Iron in PDB 4dja: Crystal Structure of A Prokaryotic (6-4) Photolyase Phrb From Agrobacterium Tumefaciens with An Fe-S Cluster and A 6,7-Dimethyl-8- Ribityllumazine Antenna Chromophore at 1.45A Resolution

The structure of Crystal Structure of A Prokaryotic (6-4) Photolyase Phrb From Agrobacterium Tumefaciens with An Fe-S Cluster and A 6,7-Dimethyl-8- Ribityllumazine Antenna Chromophore at 1.45A Resolution, PDB code: 4dja was solved by P.Scheerer, F.Zhang, I.Oberpichler, T.Lamparter, N.Krauss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.95 / 1.45
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	98.388, 106.786, 55.913, 90.00, 90.00, 90.00
R / Rfree (%)	13.8 / 18

The structure of Crystal Structure of A Prokaryotic (6-4) Photolyase Phrb From Agrobacterium Tumefaciens with An Fe-S Cluster and A 6,7-Dimethyl-8- Ribityllumazine Antenna Chromophore at 1.45A Resolution also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Iron atom in the Crystal Structure of A Prokaryotic (6-4) Photolyase Phrb From Agrobacterium Tumefaciens with An Fe-S Cluster and A 6,7-Dimethyl-8- Ribityllumazine Antenna Chromophore at 1.45A Resolution (pdb code 4dja). 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 A Prokaryotic (6-4) Photolyase Phrb From Agrobacterium Tumefaciens with An Fe-S Cluster and A 6,7-Dimethyl-8- Ribityllumazine Antenna Chromophore at 1.45A Resolution, PDB code: 4dja:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of A Prokaryotic (6-4) Photolyase Phrb From Agrobacterium Tumefaciens with An Fe-S Cluster and A 6,7-Dimethyl-8- Ribityllumazine Antenna Chromophore at 1.45A Resolution


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 A Prokaryotic (6-4) Photolyase Phrb From Agrobacterium Tumefaciens with An Fe-S Cluster and A 6,7-Dimethyl-8- Ribityllumazine Antenna Chromophore at 1.45A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:14.7 occ:1.00 FE1 A:SF4603 0.0 14.7 1.0 S4 A:SF4603 2.2 13.6 1.0 S2 A:SF4603 2.3 14.4 1.0 S3 A:SF4603 2.3 14.9 1.0 SG A:CYS438 2.3 13.5 1.0 FE2 A:SF4603 2.6 14.3 1.0 FE4 A:SF4603 2.7 14.7 1.0 FE3 A:SF4603 2.7 13.9 1.0 CB A:CYS438 3.3 13.2 1.0 CA A:CYS438 3.6 13.9 1.0 S1 A:SF4603 3.8 13.4 1.0 N A:CYS438 4.0 13.6 1.0 CG2 A:ILE431 4.4 12.1 1.0 CB A:PRO445 4.5 16.2 1.0 CB A:CYS441 4.6 14.9 1.0 SG A:CYS454 4.6 12.2 1.0 SG A:CYS441 4.7 13.7 1.0 C A:TYR437 4.7 13.6 1.0 SG A:CYS350 4.8 12.2 1.0 CD A:PRO445 4.8 16.5 1.0 CG A:PRO445 4.8 16.0 1.0 CB A:ILE431 5.0 11.5 1.0

Iron binding site 2 out of 4 in the Crystal Structure of A Prokaryotic (6-4) Photolyase Phrb From Agrobacterium Tumefaciens with An Fe-S Cluster and A 6,7-Dimethyl-8- Ribityllumazine Antenna Chromophore at 1.45A Resolution


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 A Prokaryotic (6-4) Photolyase Phrb From Agrobacterium Tumefaciens with An Fe-S Cluster and A 6,7-Dimethyl-8- Ribityllumazine Antenna Chromophore at 1.45A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:14.3 occ:1.00 FE2 A:SF4603 0.0 14.3 1.0 S1 A:SF4603 2.3 13.4 1.0 S3 A:SF4603 2.3 14.9 1.0 SG A:CYS454 2.3 12.2 1.0 S4 A:SF4603 2.3 13.6 1.0 FE1 A:SF4603 2.6 14.7 1.0 FE4 A:SF4603 2.7 14.7 1.0 FE3 A:SF4603 2.8 13.9 1.0 CB A:CYS454 3.2 12.3 1.0 S2 A:SF4603 3.9 14.4 1.0 CA A:CYS454 4.0 12.3 1.0 CD2 A:PHE456 4.1 12.0 1.0 CD A:PRO455 4.6 11.2 1.0 C A:CYS454 4.7 12.6 1.0 CB A:TYR443 4.7 13.3 1.0 CE2 A:PHE456 4.7 12.7 1.0 SG A:CYS438 4.7 13.5 1.0 CA A:GLY428 4.7 16.9 1.0 N A:PRO455 4.8 11.2 1.0 SG A:CYS441 4.8 13.7 1.0 SG A:CYS350 4.9 12.2 1.0 CB A:PRO445 5.0 16.2 1.0 CA A:PRO445 5.0 16.2 1.0

Iron binding site 3 out of 4 in the Crystal Structure of A Prokaryotic (6-4) Photolyase Phrb From Agrobacterium Tumefaciens with An Fe-S Cluster and A 6,7-Dimethyl-8- Ribityllumazine Antenna Chromophore at 1.45A Resolution


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 A Prokaryotic (6-4) Photolyase Phrb From Agrobacterium Tumefaciens with An Fe-S Cluster and A 6,7-Dimethyl-8- Ribityllumazine Antenna Chromophore at 1.45A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:13.9 occ:1.00 FE3 A:SF4603 0.0 13.9 1.0 S1 A:SF4603 2.3 13.4 1.0 S4 A:SF4603 2.3 13.6 1.0 S2 A:SF4603 2.3 14.4 1.0 SG A:CYS350 2.3 12.2 1.0 FE4 A:SF4603 2.7 14.7 1.0 FE1 A:SF4603 2.7 14.7 1.0 FE2 A:SF4603 2.8 14.3 1.0 CB A:CYS350 3.3 11.1 1.0 N A:CYS350 3.8 12.0 1.0 S3 A:SF4603 3.9 14.9 1.0 CE2 A:PHE456 4.1 12.7 1.0 CA A:CYS350 4.2 11.2 1.0 CD2 A:PHE456 4.4 12.0 1.0 CG2 A:ILE431 4.4 12.1 1.0 N A:ASN349 4.5 11.9 1.0 SG A:CYS441 4.7 13.7 1.0 CD1 A:ILE431 4.8 11.7 1.0 SG A:CYS438 4.8 13.5 1.0 SG A:CYS454 4.8 12.2 1.0 CB A:MET348 4.8 11.9 1.0 C A:MET348 4.8 11.6 1.0 C A:ASN349 5.0 11.3 1.0 CA A:MET348 5.0 11.7 1.0

Iron binding site 4 out of 4 in the Crystal Structure of A Prokaryotic (6-4) Photolyase Phrb From Agrobacterium Tumefaciens with An Fe-S Cluster and A 6,7-Dimethyl-8- Ribityllumazine Antenna Chromophore at 1.45A Resolution


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 A Prokaryotic (6-4) Photolyase Phrb From Agrobacterium Tumefaciens with An Fe-S Cluster and A 6,7-Dimethyl-8- Ribityllumazine Antenna Chromophore at 1.45A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:14.7 occ:1.00 FE4 A:SF4603 0.0 14.7 1.0 S1 A:SF4603 2.2 13.4 1.0 S3 A:SF4603 2.3 14.9 1.0 SG A:CYS441 2.3 13.7 1.0 S2 A:SF4603 2.3 14.4 1.0 FE1 A:SF4603 2.7 14.7 1.0 FE2 A:SF4603 2.7 14.3 1.0 FE3 A:SF4603 2.7 13.9 1.0 CB A:CYS441 3.2 14.9 1.0 S4 A:SF4603 3.8 13.6 1.0 N A:ASN349 4.0 11.9 1.0 CB A:TYR443 4.2 13.3 1.0 CD2 A:TYR443 4.3 14.4 1.0 CA A:MET348 4.6 11.7 1.0 CA A:CYS441 4.6 14.9 1.0 O A:TYR443 4.6 16.7 1.0 C A:MET348 4.7 11.6 1.0 CB A:ASN349 4.7 13.5 1.0 SG A:CYS350 4.7 12.2 1.0 CG A:TYR443 4.7 14.2 1.0 CA A:CYS438 4.8 13.9 1.0 SG A:CYS438 4.8 13.5 1.0 N A:CYS350 4.8 12.0 1.0 N A:TYR443 4.8 15.9 1.0 SG A:CYS454 4.9 12.2 1.0 CA A:TYR443 4.9 14.2 1.0 CA A:ASN349 4.9 11.7 1.0 C A:TYR443 5.0 14.0 1.0

F.Zhang, P.Scheerer, I.Oberpichler, T.Lamparter, N.Krauss. Crystal Structure of A Prokaryotic (6-4) Photolyase with An Fe-S Cluster and A 6,7-Dimethyl-8-Ribityllumazine Antenna Chromophore. Proc.Natl.Acad.Sci.Usa V. 110 7217 2013.
ISSN: ISSN 0027-8424
PubMed: 23589886
DOI: 10.1073/PNAS.1302377110