Iron in PDB 4k9r: Spore Photoproduct Lyase Y98F Mutant

All present enzymatic activity of Spore Photoproduct Lyase Y98F Mutant:
4.1.99.14;

The structure of Spore Photoproduct Lyase Y98F Mutant, PDB code: 4k9r was solved by L.Yang, R.S.Nelson, A.Benjdia, G.Lin, J.Telser, S.Stoll, I.Schlichting, L.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.06 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.020, 62.720, 142.620, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 26.4

The binding sites of Iron atom in the Spore Photoproduct Lyase Y98F Mutant (pdb code 4k9r). 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 Y98F Mutant, PDB code: 4k9r:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Spore Photoproduct Lyase Y98F Mutant


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 Y98F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:25.4 occ:1.00 FE1 A:SF4401 0.0 25.4 1.0 O A:EEM402 2.2 28.9 1.0 S4 A:SF4401 2.3 24.1 1.0 S2 A:SF4401 2.3 23.8 1.0 S3 A:SF4401 2.3 24.4 1.0 N A:EEM402 2.3 29.2 1.0 FE2 A:SF4401 2.7 25.8 1.0 FE4 A:SF4401 2.8 26.5 1.0 FE3 A:SF4401 2.8 22.9 1.0 C A:EEM402 3.1 29.1 1.0 CA A:EEM402 3.2 29.2 1.0 SE A:EEM402 3.6 34.2 1.0 NZ A:LYS174 3.6 24.2 1.0 CG A:EEM402 3.8 30.4 1.0 S1 A:SF4401 3.9 24.3 1.0 CB A:EEM402 4.0 29.4 1.0 OXT A:EEM402 4.2 28.4 1.0 CE A:EEM402 4.5 34.9 1.0 OD1 A:ASP143 4.6 26.6 1.0 SG A:CYS90 4.6 27.4 1.0 SG A:CYS94 4.8 26.7 1.0 CE A:LYS174 4.9 25.1 1.0 SG A:CYS97 4.9 27.9 1.0 C2' A:EEM402 4.9 27.2 1.0 CD A:LYS174 4.9 26.0 1.0

Iron binding site 2 out of 4 in the Spore Photoproduct Lyase Y98F Mutant


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 Y98F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:25.8 occ:1.00 FE2 A:SF4401 0.0 25.8 1.0 S4 A:SF4401 2.3 24.1 1.0 S1 A:SF4401 2.3 24.3 1.0 S3 A:SF4401 2.3 24.4 1.0 SG A:CYS90 2.4 27.4 1.0 FE3 A:SF4401 2.7 22.9 1.0 FE1 A:SF4401 2.7 25.4 1.0 FE4 A:SF4401 2.8 26.5 1.0 CB A:CYS90 3.2 27.3 1.0 N A:EEM402 3.7 29.2 1.0 S2 A:SF4401 3.8 23.8 1.0 CA A:GLY92 4.2 27.6 1.0 N A:GLY92 4.3 27.8 1.0 CA A:CYS90 4.6 27.5 1.0 O A:EEM402 4.7 28.9 1.0 C A:GLY92 4.7 27.3 1.0 CB A:ASP143 4.7 25.8 1.0 O A:GLY92 4.8 27.3 1.0 SG A:CYS97 4.8 27.9 1.0 SG A:CYS94 4.8 26.7 1.0 OH A:TYR175 4.9 30.4 1.0 OD1 A:ASP143 4.9 26.6 1.0

Iron binding site 3 out of 4 in the Spore Photoproduct Lyase Y98F Mutant


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 Y98F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:22.9 occ:1.00 FE3 A:SF4401 0.0 22.9 1.0 S4 A:SF4401 2.3 24.1 1.0 S2 A:SF4401 2.3 23.8 1.0 S1 A:SF4401 2.3 24.3 1.0 SG A:CYS94 2.3 26.7 1.0 FE2 A:SF4401 2.7 25.8 1.0 FE4 A:SF4401 2.7 26.5 1.0 FE1 A:SF4401 2.8 25.4 1.0 CB A:CYS94 3.0 26.2 1.0 NZ A:LYS174 3.7 24.2 1.0 S3 A:SF4401 3.9 24.4 1.0 N A:CYS94 4.0 26.4 1.0 CA A:CYS94 4.1 26.3 1.0 O A:EEM402 4.2 28.9 1.0 CD A:LYS174 4.4 26.0 1.0 CE A:LYS174 4.4 25.1 1.0 CG2 A:THR209 4.5 29.2 1.0 SG A:CYS97 4.7 27.9 1.0 CB A:CYS97 4.8 28.7 1.0 N A:EEM402 4.8 29.2 1.0 SG A:CYS90 4.8 27.4 1.0 CA A:GLY92 4.9 27.6 1.0 C A:GLY92 5.0 27.3 1.0

Iron binding site 4 out of 4 in the Spore Photoproduct Lyase Y98F Mutant


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 Y98F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:26.5 occ:1.00 FE4 A:SF4401 0.0 26.5 1.0 S2 A:SF4401 2.3 23.8 1.0 S3 A:SF4401 2.3 24.4 1.0 S1 A:SF4401 2.3 24.3 1.0 SG A:CYS97 2.3 27.9 1.0 FE3 A:SF4401 2.7 22.9 1.0 FE1 A:SF4401 2.8 25.4 1.0 FE2 A:SF4401 2.8 25.8 1.0 CB A:CYS97 3.2 28.7 1.0 S4 A:SF4401 3.9 24.1 1.0 CA A:CYS97 4.1 28.8 1.0 CB A:CYS94 4.4 26.2 1.0 CD1 A:LEU99 4.4 36.6 1.0 CE A:EEM402 4.6 34.9 1.0 SG A:CYS94 4.6 26.7 1.0 N A:EEM402 4.7 29.2 1.0 SE A:EEM402 4.8 34.2 1.0 O A:EEM402 4.8 28.9 1.0 CG A:LEU99 4.9 35.6 1.0 SG A:CYS90 4.9 27.4 1.0 CB A:CYS90 4.9 27.3 1.0

L.Yang, R.S.Nelson, A.Benjdia, G.Lin, J.Telser, S.Stoll, I.Schlichting, L.Li. A Radical Transfer Pathway in Spore Photoproduct Lyase. Biochemistry V. 52 3041 2013.
ISSN: ISSN 0006-2960
PubMed: 23607538
DOI: 10.1021/BI3016247