.8 94.0 1.0 C A:SER319 4.8 74.2 1.0 CA A:SER319 4.9 73.8 1.0 N A:SER319 4.9 73.3 1.0 CA A:LEU259 4.9 53.6 1.0 CD A:ARG258 4.9 52.2 1.0 O A:ALA255 5.0 49.5 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Deinococcus Radiodurans Endonuclease III-3 Double Mutant


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-3 Double Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:46.8 occ:1.00 FE2 A:SF4401 0.0 46.8 1.0 SG A:CYS301 1.8 64.8 1.0 S1 A:SF4401 2.2 41.6 1.0 S3 A:SF4401 2.3 72.3 1.0 S4 A:SF4401 2.3 60.9 1.0 FE4 A:SF4401 2.7 42.0 1.0 FE3 A:SF4401 2.8 45.4 1.0 FE1 A:SF4401 2.8 38.6 1.0 CB A:CYS301 3.0 58.7 1.0 S2 A:SF4401 3.8 19.3 1.0 CD A:ARG258 3.9 52.2 1.0 CA A:CYS301 3.9 58.2 1.0 CB A:ARG258 4.1 56.2 1.0 NH2 A:ARG258 4.5 52.2 1.0 CE1 A:HIS296 4.5 55.1 1.0 CB A:PRO306 4.5 61.7 1.0 SG A:CYS311 4.6 94.0 1.0 CG A:ARG258 4.6 52.8 1.0 CA A:ALA255 4.6 48.3 1.0 CB A:ALA255 4.6 47.8 1.0 NE2 A:HIS296 4.7 55.5 1.0 C A:CYS301 4.8 59.7 1.0 O A:CYS301 4.9 58.2 1.0 NE A:ARG258 4.9 53.0 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Deinococcus Radiodurans Endonuclease III-3 Double Mutant


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-3 Double Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:45.4 occ:1.00 FE3 A:SF4401 0.0 45.4 1.0 S4 A:SF4401 2.3 60.9 1.0 S2 A:SF4401 2.3 19.3 1.0 S1 A:SF4401 2.3 41.6 1.0 SG A:CYS308 2.7 73.1 1.0 FE1 A:SF4401 2.7 38.6 1.0 FE2 A:SF4401 2.8 46.8 1.0 FE4 A:SF4401 2.8 42.0 1.0 CB A:CYS308 3.6 63.0 1.0 CA A:CYS308 3.7 64.5 1.0 S3 A:SF4401 3.9 72.3 1.0 CB A:PRO306 4.2 61.7 1.0 N A:CYS308 4.3 62.1 1.0 SG A:CYS301 4.3 64.8 1.0 SG A:CYS311 4.3 94.0 1.0 CD2 A:PHE323 4.4 75.1 1.0 CG A:PRO306 4.5 63.0 1.0 CA A:ALA320 4.6 74.2 1.0 SG A:CYS317 4.6 72.2 1.0 CE2 A:PHE323 4.7 74.9 1.0 N A:ALA320 4.7 73.8 1.0 CB A:ALA320 4.8 73.8 1.0 CB A:CYS311 5.0 85.3 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Deinococcus Radiodurans Endonuclease III-3 Double Mutant


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-3 Double Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:42.0 occ:1.00 FE4 A:SF4401 0.0 42.0 1.0 SG A:CYS311 2.2 94.0 1.0 S2 A:SF4401 2.2 19.3 1.0 S1 A:SF4401 2.3 41.6 1.0 S3 A:SF4401 2.3 72.3 1.0 FE2 A:SF4401 2.7 46.8 1.0 FE1 A:SF4401 2.7 38.6 1.0 FE3 A:SF4401 2.8 45.4 1.0 CB A:CYS311 3.6 85.3 1.0 NE2 A:HIS296 3.8 55.5 1.0 S4 A:SF4401 3.9 60.9 1.0 SG A:CYS301 4.3 64.8 1.0 CE1 A:HIS296 4.3 55.1 1.0 CB A:CYS317 4.5 75.2 1.0 CB A:CYS301 4.6 58.7 1.0 SG A:CYS317 4.6 72.2 1.0 CB A:LEU313 4.8 69.9 1.0 CA A:CYS311 4.9 72.1 1.0 O A:LEU313 5.0 70.7 1.0 CA A:CYS308 5.0 64.5 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