Iron in PDB 8a1h: Bacterial 6-4 Photolyase From Vibrio Cholerase

The structure of Bacterial 6-4 Photolyase From Vibrio Cholerase, PDB code: 8a1h was solved by L.-O.Essen, H.J.Emmerich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.59 / 1.65
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	199.687, 199.687, 76.996, 90, 90, 120
R / Rfree (%)	11.9 / 13.6

The structure of Bacterial 6-4 Photolyase From Vibrio Cholerase also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Sodium	(Na)	6 atoms

The binding sites of Iron atom in the Bacterial 6-4 Photolyase From Vibrio Cholerase (pdb code 8a1h). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Bacterial 6-4 Photolyase From Vibrio Cholerase, PDB code: 8a1h:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Bacterial 6-4 Photolyase From Vibrio Cholerase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Bacterial 6-4 Photolyase From Vibrio Cholerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:19.6 occ:1.00 FE1 A:SF4603 0.0 19.6 1.0 S4 A:SF4603 2.2 19.5 1.0 SG A:CYS465 2.3 19.6 1.0 S2 A:SF4603 2.3 18.8 1.0 S3 A:SF4603 2.3 20.0 1.0 FE2 A:SF4603 2.7 20.6 1.0 FE4 A:SF4603 2.7 20.1 1.0 FE3 A:SF4603 2.8 19.8 1.0 HA A:CYS465 3.1 22.4 1.0 CB A:CYS465 3.3 19.1 1.0 HB3 A:CYS465 3.4 22.8 1.0 HB A:VAL472 3.6 26.3 1.0 CA A:CYS465 3.6 18.8 1.0 HG22 A:ILE458 3.7 22.7 1.0 HG21 A:ILE458 3.7 22.7 1.0 S1 A:SF4603 3.9 21.3 1.0 HG21 A:VAL472 4.0 28.0 1.0 HB A:ILE458 4.0 25.8 1.0 N A:CYS465 4.0 18.4 1.0 HG23 A:VAL472 4.0 28.0 1.0 CG2 A:ILE458 4.1 18.9 1.0 H A:CYS465 4.1 22.1 1.0 HB2 A:CYS465 4.2 22.8 1.0 CG2 A:VAL472 4.3 23.3 1.0 HB2 A:CYS468 4.3 24.9 1.0 CB A:VAL472 4.4 21.9 1.0 HB2 A:TYR464 4.4 22.4 1.0 HB3 A:CYS377 4.5 20.5 1.0 SG A:CYS481 4.6 21.6 1.0 CB A:ILE458 4.6 21.5 1.0 HB3 A:TYR464 4.6 22.4 1.0 HB3 A:CYS468 4.6 24.9 1.0 C A:TYR464 4.6 18.9 1.0 SG A:CYS468 4.7 20.4 1.0 HB2 A:CYS481 4.8 25.9 1.0 CB A:CYS468 4.8 20.7 1.0 HA3 A:GLY455 4.8 24.7 1.0 H A:CYS377 4.8 22.4 1.0 HA2 A:GLY455 4.8 24.7 1.0 HB2 A:ASN459 4.9 23.7 1.0 SG A:CYS377 4.9 20.4 1.0 CB A:TYR464 5.0 18.7 1.0 C A:CYS465 5.0 19.7 1.0 O A:GLY455 5.0 23.9 1.0 O A:TYR464 5.0 19.2 1.0 HG13 A:ILE458 5.0 27.1 1.0

Iron binding site 2 out of 4 in the Bacterial 6-4 Photolyase From Vibrio Cholerase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Bacterial 6-4 Photolyase From Vibrio Cholerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:20.6 occ:1.00 FE2 A:SF4603 0.0 20.6 1.0 S3 A:SF4603 2.3 20.0 1.0 S4 A:SF4603 2.3 19.5 1.0 S1 A:SF4603 2.3 21.3 1.0 SG A:CYS481 2.3 21.6 1.0 FE1 A:SF4603 2.7 19.6 1.0 FE4 A:SF4603 2.7 20.1 1.0 FE3 A:SF4603 2.7 19.8 1.0 HB2 A:CYS481 3.1 25.9 1.0 CB A:CYS481 3.3 21.6 1.0 HA A:CYS481 3.6 28.4 1.0 S2 A:SF4603 3.9 18.8 1.0 HG23 A:VAL472 3.9 28.0 1.0 HD2 A:PRO482 4.0 30.9 1.0 CA A:CYS481 4.0 23.7 1.0 HA3 A:GLY455 4.1 24.7 1.0 HB3 A:CYS481 4.1 25.9 1.0 HD12 A:LEU483 4.1 27.2 1.0 HB2 A:TYR470 4.1 29.5 1.0 HG A:LEU483 4.2 25.6 1.0 H A:LEU483 4.2 29.0 1.0 HB A:VAL472 4.3 26.3 1.0 HB2 A:LEU483 4.3 24.8 1.0 HE3 A:MET375 4.4 28.6 1.0 HA2 A:GLY455 4.4 24.7 1.0 HA A:VAL472 4.5 25.3 1.0 CD A:PRO482 4.7 25.7 1.0 C A:CYS481 4.7 22.0 1.0 CG2 A:VAL472 4.7 23.3 1.0 SG A:CYS465 4.7 19.6 1.0 CA A:GLY455 4.7 20.6 1.0 HD3 A:PRO482 4.8 30.9 1.0 CD1 A:LEU483 4.8 22.6 1.0 HB3 A:TYR470 4.8 29.5 1.0 CG A:LEU483 4.8 21.3 1.0 HG21 A:VAL472 4.8 28.0 1.0 N A:PRO482 4.8 22.6 1.0 SG A:CYS377 4.8 20.4 1.0 SG A:CYS468 4.8 20.4 1.0 CB A:TYR470 4.9 24.6 1.0 CB A:VAL472 4.9 21.9 1.0 HD11 A:LEU483 5.0 27.2 1.0

Iron binding site 3 out of 4 in the Bacterial 6-4 Photolyase From Vibrio Cholerase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Bacterial 6-4 Photolyase From Vibrio Cholerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:19.8 occ:1.00 FE3 A:SF4603 0.0 19.8 1.0 S4 A:SF4603 2.3 19.5 1.0 S2 A:SF4603 2.3 18.8 1.0 S1 A:SF4603 2.3 21.3 1.0 SG A:CYS377 2.3 20.4 1.0 FE2 A:SF4603 2.7 20.6 1.0 FE4 A:SF4603 2.7 20.1 1.0 FE1 A:SF4603 2.8 19.6 1.0 HB3 A:CYS377 3.1 20.5 1.0 H A:CYS377 3.1 22.4 1.0 CB A:CYS377 3.3 17.1 1.0 HG21 A:ILE458 3.5 22.7 1.0 HB3 A:MET375 3.8 24.3 1.0 N A:CYS377 3.9 18.6 1.0 S3 A:SF4603 3.9 20.0 1.0 HB2 A:CYS377 4.0 20.5 1.0 HD12 A:LEU483 4.1 27.2 1.0 HE3 A:MET375 4.2 28.6 1.0 H A:ARG376 4.2 24.9 1.0 HD11 A:LEU483 4.2 27.2 1.0 HG13 A:ILE458 4.2 27.1 1.0 CA A:CYS377 4.3 17.2 1.0 HE2 A:MET375 4.3 28.6 1.0 CG2 A:ILE458 4.4 18.9 1.0 HG A:LEU483 4.5 25.6 1.0 N A:ARG376 4.5 20.7 1.0 HG22 A:ILE458 4.6 22.7 1.0 CD1 A:LEU483 4.6 22.6 1.0 H A:LEU378 4.6 22.6 1.0 HA A:MET375 4.6 24.2 1.0 HB3 A:ARG376 4.6 23.5 0.6 HB3 A:ARG376 4.6 23.5 0.5 HB A:ILE458 4.6 25.8 1.0 HB3 A:TYR464 4.7 22.4 1.0 SG A:CYS468 4.7 20.4 1.0 CB A:MET375 4.7 20.2 1.0 SG A:CYS481 4.7 21.6 1.0 CE A:MET375 4.7 23.9 1.0 SG A:CYS465 4.8 19.6 1.0 C A:MET375 4.9 19.8 1.0 HG2 A:MET375 4.9 25.4 1.0 HA A:CYS377 4.9 20.7 1.0 CB A:ILE458 5.0 21.5 1.0 CA A:MET375 5.0 20.2 1.0 HB2 A:TYR464 5.0 22.4 1.0

Iron binding site 4 out of 4 in the Bacterial 6-4 Photolyase From Vibrio Cholerase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Bacterial 6-4 Photolyase From Vibrio Cholerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:20.1 occ:1.00 FE4 A:SF4603 0.0 20.1 1.0 S1 A:SF4603 2.2 21.3 1.0 S3 A:SF4603 2.3 20.0 1.0 SG A:CYS468 2.3 20.4 1.0 S2 A:SF4603 2.3 18.8 1.0 FE2 A:SF4603 2.7 20.6 1.0 FE3 A:SF4603 2.7 19.8 1.0 FE1 A:SF4603 2.7 19.6 1.0 HB2 A:CYS468 3.1 24.9 1.0 CB A:CYS468 3.2 20.7 1.0 HB2 A:TYR470 3.3 29.5 1.0 HB3 A:CYS468 3.3 24.9 1.0 H A:ARG376 3.3 24.9 1.0 HD2 A:TYR470 3.7 27.6 1.0 HA A:CYS465 3.8 22.4 1.0 S4 A:SF4603 3.8 19.5 1.0 HA A:MET375 3.8 24.2 1.0 HB3 A:ARG376 3.9 23.5 0.5 HB3 A:ARG376 3.9 23.5 0.6 N A:ARG376 4.1 20.7 1.0 H A:CYS377 4.1 22.4 1.0 H A:TYR470 4.1 26.9 1.0 CB A:TYR470 4.3 24.6 1.0 CD2 A:TYR470 4.5 23.0 1.0 HB3 A:MET375 4.6 24.3 1.0 CA A:MET375 4.6 20.2 1.0 CA A:CYS468 4.7 20.9 1.0 CB A:ARG376 4.7 19.6 0.6 CA A:CYS465 4.7 18.8 1.0 CB A:ARG376 4.7 19.6 0.5 HB3 A:TYR470 4.7 29.5 1.0 SG A:CYS377 4.7 20.4 1.0 HB2 A:CYS481 4.7 25.9 1.0 O A:TYR470 4.7 24.0 1.0 HB2 A:ARG376 4.8 23.5 0.6 HG2 A:MET375 4.8 25.4 1.0 SG A:CYS465 4.8 19.6 1.0 C A:MET375 4.8 19.8 1.0 HB2 A:ARG376 4.8 23.5 0.5 HA A:CYS481 4.8 28.4 1.0 SG A:CYS481 4.9 21.6 1.0 N A:TYR470 4.9 22.4 1.0 HA A:CYS468 4.9 25.1 1.0 HB3 A:CYS465 4.9 22.8 1.0 CG A:TYR470 4.9 21.0 1.0 N A:CYS377 4.9 18.6 1.0 CA A:ARG376 5.0 18.2 0.6 HD2 A:PRO482 5.0 30.9 1.0 CA A:ARG376 5.0 18.1 0.5 CA A:TYR470 5.0 21.9 1.0

H.J.Emmerich, L.Schneider, L.O.Essen. Structural and Functional Analysis of A Prokaryotic (6-4) Photolyase From the Aquatic Pathogen Vibrio Cholerae. Photochem.Photobiol. 2023.
ISSN: ISSN 0031-8655
PubMed: 36692077
DOI: 10.1111/PHP.13783