Iron in PDB 9hnm: Structure of the (6-4) Photolyase of Caulobacter Crescentus in Its Dark Adapted and Oxidized State Determined By Serial Femtosecond Crystallography

The structure of Structure of the (6-4) Photolyase of Caulobacter Crescentus in Its Dark Adapted and Oxidized State Determined By Serial Femtosecond Crystallography, PDB code: 9hnm 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)	24.23 / 1.71
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.8, 103.4, 104.8, 90, 90, 90
R / Rfree (%)	15.9 / 18.7

The binding sites of Iron atom in the Structure of the (6-4) Photolyase of Caulobacter Crescentus in Its Dark Adapted and Oxidized State Determined By Serial Femtosecond Crystallography (pdb code 9hnm). 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 Dark Adapted and Oxidized State Determined By Serial Femtosecond Crystallography, PDB code: 9hnm:
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 Dark Adapted and Oxidized State Determined By Serial Femtosecond Crystallography


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 Dark Adapted and Oxidized State Determined By Serial Femtosecond Crystallography within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:27.2 occ:1.00 FE1 A:SF4603 0.0 27.2 1.0 S4 A:SF4603 2.3 26.6 1.0 S2 A:SF4603 2.3 26.8 1.0 S3 A:SF4603 2.3 27.7 1.0 SG A:CYS437 2.3 32.0 1.0 FE2 A:SF4603 2.7 27.1 1.0 FE3 A:SF4603 2.7 26.1 1.0 FE4 A:SF4603 2.8 28.1 1.0 CB A:CYS437 3.3 31.2 1.0 CA A:CYS437 3.6 32.3 1.0 S1 A:SF4603 3.9 27.2 1.0 N A:CYS437 4.2 32.6 1.0 CG2 A:VAL444 4.3 37.2 1.0 CG2 A:ILE430 4.5 29.8 1.0 CB A:VAL444 4.6 36.2 1.0 CB A:CYS440 4.6 31.2 1.0 SG A:CYS453 4.7 30.2 1.0 C A:TYR436 4.7 30.0 1.0 SG A:CYS440 4.8 29.5 1.0 CB A:TYR436 4.8 29.3 1.0 SG A:CYS349 4.8 25.5 1.0 CB A:ILE430 4.9 29.0 1.0 C A:CYS437 5.0 32.6 1.0

Iron binding site 2 out of 4 in the Structure of the (6-4) Photolyase of Caulobacter Crescentus in Its Dark Adapted and Oxidized State Determined By Serial Femtosecond Crystallography


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 Dark Adapted and Oxidized State Determined By Serial Femtosecond Crystallography within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:27.1 occ:1.00 FE2 A:SF4603 0.0 27.1 1.0 S3 A:SF4603 2.2 27.7 1.0 S1 A:SF4603 2.3 27.2 1.0 S4 A:SF4603 2.3 26.6 1.0 SG A:CYS453 2.3 30.2 1.0 FE4 A:SF4603 2.7 28.1 1.0 FE1 A:SF4603 2.7 27.2 1.0 FE3 A:SF4603 2.8 26.1 1.0 CB A:CYS453 3.3 30.1 1.0 S2 A:SF4603 3.9 26.8 1.0 CA A:CYS453 4.1 30.2 1.0 CD1 A:PHE455 4.2 28.5 1.0 CG2 A:VAL444 4.6 37.2 1.0 CD A:PRO454 4.7 30.7 1.0 SG A:CYS437 4.7 32.0 1.0 C A:CYS453 4.8 30.6 1.0 CE1 A:PHE455 4.8 30.7 1.0 CB A:TYR442 4.8 36.8 1.0 SG A:CYS440 4.8 29.5 1.0 SG A:CYS349 4.9 25.5 1.0 CA A:GLY427 4.9 30.3 1.0 CB A:VAL444 4.9 36.2 1.0 N A:PRO454 4.9 30.8 1.0

Iron binding site 3 out of 4 in the Structure of the (6-4) Photolyase of Caulobacter Crescentus in Its Dark Adapted and Oxidized State Determined By Serial Femtosecond Crystallography


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 Dark Adapted and Oxidized State Determined By Serial Femtosecond Crystallography within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:26.1 occ:1.00 FE3 A:SF4603 0.0 26.1 1.0 S2 A:SF4603 2.2 26.8 1.0 S4 A:SF4603 2.3 26.6 1.0 SG A:CYS349 2.3 25.5 1.0 S1 A:SF4603 2.3 27.2 1.0 FE1 A:SF4603 2.7 27.2 1.0 FE4 A:SF4603 2.8 28.1 1.0 FE2 A:SF4603 2.8 27.1 1.0 CB A:CYS349 3.4 25.1 1.0 S3 A:SF4603 3.9 27.7 1.0 N A:CYS349 3.9 24.8 1.0 CE1 A:PHE455 4.1 30.7 1.0 CA A:CYS349 4.3 24.2 1.0 CD1 A:PHE455 4.4 28.5 1.0 CG2 A:ILE430 4.5 29.8 1.0 N A:ALA348 4.5 26.1 1.0 CD1 A:ILE430 4.6 29.9 1.0 CB A:MET347 4.7 29.8 1.0 SG A:CYS440 4.8 29.5 1.0 SG A:CYS437 4.8 32.0 1.0 SG A:CYS453 4.8 30.2 1.0 C A:MET347 4.8 29.5 1.0 CA A:MET347 5.0 28.9 1.0

Iron binding site 4 out of 4 in the Structure of the (6-4) Photolyase of Caulobacter Crescentus in Its Dark Adapted and Oxidized State Determined By Serial Femtosecond Crystallography


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 Dark Adapted and Oxidized State Determined By Serial Femtosecond Crystallography within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:28.1 occ:1.00 FE4 A:SF4603 0.0 28.1 1.0 S1 A:SF4603 2.2 27.2 1.0 S3 A:SF4603 2.3 27.7 1.0 SG A:CYS440 2.3 29.5 1.0 S2 A:SF4603 2.3 26.8 1.0 FE2 A:SF4603 2.7 27.1 1.0 FE3 A:SF4603 2.8 26.1 1.0 FE1 A:SF4603 2.8 27.2 1.0 CB A:CYS440 3.1 31.2 1.0 S4 A:SF4603 3.9 26.6 1.0 N A:ALA348 4.1 26.1 1.0 CB A:TYR442 4.3 36.8 1.0 CD2 A:TYR442 4.5 37.4 1.0 CA A:CYS440 4.5 33.4 1.0 CA A:MET347 4.6 28.9 1.0 CB A:ALA348 4.7 25.9 1.0 SG A:CYS349 4.7 25.5 1.0 C A:MET347 4.8 29.5 1.0 O A:TYR442 4.8 40.7 1.0 CA A:CYS437 4.8 32.3 1.0 SG A:CYS437 4.9 32.0 1.0 N A:TYR442 4.9 39.1 1.0 CG A:TYR442 4.9 39.2 1.0 SG A:CYS453 4.9 30.2 1.0 CB A:MET347 4.9 29.8 1.0 CA A:ALA348 5.0 25.9 1.0 N A:CYS349 5.0 24.8 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