Iron in PDB 9hnk: Structure of the (6-4) Photolyase of Caulobacter Crescentus in Its Oxidizd State - Singal Crystal / Synchrotron

The structure of Structure of the (6-4) Photolyase of Caulobacter Crescentus in Its Oxidizd State - Singal Crystal / Synchrotron, PDB code: 9hnk was solved by W.Po Hsun, M.Maestre-Reyna, L.-O.Essen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.36 / 1.59
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.274, 102.73, 103.893, 90, 90, 90
R / Rfree (%)	18.1 / 20.2

The binding sites of Iron atom in the Structure of the (6-4) Photolyase of Caulobacter Crescentus in Its Oxidizd State - Singal Crystal / Synchrotron (pdb code 9hnk). 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 the (6-4) Photolyase of Caulobacter Crescentus in Its Oxidizd State - Singal Crystal / Synchrotron, PDB code: 9hnk:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of the (6-4) Photolyase of Caulobacter Crescentus in Its Oxidizd State - Singal Crystal / Synchrotron


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of the (6-4) Photolyase of Caulobacter Crescentus in Its Oxidizd State - Singal Crystal / Synchrotron within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:21.4 occ:1.00 FE1 A:SF4603 0.0 21.4 1.0 S4 A:SF4603 2.2 21.1 1.0 S3 A:SF4603 2.3 21.8 1.0 SG A:CYS437 2.3 24.4 1.0 S2 A:SF4603 2.3 20.7 1.0 FE2 A:SF4603 2.7 20.9 1.0 FE3 A:SF4603 2.7 20.3 1.0 FE4 A:SF4603 2.8 20.9 1.0 HA A:CYS437 3.0 28.5 1.0 CB A:CYS437 3.3 24.2 1.0 HB3 A:CYS437 3.4 29.0 1.0 CA A:CYS437 3.6 23.7 1.0 HB A:VAL444 3.7 32.4 1.0 HG21 A:VAL444 3.8 32.8 1.0 S1 A:SF4603 3.9 20.8 1.0 HG22 A:ILE430 4.0 27.1 1.0 HG23 A:VAL444 4.0 32.8 1.0 HG21 A:ILE430 4.1 27.1 1.0 N A:CYS437 4.2 23.9 1.0 HB2 A:CYS437 4.2 29.0 1.0 CG2 A:VAL444 4.2 27.4 1.0 HB2 A:TYR436 4.2 27.9 1.0 HB3 A:TYR436 4.3 27.9 1.0 HB3 A:CYS440 4.3 28.6 1.0 HB A:ILE430 4.3 27.4 1.0 HB2 A:CYS440 4.3 28.6 1.0 H A:CYS437 4.4 28.6 1.0 CG2 A:ILE430 4.5 22.6 1.0 CB A:VAL444 4.5 27.0 1.0 HB3 A:CYS349 4.6 22.6 1.0 CB A:CYS440 4.7 23.8 1.0 SG A:CYS453 4.7 23.6 1.0 SG A:CYS440 4.7 22.9 1.0 HB2 A:ASP431 4.7 34.0 1.0 CB A:TYR436 4.7 23.2 1.0 C A:TYR436 4.8 23.4 1.0 HB2 A:CYS453 4.8 28.4 1.0 SG A:CYS349 4.8 19.5 1.0 H A:CYS349 4.9 22.5 1.0 C A:CYS437 4.9 23.9 1.0 CB A:ILE430 5.0 22.8 1.0 HA A:ASP431 5.0 34.1 1.0 O A:GLY427 5.0 25.1 1.0 HA3 A:GLY427 5.0 29.5 1.0

Iron binding site 2 out of 4 in the Structure of the (6-4) Photolyase of Caulobacter Crescentus in Its Oxidizd State - Singal Crystal / Synchrotron


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of the (6-4) Photolyase of Caulobacter Crescentus in Its Oxidizd State - Singal Crystal / Synchrotron within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:20.9 occ:1.00 FE2 A:SF4603 0.0 20.9 1.0 S3 A:SF4603 2.2 21.8 1.0 S4 A:SF4603 2.2 21.1 1.0 S1 A:SF4603 2.3 20.8 1.0 SG A:CYS453 2.3 23.6 1.0 FE1 A:SF4603 2.7 21.4 1.0 FE3 A:SF4603 2.7 20.3 1.0 FE4 A:SF4603 2.7 20.9 1.0 HB2 A:CYS453 3.0 28.4 1.0 CB A:CYS453 3.2 23.7 1.0 HD1 A:PHE455 3.5 25.5 1.0 HG23 A:VAL444 3.7 32.8 1.0 HA A:CYS453 3.7 27.1 1.0 S2 A:SF4603 3.9 20.7 1.0 HB3 A:CYS453 4.0 28.4 1.0 CA A:CYS453 4.0 22.6 1.0 HD2 A:PRO454 4.0 24.9 1.0 HA3 A:GLY427 4.1 29.5 1.0 HB2 A:TYR442 4.1 31.9 1.0 CD1 A:PHE455 4.2 21.2 1.0 HB2 A:PHE455 4.3 27.2 1.0 HB A:VAL444 4.3 32.4 1.0 H A:PHE455 4.4 25.7 1.0 HA A:VAL444 4.5 32.1 1.0 CG2 A:VAL444 4.5 27.4 1.0 HA2 A:GLY427 4.5 29.5 1.0 HG21 A:VAL444 4.6 32.8 1.0 HB3 A:TYR442 4.7 31.9 1.0 HE1 A:PHE455 4.7 25.0 1.0 SG A:CYS437 4.7 24.4 1.0 C A:CYS453 4.7 22.2 1.0 CA A:GLY427 4.8 24.6 1.0 HD2 A:TYR442 4.8 30.1 1.0 CD A:PRO454 4.8 20.8 1.0 SG A:CYS440 4.8 22.9 1.0 CB A:TYR442 4.8 26.6 1.0 SG A:CYS349 4.8 19.5 1.0 CB A:VAL444 4.9 27.0 1.0 CE1 A:PHE455 4.9 20.8 1.0 HD3 A:PRO454 4.9 24.9 1.0 N A:PRO454 4.9 21.4 1.0 HG2 A:MET347 5.0 26.3 1.0

Iron binding site 3 out of 4 in the Structure of the (6-4) Photolyase of Caulobacter Crescentus in Its Oxidizd State - Singal Crystal / Synchrotron


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of the (6-4) Photolyase of Caulobacter Crescentus in Its Oxidizd State - Singal Crystal / Synchrotron within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:20.3 occ:1.00 FE3 A:SF4603 0.0 20.3 1.0 S4 A:SF4603 2.2 21.1 1.0 S2 A:SF4603 2.3 20.7 1.0 S1 A:SF4603 2.3 20.8 1.0 SG A:CYS349 2.3 19.5 1.0 FE2 A:SF4603 2.7 20.9 1.0 FE4 A:SF4603 2.7 20.9 1.0 FE1 A:SF4603 2.7 21.4 1.0 H A:CYS349 3.1 22.5 1.0 HB3 A:CYS349 3.2 22.6 1.0 CB A:CYS349 3.4 18.8 1.0 HG21 A:ILE430 3.6 27.1 1.0 HE1 A:PHE455 3.7 25.0 1.0 S3 A:SF4603 3.9 21.8 1.0 N A:CYS349 3.9 18.8 1.0 HB3 A:MET347 3.9 25.8 1.0 HD1 A:PHE455 4.0 25.5 1.0 HD13 A:ILE430 4.0 24.6 1.0 HB2 A:CYS349 4.1 22.6 1.0 H A:ALA348 4.2 24.8 1.0 CE1 A:PHE455 4.2 20.8 1.0 HD12 A:ILE430 4.3 24.6 1.0 CA A:CYS349 4.3 18.5 1.0 CD1 A:PHE455 4.4 21.2 1.0 CG2 A:ILE430 4.4 22.6 1.0 HG22 A:ILE430 4.4 27.1 1.0 HA A:MET347 4.5 25.7 1.0 N A:ALA348 4.5 20.7 1.0 HB A:ILE430 4.6 27.4 1.0 H A:VAL350 4.6 20.9 1.0 HB3 A:TYR436 4.6 27.9 1.0 CD1 A:ILE430 4.6 20.5 1.0 SG A:CYS440 4.7 22.9 1.0 SG A:CYS453 4.7 23.6 1.0 HB3 A:ALA348 4.7 24.2 1.0 CB A:MET347 4.8 21.5 1.0 SG A:CYS437 4.8 24.4 1.0 HG23 A:VAL350 4.8 21.8 1.0 C A:MET347 4.9 21.2 1.0 HB2 A:TYR436 4.9 27.9 1.0 CA A:MET347 4.9 21.4 1.0 HG2 A:MET347 5.0 26.3 1.0 HA A:CYS349 5.0 22.2 1.0

Iron binding site 4 out of 4 in the Structure of the (6-4) Photolyase of Caulobacter Crescentus in Its Oxidizd State - Singal Crystal / Synchrotron


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of the (6-4) Photolyase of Caulobacter Crescentus in Its Oxidizd State - Singal Crystal / Synchrotron within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:20.9 occ:1.00 FE4 A:SF4603 0.0 20.9 1.0 S1 A:SF4603 2.2 20.8 1.0 SG A:CYS440 2.3 22.9 1.0 S2 A:SF4603 2.3 20.7 1.0 S3 A:SF4603 2.3 21.8 1.0 FE2 A:SF4603 2.7 20.9 1.0 FE3 A:SF4603 2.7 20.3 1.0 FE1 A:SF4603 2.8 21.4 1.0 CB A:CYS440 3.1 23.8 1.0 HB2 A:CYS440 3.1 28.6 1.0 HB3 A:CYS440 3.2 28.6 1.0 HB2 A:TYR442 3.2 31.9 1.0 H A:ALA348 3.3 24.8 1.0 HD2 A:TYR442 3.5 30.1 1.0 HA A:MET347 3.7 25.7 1.0 S4 A:SF4603 3.8 21.1 1.0 HA A:CYS437 3.9 28.5 1.0 N A:ALA348 4.0 20.7 1.0 HB3 A:ALA348 4.1 24.2 1.0 H A:CYS349 4.1 22.5 1.0 CB A:TYR442 4.2 26.6 1.0 H A:TYR442 4.3 32.3 1.0 CD2 A:TYR442 4.4 25.1 1.0 CA A:MET347 4.5 21.4 1.0 HB3 A:TYR442 4.6 31.9 1.0 HB3 A:MET347 4.6 25.8 1.0 CA A:CYS440 4.6 23.9 1.0 HB2 A:CYS453 4.7 28.4 1.0 C A:MET347 4.7 21.2 1.0 HG2 A:MET347 4.7 26.3 1.0 CB A:ALA348 4.7 20.2 1.0 SG A:CYS349 4.8 19.5 1.0 HB2 A:ALA348 4.8 24.2 1.0 SG A:CYS437 4.8 24.4 1.0 CG A:TYR442 4.8 25.8 1.0 CA A:CYS437 4.8 23.7 1.0 HA A:CYS440 4.9 28.7 1.0 SG A:CYS453 4.9 23.6 1.0 HA A:CYS453 4.9 27.1 1.0 N A:CYS349 4.9 18.8 1.0 HB3 A:TYR436 4.9 27.9 1.0 CA A:ALA348 4.9 20.1 1.0 N A:TYR442 5.0 26.9 1.0 O A:ASP346 5.0 26.8 1.0 O A:TYR442 5.0 28.8 1.0

P.H.Wang, Y.Hosokawa, J.C Soares, H.J.Emmerich, V.Fuchs, N.Caramello, S.Engilberge, A.Bologna, C.J.Rosner, M.Nakamura, M.Watad, F.Luo, S.Owada, T.Tosha, J.Kang, K.Tono, Y.Bessho, E.Nango, A.J.Pierik, A.Royant, M.D.Tsai, J.Yamamoto, M.Maestre-Reyna, L.O.Essen. Redox-State-Dependent Structural Changes Within A Prokaryotic 6-4 Photolyase. J.Am.Chem.Soc. 2025.
ISSN: ESSN 1520-5126
PubMed: 40298610
DOI: 10.1021/JACS.4C18116