Iron in PDB 4uob: Crystal Structure of Deinococcus Radiodurans Endonuclease III-3

All present enzymatic activity of Crystal Structure of Deinococcus Radiodurans Endonuclease III-3:
4.2.99.18;

The structure of Crystal Structure of Deinococcus Radiodurans Endonuclease III-3, PDB code: 4uob was solved by A.Sarre, M.Okvist, T.Klar, D.Hall, A.O.Smalas, S.Mcsweeney, J.Timmins, E.Moe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.932 / 1.31
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	91.240, 40.510, 72.150, 90.00, 102.34, 90.00
R / Rfree (%)	13.35 / 15.93

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

Cobalt

(Co)

1 atom

The binding sites of Iron atom in the Crystal Structure of Deinococcus Radiodurans Endonuclease III-3 (pdb code 4uob). 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, PDB code: 4uob:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1329 b:11.1 occ:1.00 FE1 A:SF41329 0.0 11.1 1.0 S3 A:SF41329 2.3 10.8 1.0 S2 A:SF41329 2.3 11.5 1.0 SG A:CYS317 2.3 13.0 1.0 S4 A:SF41329 2.3 11.2 1.0 FE4 A:SF41329 2.7 10.3 1.0 FE3 A:SF41329 2.7 11.2 1.0 FE2 A:SF41329 2.7 10.7 1.0 HB2 A:CYS317 3.1 15.5 1.0 CB A:CYS317 3.1 12.9 1.0 HB3 A:CYS317 3.3 15.5 1.0 HB3 A:ALA320 3.8 18.5 1.0 HB3 A:ARG258 3.9 12.5 1.0 S1 A:SF41329 3.9 10.3 1.0 HB2 A:SER319 3.9 16.0 1.0 HD21 A:LEU259 4.0 13.1 1.0 HD22 A:LEU259 4.1 13.1 1.0 H A:ALA320 4.2 17.9 1.0 HG A:LEU259 4.2 12.6 1.0 HA A:ALA320 4.4 18.9 1.0 CD2 A:LEU259 4.5 10.9 1.0 N A:ALA320 4.5 15.0 1.0 HA A:ARG314 4.5 17.1 1.0 H A:SER319 4.5 17.2 1.0 CA A:CYS317 4.6 13.3 1.0 HB2 A:ARG258 4.6 12.5 1.0 HB2 A:LEU313 4.7 13.8 1.0 CB A:ARG258 4.7 10.4 1.0 SG A:CYS308 4.7 12.8 1.0 CB A:ALA320 4.7 15.4 1.0 HD3 A:ARG258 4.7 13.4 1.0 HA A:CYS317 4.8 16.0 1.0 CA A:ALA320 4.8 15.7 1.0 SG A:CYS301 4.8 10.4 1.0 SG A:CYS311 4.8 10.6 1.0 CG A:LEU259 4.8 10.5 1.0 CB A:SER319 4.9 13.3 1.0 HA A:LEU259 5.0 13.4 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1329 b:10.7 occ:1.00 FE2 A:SF41329 0.0 10.7 1.0 SG A:CYS301 2.3 10.4 1.0 S1 A:SF41329 2.3 10.3 1.0 S4 A:SF41329 2.3 11.2 1.0 S3 A:SF41329 2.3 10.8 1.0 FE4 A:SF41329 2.7 10.3 1.0 FE3 A:SF41329 2.7 11.2 1.0 FE1 A:SF41329 2.7 11.1 1.0 HB2 A:CYS301 3.1 12.8 1.0 CB A:CYS301 3.2 10.7 1.0 HA A:CYS301 3.3 11.4 1.0 HD3 A:ARG258 3.5 13.4 1.0 CA A:CYS301 3.8 9.5 1.0 HE1 A:HIS296 3.8 11.9 1.0 S2 A:SF41329 3.9 11.5 1.0 HH21 A:ARG258 3.9 13.7 1.0 HB3 A:CYS301 4.0 12.8 1.0 HB2 A:PRO306 4.1 14.2 1.0 HE2 A:HIS296 4.2 12.2 1.0 HD2 A:ARG258 4.2 13.4 1.0 HB3 A:ARG258 4.3 12.5 1.0 HB2 A:ARG258 4.3 12.5 1.0 HA A:ALA255 4.3 11.8 1.0 CD A:ARG258 4.3 11.2 1.0 HB3 A:PRO306 4.4 14.2 1.0 CE1 A:HIS296 4.4 9.9 1.0 HB2 A:ALA255 4.6 12.5 1.0 NE2 A:HIS296 4.6 10.2 1.0 CB A:ARG258 4.7 10.4 1.0 CB A:PRO306 4.7 11.8 1.0 HB3 A:ALA255 4.7 12.5 1.0 NH2 A:ARG258 4.7 11.4 1.0 HG23 A:THR300 4.8 14.2 1.0 SG A:CYS311 4.8 10.6 1.0 N A:CYS301 4.8 10.6 1.0 SG A:CYS308 4.8 12.8 1.0 SG A:CYS317 4.8 13.0 1.0 C A:CYS301 4.9 10.6 1.0 CB A:ALA255 5.0 10.4 1.0 HG A:LEU259 5.0 12.6 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1329 b:11.2 occ:1.00 FE3 A:SF41329 0.0 11.2 1.0 SG A:CYS308 2.3 12.8 1.0 S4 A:SF41329 2.3 11.2 1.0 S2 A:SF41329 2.3 11.5 1.0 S1 A:SF41329 2.3 10.3 1.0 FE1 A:SF41329 2.7 11.1 1.0 FE2 A:SF41329 2.7 10.7 1.0 FE4 A:SF41329 2.7 10.3 1.0 HA A:CYS308 3.0 14.9 1.0 CB A:CYS308 3.2 12.3 1.0 HB3 A:CYS308 3.2 14.8 1.0 HB2 A:PRO306 3.4 14.2 1.0 CA A:CYS308 3.5 12.4 1.0 HA A:ALA320 3.7 18.9 1.0 S3 A:SF41329 3.9 10.8 1.0 H A:CYS308 3.9 13.8 1.0 N A:CYS308 4.0 11.5 1.0 HB3 A:ALA320 4.0 18.5 1.0 HB2 A:CYS308 4.1 14.8 1.0 HD2 A:PHE323 4.2 16.8 1.0 CB A:PRO306 4.3 11.8 1.0 HB3 A:CYS311 4.4 13.6 1.0 HB2 A:CYS311 4.4 13.6 1.0 HG2 A:PRO306 4.4 14.8 1.0 CA A:ALA320 4.5 15.7 1.0 HB3 A:PRO306 4.6 14.2 1.0 CB A:ALA320 4.6 15.4 1.0 HA A:CYS301 4.6 11.4 1.0 HG3 A:PRO306 4.7 14.8 1.0 SG A:CYS317 4.7 13.0 1.0 HB2 A:ALA320 4.7 18.5 1.0 CG A:PRO306 4.7 12.3 1.0 CB A:CYS311 4.7 11.3 1.0 SG A:CYS301 4.7 10.4 1.0 CD2 A:PHE323 4.8 14.0 1.0 SG A:CYS311 4.8 10.6 1.0 C A:CYS308 4.8 12.4 1.0 HD3 A:ARG258 4.9 13.4 1.0 N A:ALA320 4.9 15.0 1.0 C A:LEU307 4.9 10.9 1.0 HB2 A:PHE323 5.0 18.6 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1329 b:10.3 occ:1.00 FE4 A:SF41329 0.0 10.3 1.0 S3 A:SF41329 2.3 10.8 1.0 S2 A:SF41329 2.3 11.5 1.0 S1 A:SF41329 2.3 10.3 1.0 SG A:CYS311 2.3 10.6 1.0 FE1 A:SF41329 2.7 11.1 1.0 FE2 A:SF41329 2.7 10.7 1.0 FE3 A:SF41329 2.7 11.2 1.0 HE2 A:HIS296 3.1 12.2 1.0 CB A:CYS311 3.1 11.3 1.0 HB3 A:CYS311 3.1 13.6 1.0 HB2 A:CYS311 3.2 13.6 1.0 HB2 A:LEU313 3.6 13.8 1.0 HA A:CYS308 3.7 14.9 1.0 NE2 A:HIS296 3.9 10.2 1.0 S4 A:SF41329 3.9 11.2 1.0 HG23 A:THR300 4.1 14.2 1.0 HE1 A:HIS296 4.2 11.9 1.0 HA A:ARG314 4.4 17.1 1.0 HB2 A:CYS301 4.4 12.8 1.0 H A:LEU313 4.4 13.4 1.0 CE1 A:HIS296 4.4 9.9 1.0 HD13 A:LEU313 4.5 15.0 1.0 HB2 A:CYS317 4.5 15.5 1.0 CB A:LEU313 4.6 11.5 1.0 HG22 A:THR300 4.6 14.2 1.0 CA A:CYS311 4.6 12.2 1.0 CA A:CYS308 4.6 12.4 1.0 HD22 A:LEU259 4.7 13.1 1.0 SG A:CYS301 4.8 10.4 1.0 N A:ARG314 4.8 12.6 1.0 HB3 A:CYS308 4.8 14.8 1.0 SG A:CYS308 4.8 12.8 1.0 CG2 A:THR300 4.8 11.9 1.0 HB2 A:ARG314 4.8 19.7 1.0 SG A:CYS317 4.8 13.0 1.0 H A:ARG314 4.8 15.1 1.0 HB3 A:CYS317 4.9 15.5 1.0 HA A:CYS301 4.9 11.4 1.0 HA A:CYS311 4.9 14.6 1.0 C A:LEU313 4.9 12.2 1.0 CB A:CYS317 4.9 12.9 1.0 CB A:CYS308 5.0 12.3 1.0

A.Sarre, M.Okvist, T.Klar, D.R.Hall, A.O.Smalas, S.Mcsweeney, J.Timmins, E.Moe. Structural and Functional Characterization of Two Unusual Endonuclease III Enzymes From Deinococcus Radiodurans. J.Struct.Biol. V. 191 87 2015.
ISSN: ISSN 1047-8477
PubMed: 26172070
DOI: 10.1016/J.JSB.2015.05.009