Iron in PDB 7ykn: Crystal Structure of (6-4) Photolyase From Vibrio Cholerae

The structure of Crystal Structure of (6-4) Photolyase From Vibrio Cholerae, PDB code: 7ykn was solved by B.Cakilkaya, I.H.Kavakli, H.Demirci, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.62 / 2.50
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	200.751, 200.751, 77.023, 90, 90, 120
R / Rfree (%)	22.5 / 28.3

The binding sites of Iron atom in the Crystal Structure of (6-4) Photolyase From Vibrio Cholerae (pdb code 7ykn). 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 (6-4) Photolyase From Vibrio Cholerae, PDB code: 7ykn:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of (6-4) Photolyase From Vibrio Cholerae


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 (6-4) Photolyase From Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe606 b:17.6 occ:1.00 FE1 A:SF4606 0.0 17.6 1.0 SG A:CYS445 2.3 14.6 1.0 S2 A:SF4606 2.3 11.6 1.0 S3 A:SF4606 2.3 14.0 1.0 S4 A:SF4606 2.3 12.7 1.0 FE4 A:SF4606 2.7 18.1 1.0 FE2 A:SF4606 2.7 18.8 1.0 FE3 A:SF4606 2.7 17.0 1.0 CB A:CYS445 3.2 17.8 1.0 CA A:CYS445 3.5 18.5 1.0 N A:CYS445 3.7 14.0 1.0 S1 A:SF4606 3.9 18.3 1.0 CG2 A:ILE438 4.0 15.8 1.0 CG2 A:VAL452 4.2 14.8 1.0 C A:TYR444 4.4 17.7 1.0 CB A:VAL452 4.5 19.1 1.0 CB A:CYS448 4.5 16.1 1.0 SG A:CYS461 4.7 14.2 1.0 CB A:ILE438 4.7 15.7 1.0 SG A:CYS357 4.8 15.0 1.0 CB A:TYR444 4.8 15.3 1.0 SG A:CYS448 4.8 20.1 1.0 O A:TYR444 4.8 15.9 1.0 O A:GLY435 4.9 17.7 1.0 C A:CYS445 4.9 20.7 1.0

Iron binding site 2 out of 4 in the Crystal Structure of (6-4) Photolyase From Vibrio Cholerae


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 (6-4) Photolyase From Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe606 b:18.8 occ:1.00 FE2 A:SF4606 0.0 18.8 1.0 SG A:CYS461 2.3 14.2 1.0 S4 A:SF4606 2.3 12.7 1.0 S1 A:SF4606 2.3 18.3 1.0 S3 A:SF4606 2.3 14.0 1.0 FE4 A:SF4606 2.7 18.1 1.0 FE1 A:SF4606 2.7 17.6 1.0 FE3 A:SF4606 2.7 17.0 1.0 CB A:CYS461 3.2 17.9 1.0 S2 A:SF4606 3.9 11.6 1.0 CA A:CYS461 4.1 19.2 1.0 CG2 A:VAL452 4.4 14.8 1.0 CD1 A:LEU463 4.5 12.9 1.0 CA A:GLY435 4.6 22.1 1.0 CD A:PRO462 4.6 15.2 1.0 SG A:CYS445 4.7 14.6 1.0 C A:CYS461 4.8 16.2 1.0 SG A:CYS448 4.8 20.1 1.0 CB A:TYR450 4.8 16.7 1.0 CB A:VAL452 4.8 19.1 1.0 SG A:CYS357 4.9 15.0 1.0 N A:PRO462 4.9 14.3 1.0 CG A:LEU463 5.0 12.7 1.0

Iron binding site 3 out of 4 in the Crystal Structure of (6-4) Photolyase From Vibrio Cholerae


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 (6-4) Photolyase From Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe606 b:17.0 occ:1.00 FE3 A:SF4606 0.0 17.0 1.0 SG A:CYS357 2.3 15.0 1.0 S2 A:SF4606 2.3 11.6 1.0 S4 A:SF4606 2.3 12.7 1.0 S1 A:SF4606 2.3 18.3 1.0 FE4 A:SF4606 2.7 18.1 1.0 FE2 A:SF4606 2.7 18.8 1.0 FE1 A:SF4606 2.7 17.6 1.0 CB A:CYS357 3.5 16.0 1.0 S3 A:SF4606 3.9 14.0 1.0 N A:CYS357 3.9 17.0 1.0 CD1 A:LEU463 4.2 12.9 1.0 CG2 A:ILE438 4.4 15.8 1.0 CA A:CYS357 4.4 15.7 1.0 N A:ARG356 4.5 15.9 1.0 CB A:MET355 4.7 15.9 1.0 SG A:CYS461 4.7 14.2 1.0 SG A:CYS448 4.7 20.1 1.0 CE A:MET355 4.7 14.5 1.0 SG A:CYS445 4.9 14.6 1.0 C A:MET355 4.9 16.8 1.0 CA A:MET355 5.0 17.4 1.0 CB A:ILE438 5.0 15.7 1.0

Iron binding site 4 out of 4 in the Crystal Structure of (6-4) Photolyase From Vibrio Cholerae


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 (6-4) Photolyase From Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe606 b:18.1 occ:1.00 FE4 A:SF4606 0.0 18.1 1.0 SG A:CYS448 2.3 20.1 1.0 S3 A:SF4606 2.3 14.0 1.0 S1 A:SF4606 2.3 18.3 1.0 S2 A:SF4606 2.3 11.6 1.0 FE1 A:SF4606 2.7 17.6 1.0 FE2 A:SF4606 2.7 18.8 1.0 FE3 A:SF4606 2.7 17.0 1.0 CB A:CYS448 2.9 16.1 1.0 S4 A:SF4606 3.9 12.7 1.0 N A:ARG356 4.0 15.9 1.0 CB A:TYR450 4.2 16.7 1.0 CA A:CYS448 4.4 17.7 1.0 CD2 A:TYR450 4.4 19.7 1.0 CA A:MET355 4.6 17.4 1.0 CA A:CYS445 4.6 18.5 1.0 CB A:ARG356 4.6 16.1 1.0 SG A:CYS357 4.7 15.0 1.0 C A:MET355 4.8 16.8 1.0 SG A:CYS445 4.8 14.6 1.0 CG A:TYR450 4.8 20.5 1.0 O A:TYR450 4.8 20.8 1.0 N A:TYR450 4.8 24.6 1.0 SG A:CYS461 4.9 14.2 1.0 CA A:ARG356 4.9 14.5 1.0 CA A:TYR450 4.9 20.2 1.0 CB A:MET355 4.9 15.9 1.0 N A:CYS357 4.9 17.0 1.0 CB A:CYS445 5.0 17.8 1.0

B.Cakilkaya, I.H.Kavakli, H.Demirci. Crystal Structure of (6-4) Photolyase From Vibrio Cholerae To Be Published.