Iron in PDB 4fhd: Spore Photoproduct Lyase Complexed with Dinucleoside Spore Photoproduct

The structure of Spore Photoproduct Lyase Complexed with Dinucleoside Spore Photoproduct, PDB code: 4fhd was solved by A.Benjdia, K.Heil, T.R.M.Barends, T.Carell, I.Schlichting, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.93 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.320, 58.920, 131.620, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 25.4

The binding sites of Iron atom in the Spore Photoproduct Lyase Complexed with Dinucleoside Spore Photoproduct (pdb code 4fhd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Spore Photoproduct Lyase Complexed with Dinucleoside Spore Photoproduct, PDB code: 4fhd:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Spore Photoproduct Lyase Complexed with Dinucleoside Spore Photoproduct


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Spore Photoproduct Lyase Complexed with Dinucleoside Spore Photoproduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:21.9 occ:1.00 FE1 A:SF4401 0.0 21.9 1.0 S2 A:SF4401 2.3 22.8 1.0 S3 A:SF4401 2.3 23.2 1.0 SG A:CYS90 2.3 23.1 1.0 S4 A:SF4401 2.3 21.7 1.0 FE4 A:SF4401 2.7 22.1 1.0 FE3 A:SF4401 2.7 23.1 1.0 FE2 A:SF4401 2.7 22.6 1.0 CB A:CYS90 3.2 22.4 1.0 N A:EEM402 3.7 28.1 1.0 S1 A:SF4401 3.9 22.3 1.0 CA A:GLY92 4.2 24.2 1.0 N A:GLY92 4.3 24.2 1.0 CA A:CYS90 4.6 22.6 1.0 O A:EEM402 4.6 28.7 1.0 SG A:CYS97 4.7 23.4 1.0 C A:GLY92 4.7 24.2 1.0 CB A:ASP143 4.7 24.9 1.0 O A:GLY92 4.8 23.6 1.0 SG A:CYS94 4.9 24.4 1.0

Iron binding site 2 out of 4 in the Spore Photoproduct Lyase Complexed with Dinucleoside Spore Photoproduct


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Spore Photoproduct Lyase Complexed with Dinucleoside Spore Photoproduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:22.6 occ:1.00 FE2 A:SF4401 0.0 22.6 1.0 SG A:CYS97 2.2 23.4 1.0 S1 A:SF4401 2.3 22.3 1.0 S4 A:SF4401 2.3 21.7 1.0 S3 A:SF4401 2.3 23.2 1.0 FE4 A:SF4401 2.6 22.1 1.0 FE1 A:SF4401 2.7 21.9 1.0 FE3 A:SF4401 2.8 23.1 1.0 CB A:CYS97 3.2 24.4 1.0 S2 A:SF4401 3.9 22.8 1.0 CA A:CYS97 4.2 24.4 1.0 CE A:EEM402 4.4 34.5 1.0 CD1 A:LEU99 4.4 34.7 1.0 CB A:CYS94 4.5 23.9 1.0 CG A:LEU99 4.6 34.3 1.0 SE A:EEM402 4.6 29.8 1.0 SG A:CYS94 4.6 24.4 1.0 O A:EEM402 4.7 28.7 1.0 N A:EEM402 4.7 28.1 1.0 SG A:CYS90 4.8 23.1 1.0 CB A:CYS90 4.9 22.4 1.0 CB A:LEU99 5.0 33.5 1.0

Iron binding site 3 out of 4 in the Spore Photoproduct Lyase Complexed with Dinucleoside Spore Photoproduct


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Spore Photoproduct Lyase Complexed with Dinucleoside Spore Photoproduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:23.1 occ:1.00 FE3 A:SF4401 0.0 23.1 1.0 O A:EEM402 2.1 28.7 1.0 S4 A:SF4401 2.3 21.7 1.0 N A:EEM402 2.3 28.1 1.0 S2 A:SF4401 2.3 22.8 1.0 S1 A:SF4401 2.3 22.3 1.0 FE1 A:SF4401 2.7 21.9 1.0 FE4 A:SF4401 2.8 22.1 1.0 FE2 A:SF4401 2.8 22.6 1.0 C A:EEM402 2.9 28.3 1.0 CA A:EEM402 3.1 27.9 1.0 SE A:EEM402 3.5 29.8 1.0 CG A:EEM402 3.7 28.9 1.0 NZ A:LYS174 3.8 25.2 1.0 CB A:EEM402 3.9 27.9 1.0 S3 A:SF4401 4.0 23.2 1.0 OXT A:EEM402 4.1 27.6 1.0 CE A:EEM402 4.4 34.5 1.0 CD A:LYS174 4.5 24.2 1.0 SG A:CYS90 4.6 23.1 1.0 OD1 A:ASP143 4.6 24.5 1.0 CE A:LYS174 4.7 25.0 1.0 SG A:CYS94 4.8 24.4 1.0 SG A:CYS97 4.9 23.4 1.0 C2' A:EEM402 4.9 24.4 1.0 CG A:LYS174 4.9 24.2 1.0

Iron binding site 4 out of 4 in the Spore Photoproduct Lyase Complexed with Dinucleoside Spore Photoproduct


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Spore Photoproduct Lyase Complexed with Dinucleoside Spore Photoproduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:22.1 occ:1.00 FE4 A:SF4401 0.0 22.1 1.0 S2 A:SF4401 2.3 22.8 1.0 S1 A:SF4401 2.3 22.3 1.0 SG A:CYS94 2.3 24.4 1.0 S3 A:SF4401 2.3 23.2 1.0 FE2 A:SF4401 2.6 22.6 1.0 FE1 A:SF4401 2.7 21.9 1.0 FE3 A:SF4401 2.8 23.1 1.0 CB A:CYS94 3.1 23.9 1.0 NZ A:LYS174 3.8 25.2 1.0 S4 A:SF4401 3.9 21.7 1.0 N A:CYS94 4.0 24.0 1.0 CD A:LYS174 4.1 24.2 1.0 O A:EEM402 4.1 28.7 1.0 CA A:CYS94 4.2 23.9 1.0 CE A:LYS174 4.4 25.0 1.0 CG2 A:THR209 4.5 27.0 1.0 SG A:CYS97 4.6 23.4 1.0 CB A:CYS97 4.7 24.4 1.0 N A:EEM402 4.8 28.1 1.0 SG A:CYS90 4.8 23.1 1.0 CA A:GLY92 4.9 24.2 1.0

A.Benjdia, K.Heil, T.R.Barends, T.Carell, I.Schlichting. Structural Insights Into Recognition and Repair of Uv-Dna Damage By Spore Photoproduct Lyase, A Radical Sam Enzyme. Nucleic Acids Res. V. 40 9308 2012.
ISSN: ISSN 0305-1048
PubMed: 22761404
DOI: 10.1093/NAR/GKS603