Iron in PDB 6dd6: Crystal Structure of Bacterial (6-4) Photolyase Phrb From in Situ Serial Laue Diffraction

The structure of Crystal Structure of Bacterial (6-4) Photolyase Phrb From in Situ Serial Laue Diffraction, PDB code: 6dd6 was solved by Z.Ren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.68 / 2.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	99.700, 106.800, 57.300, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 23.5

The binding sites of Iron atom in the Crystal Structure of Bacterial (6-4) Photolyase Phrb From in Situ Serial Laue Diffraction (pdb code 6dd6). 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 Bacterial (6-4) Photolyase Phrb From in Situ Serial Laue Diffraction, PDB code: 6dd6:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Bacterial (6-4) Photolyase Phrb From in Situ Serial Laue Diffraction


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 Bacterial (6-4) Photolyase Phrb From in Situ Serial Laue Diffraction within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:47.9 occ:1.00 FE1 A:SF4603 0.0 47.9 1.0 S2 A:SF4603 2.1 41.2 1.0 S4 A:SF4603 2.1 33.1 1.0 S3 A:SF4603 2.1 39.1 1.0 SG A:CYS438 2.3 60.4 1.0 FE4 A:SF4603 2.9 56.7 1.0 FE2 A:SF4603 2.9 56.2 1.0 FE3 A:SF4603 3.0 53.5 1.0 CB A:CYS438 3.2 55.2 1.0 CA A:CYS438 3.5 45.9 1.0 S1 A:SF4603 3.6 34.5 1.0 N A:CYS438 3.9 45.5 1.0 CG2 A:ILE431 4.5 30.8 1.0 C A:TYR437 4.6 40.0 1.0 CB A:PRO445 4.6 53.5 1.0 SG A:CYS454 4.6 0.4 1.0 CB A:CYS441 4.7 40.3 1.0 CB A:ILE431 4.7 35.8 1.0 C A:CYS438 4.9 58.8 1.0 SG A:CYS441 4.9 48.5 1.0 SG A:CYS350 4.9 39.8 1.0 CG A:PRO445 4.9 49.3 1.0 O A:TYR437 4.9 41.7 1.0 CD A:PRO445 5.0 54.2 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Bacterial (6-4) Photolyase Phrb From in Situ Serial Laue Diffraction


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 Bacterial (6-4) Photolyase Phrb From in Situ Serial Laue Diffraction within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:56.2 occ:1.00 FE2 A:SF4603 0.0 56.2 1.0 S3 A:SF4603 2.1 39.1 1.0 S4 A:SF4603 2.1 33.1 1.0 S1 A:SF4603 2.2 34.5 1.0 SG A:CYS454 2.2 0.4 1.0 CB A:CYS454 2.5 90.7 1.0 FE1 A:SF4603 2.9 47.9 1.0 FE3 A:SF4603 3.1 53.5 1.0 FE4 A:SF4603 3.2 56.7 1.0 S2 A:SF4603 3.8 41.2 1.0 CA A:CYS454 3.9 57.8 1.0 CD1 A:PHE456 4.0 40.7 1.0 CA A:GLY428 4.4 40.0 1.0 CE1 A:PHE456 4.6 37.4 1.0 C A:CYS454 4.7 40.5 1.0 SG A:CYS438 4.8 60.4 1.0 CB A:PRO445 4.8 53.5 1.0 CG A:PHE456 4.8 29.7 1.0 CB A:PHE456 4.9 30.8 1.0 CA A:PRO445 4.9 49.7 1.0 N A:CYS454 4.9 53.8 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Bacterial (6-4) Photolyase Phrb From in Situ Serial Laue Diffraction


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 Bacterial (6-4) Photolyase Phrb From in Situ Serial Laue Diffraction within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:53.5 occ:1.00 FE3 A:SF4603 0.0 53.5 1.0 S1 A:SF4603 2.1 34.5 1.0 S2 A:SF4603 2.1 41.2 1.0 S4 A:SF4603 2.1 33.1 1.0 SG A:CYS350 2.3 39.8 1.0 FE4 A:SF4603 3.0 56.7 1.0 FE1 A:SF4603 3.0 47.9 1.0 FE2 A:SF4603 3.1 56.2 1.0 CB A:CYS350 3.4 39.4 1.0 S3 A:SF4603 3.7 39.1 1.0 N A:CYS350 3.8 37.7 1.0 CE1 A:PHE456 3.9 37.4 1.0 SG A:CYS454 3.9 0.4 1.0 CA A:CYS350 4.2 37.3 1.0 CD1 A:PHE456 4.3 40.7 1.0 N A:ASN349 4.4 42.4 1.0 CB A:MET348 4.6 41.7 1.0 C A:MET348 4.6 42.8 1.0 CA A:MET348 4.7 42.0 1.0 CG2 A:ILE431 4.7 30.8 1.0 CD1 A:ILE431 4.7 29.1 1.0 SG A:CYS441 4.8 48.5 1.0 C A:ASN349 4.9 33.6 1.0 N A:MET351 4.9 29.6 1.0 CZ A:PHE456 5.0 27.9 1.0 CG A:MET348 5.0 42.4 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Bacterial (6-4) Photolyase Phrb From in Situ Serial Laue Diffraction


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 Bacterial (6-4) Photolyase Phrb From in Situ Serial Laue Diffraction within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:56.7 occ:1.00 FE4 A:SF4603 0.0 56.7 1.0 S1 A:SF4603 2.1 34.5 1.0 S3 A:SF4603 2.1 39.1 1.0 S2 A:SF4603 2.1 41.2 1.0 SG A:CYS441 2.3 48.5 1.0 FE1 A:SF4603 2.9 47.9 1.0 FE3 A:SF4603 3.0 53.5 1.0 CB A:CYS441 3.0 40.3 1.0 FE2 A:SF4603 3.2 56.2 1.0 SG A:CYS454 3.2 0.4 1.0 S4 A:SF4603 3.7 33.1 1.0 CD2 A:TYR443 4.1 39.1 1.0 CB A:TYR443 4.2 51.6 1.0 N A:ASN349 4.3 42.4 1.0 CB A:CYS454 4.4 90.7 1.0 CA A:CYS441 4.5 44.1 1.0 O A:TYR443 4.5 52.9 1.0 N A:TYR443 4.6 43.6 1.0 CG A:TYR443 4.7 48.8 1.0 CA A:CYS438 4.7 45.9 1.0 CA A:MET348 4.8 42.0 1.0 CB A:ASN349 4.8 39.8 1.0 CA A:TYR443 4.8 44.7 1.0 C A:TYR443 4.9 49.0 1.0 SG A:CYS438 4.9 60.4 1.0 C A:MET348 5.0 42.8 1.0 C A:CYS441 5.0 51.4 1.0

Z.Ren, M.Ayhan, S.Bandara, K.Bowatte, I.Kumarapperuma, S.Gunawardana, H.Shin, C.Wang, X.Zeng, X.Yang. Crystal-on-Crystal Chips For in Situ Serial Diffraction at Room Temperature. Lab Chip V. 18 2246 2018.
ISSN: ISSN 1473-0189
PubMed: 29952383
DOI: 10.1039/C8LC00489G