Iron in PDB 8ai2: Crystal Structure of Radical Sam Epimerase Epee From Bacillus Subtilis with [4FE-4S] Clusters, S-Adenosyl-L-Homocysteine and Ripp Peptide 5 Bound

The structure of Crystal Structure of Radical Sam Epimerase Epee From Bacillus Subtilis with [4FE-4S] Clusters, S-Adenosyl-L-Homocysteine and Ripp Peptide 5 Bound, PDB code: 8ai2 was solved by I.Polsinelli, C.D.Fyfe, P.Legrand, X.Kubiak, L.M.G.Chavas, O.Berteau, A.Benjdia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.19 / 2.39
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	79.73, 92.37, 126.72, 90, 90, 90
R / Rfree (%)	18.6 / 22.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Radical Sam Epimerase Epee From Bacillus Subtilis with [4FE-4S] Clusters, S-Adenosyl-L-Homocysteine and Ripp Peptide 5 Bound (pdb code 8ai2). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Crystal Structure of Radical Sam Epimerase Epee From Bacillus Subtilis with [4FE-4S] Clusters, S-Adenosyl-L-Homocysteine and Ripp Peptide 5 Bound, PDB code: 8ai2:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in the Crystal Structure of Radical Sam Epimerase Epee From Bacillus Subtilis with [4FE-4S] Clusters, S-Adenosyl-L-Homocysteine and Ripp Peptide 5 Bound


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 Radical Sam Epimerase Epee From Bacillus Subtilis with [4FE-4S] Clusters, S-Adenosyl-L-Homocysteine and Ripp Peptide 5 Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:53.2 occ:0.91 FE1 A:SF4401 0.0 53.2 0.9 S2 A:SF4401 2.3 50.4 0.9 S4 A:SF4401 2.3 50.0 0.9 O A:SAH403 2.3 51.2 1.0 S3 A:SF4401 2.4 49.6 0.9 N A:SAH403 2.5 50.3 1.0 FE4 A:SF4401 2.7 49.7 0.9 FE3 A:SF4401 2.8 49.4 0.9 FE2 A:SF4401 2.8 48.6 0.9 C A:SAH403 3.1 51.1 1.0 CA A:SAH403 3.3 51.0 1.0 SD A:SAH403 3.6 51.5 1.0 CG A:SAH403 3.7 51.9 1.0 NE2 A:HIS120 3.7 48.9 1.0 S1 A:SF4401 4.0 48.5 0.9 CB A:SAH403 4.0 51.5 1.0 OXT A:SAH403 4.3 51.3 1.0 CD2 A:HIS120 4.5 48.1 1.0 SG A:CYS14 4.6 50.9 1.0 CE1 A:HIS120 4.7 49.1 1.0 O A:GLY59 4.7 48.1 1.0 C2' A:SAH403 4.8 49.0 1.0 C3' A:SAH403 4.9 48.9 1.0 SG A:CYS18 4.9 51.1 1.0 SG A:CYS21 5.0 48.6 1.0 C5' A:SAH403 5.0 49.8 1.0

Iron binding site 2 out of 16 in the Crystal Structure of Radical Sam Epimerase Epee From Bacillus Subtilis with [4FE-4S] Clusters, S-Adenosyl-L-Homocysteine and Ripp Peptide 5 Bound


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 Radical Sam Epimerase Epee From Bacillus Subtilis with [4FE-4S] Clusters, S-Adenosyl-L-Homocysteine and Ripp Peptide 5 Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:48.6 occ:0.91 FE2 A:SF4401 0.0 48.6 0.9 S3 A:SF4401 2.3 49.6 0.9 S1 A:SF4401 2.3 48.5 0.9 SG A:CYS21 2.3 48.6 1.0 S4 A:SF4401 2.3 50.0 0.9 FE4 A:SF4401 2.7 49.7 0.9 FE3 A:SF4401 2.8 49.4 0.9 FE1 A:SF4401 2.8 53.2 0.9 CB A:CYS21 3.2 49.8 1.0 CB A:SER25 3.9 51.2 1.0 S2 A:SF4401 3.9 50.4 0.9 OG A:SER25 4.1 51.4 1.0 CA A:CYS21 4.2 50.1 1.0 SD A:SAH403 4.6 51.5 1.0 N A:SER25 4.7 51.8 1.0 SG A:CYS18 4.7 51.1 1.0 CA A:SER25 4.8 51.1 1.0 N A:SAH403 4.8 50.3 1.0 CB A:CYS18 4.9 51.0 1.0 SG A:CYS14 4.9 50.9 1.0

Iron binding site 3 out of 16 in the Crystal Structure of Radical Sam Epimerase Epee From Bacillus Subtilis with [4FE-4S] Clusters, S-Adenosyl-L-Homocysteine and Ripp Peptide 5 Bound


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 Radical Sam Epimerase Epee From Bacillus Subtilis with [4FE-4S] Clusters, S-Adenosyl-L-Homocysteine and Ripp Peptide 5 Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:49.4 occ:0.91 FE3 A:SF4401 0.0 49.4 0.9 SG A:CYS18 2.3 51.1 1.0 S1 A:SF4401 2.3 48.5 0.9 S2 A:SF4401 2.3 50.4 0.9 S4 A:SF4401 2.3 50.0 0.9 FE4 A:SF4401 2.7 49.7 0.9 FE2 A:SF4401 2.8 48.6 0.9 FE1 A:SF4401 2.8 53.2 0.9 CB A:CYS18 3.3 51.0 1.0 NE2 A:HIS120 3.5 48.9 1.0 CD2 A:HIS120 3.8 48.1 1.0 S3 A:SF4401 3.9 49.6 0.9 N A:CYS18 4.0 51.4 1.0 CB A:ALA16 4.2 49.0 1.0 CE1 A:HIS120 4.2 49.1 1.0 CA A:CYS18 4.2 51.4 1.0 O A:SAH403 4.3 51.2 1.0 CG A:HIS120 4.6 48.2 1.0 CE1 A:HIS20 4.6 53.2 1.0 CB A:CYS21 4.7 49.8 1.0 SG A:CYS14 4.7 50.9 1.0 SG A:CYS21 4.7 48.6 1.0 ND1 A:HIS120 4.8 49.2 1.0

Iron binding site 4 out of 16 in the Crystal Structure of Radical Sam Epimerase Epee From Bacillus Subtilis with [4FE-4S] Clusters, S-Adenosyl-L-Homocysteine and Ripp Peptide 5 Bound


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 Radical Sam Epimerase Epee From Bacillus Subtilis with [4FE-4S] Clusters, S-Adenosyl-L-Homocysteine and Ripp Peptide 5 Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:49.7 occ:0.91 FE4 A:SF4401 0.0 49.7 0.9 S3 A:SF4401 2.3 49.6 0.9 SG A:CYS14 2.3 50.9 1.0 S1 A:SF4401 2.3 48.5 0.9 S2 A:SF4401 2.3 50.4 0.9 FE2 A:SF4401 2.7 48.6 0.9 FE3 A:SF4401 2.7 49.4 0.9 FE1 A:SF4401 2.7 53.2 0.9 CB A:CYS14 3.2 51.6 1.0 N A:SAH403 3.9 50.3 1.0 S4 A:SF4401 3.9 50.0 0.9 CB A:SER25 4.0 51.2 1.0 CB A:ALA16 4.1 49.0 1.0 O A:ALA16 4.4 50.9 1.0 ND2 A:ASN87 4.5 46.5 1.0 C A:ALA16 4.6 50.5 1.0 OG A:SER25 4.7 51.4 1.0 CA A:CYS14 4.7 52.2 1.0 SG A:CYS18 4.7 51.1 1.0 CA A:ALA16 4.8 50.0 1.0 SG A:CYS21 4.8 48.6 1.0 O A:SAH403 4.8 51.2 1.0 N A:ALA16 4.8 50.6 1.0 C A:GLY59 4.9 47.5 1.0 O A:GLY59 5.0 48.1 1.0

Iron binding site 5 out of 16 in the Crystal Structure of Radical Sam Epimerase Epee From Bacillus Subtilis with [4FE-4S] Clusters, S-Adenosyl-L-Homocysteine and Ripp Peptide 5 Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Radical Sam Epimerase Epee From Bacillus Subtilis with [4FE-4S] Clusters, S-Adenosyl-L-Homocysteine and Ripp Peptide 5 Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:53.9 occ:0.85 FE1 A:SF4402 0.0 53.9 0.8 SG A:CYS292 2.2 62.1 1.0 S2 A:SF4402 2.3 53.7 0.8 S3 A:SF4402 2.3 53.7 0.8 S4 A:SF4402 2.3 54.1 0.8 FE4 A:SF4402 2.7 53.2 0.8 FE2 A:SF4402 2.7 55.1 0.8 FE3 A:SF4402 2.8 54.0 0.8 CB A:CYS292 2.9 61.2 1.0 S1 A:SF4402 3.9 53.5 0.8 CZ A:PHE263 4.2 57.2 1.0 CD1 A:ILE227 4.4 48.7 1.0 CA A:CYS292 4.4 60.8 1.0 SG A:CYS222 4.7 57.0 1.0 SG A:CYS206 4.7 60.2 1.0 CA A:CYS289 4.7 60.2 1.0 CD2 A:LEU258 4.8 55.9 1.0 SG A:CYS289 4.8 60.6 1.0 CE1 A:PHE263 4.9 57.6 1.0 CB A:CYS289 5.0 60.8 1.0

Iron binding site 6 out of 16 in the Crystal Structure of Radical Sam Epimerase Epee From Bacillus Subtilis with [4FE-4S] Clusters, S-Adenosyl-L-Homocysteine and Ripp Peptide 5 Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Radical Sam Epimerase Epee From Bacillus Subtilis with [4FE-4S] Clusters, S-Adenosyl-L-Homocysteine and Ripp Peptide 5 Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:55.1 occ:0.85 FE2 A:SF4402 0.0 55.1 0.8 S4 A:SF4402 2.3 54.1 0.8 S3 A:SF4402 2.3 53.7 0.8 S1 A:SF4402 2.3 53.5 0.8 SG A:CYS289 2.3 60.6 1.0 FE4 A:SF4402 2.7 53.2 0.8 FE1 A:SF4402 2.7 53.9 0.8 FE3 A:SF4402 2.7 54.0 0.8 CB A:CYS289 3.3 60.8 1.0 CA A:CYS289 3.6 60.2 1.0 CB A:SER224 3.9 56.6 1.0 S2 A:SF4402 3.9 53.7 0.8 OG A:SER224 3.9 58.8 1.0 N A:CYS289 4.2 60.0 1.0 CD A:PRO207 4.2 61.5 1.0 SG A:CYS222 4.6 57.0 1.0 CB A:CYS292 4.6 61.2 1.0 CB C:GLU6 4.8 72.0 0.7 SG A:CYS292 4.8 62.1 1.0 SG A:CYS206 4.9 60.2 1.0 C A:CYS289 4.9 60.1 1.0 CG A:PRO207 4.9 62.9 1.0

Iron binding site 7 out of 16 in the Crystal Structure of Radical Sam Epimerase Epee From Bacillus Subtilis with [4FE-4S] Clusters, S-Adenosyl-L-Homocysteine and Ripp Peptide 5 Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Radical Sam Epimerase Epee From Bacillus Subtilis with [4FE-4S] Clusters, S-Adenosyl-L-Homocysteine and Ripp Peptide 5 Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:54.0 occ:0.85 FE3 A:SF4402 0.0 54.0 0.8 SG A:CYS206 2.3 60.2 1.0 S2 A:SF4402 2.3 53.7 0.8 S1 A:SF4402 2.3 53.5 0.8 S4 A:SF4402 2.3 54.1 0.8 FE4 A:SF4402 2.7 53.2 0.8 FE2 A:SF4402 2.7 55.1 0.8 FE1 A:SF4402 2.8 53.9 0.8 CB A:CYS206 3.2 62.8 1.0 CD A:PRO207 3.7 61.5 1.0 CA A:CYS206 3.9 63.9 1.0 S3 A:SF4402 3.9 53.7 0.8 N A:PRO207 4.3 61.9 1.0 O A:GLY208 4.4 57.6 1.0 C A:CYS206 4.5 62.5 1.0 SG A:CYS222 4.6 57.0 1.0 CE1 A:TYR209 4.6 57.7 1.0 SG A:CYS292 4.8 62.1 1.0 CB A:CYS222 4.8 53.5 1.0 N A:GLY208 4.9 61.1 1.0 CG A:PRO207 4.9 62.9 1.0 SG A:CYS289 4.9 60.6 1.0 CD1 A:TYR209 5.0 56.2 1.0

Iron binding site 8 out of 16 in the Crystal Structure of Radical Sam Epimerase Epee From Bacillus Subtilis with [4FE-4S] Clusters, S-Adenosyl-L-Homocysteine and Ripp Peptide 5 Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Radical Sam Epimerase Epee From Bacillus Subtilis with [4FE-4S] Clusters, S-Adenosyl-L-Homocysteine and Ripp Peptide 5 Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:53.2 occ:0.85 FE4 A:SF4402 0.0 53.2 0.8 SG A:CYS222 2.1 57.0 1.0 S3 A:SF4402 2.3 53.7 0.8 S1 A:SF4402 2.3 53.5 0.8 S2 A:SF4402 2.3 53.7 0.8 FE3 A:SF4402 2.7 54.0 0.8 FE2 A:SF4402 2.7 55.1 0.8 FE1 A:SF4402 2.7 53.9 0.8 CB A:CYS222 3.2 53.5 1.0 S4 A:SF4402 3.9 54.1 0.8 CB A:SER224 3.9 56.6 1.0 CD1 A:ILE227 4.1 48.7 1.0 CB A:ILE227 4.4 48.9 1.0 CG1 A:ILE227 4.5 48.7 1.0 CA A:CYS222 4.5 52.8 1.0 OG A:SER224 4.7 58.8 1.0 SG A:CYS289 4.7 60.6 1.0 SG A:CYS292 4.7 62.1 1.0 SG A:CYS206 4.7 60.2 1.0 N A:SER224 4.9 56.6 1.0 N A:CYS222 4.9 51.3 1.0

Iron binding site 9 out of 16 in the Crystal Structure of Radical Sam Epimerase Epee From Bacillus Subtilis with [4FE-4S] Clusters, S-Adenosyl-L-Homocysteine and Ripp Peptide 5 Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Radical Sam Epimerase Epee From Bacillus Subtilis with [4FE-4S] Clusters, S-Adenosyl-L-Homocysteine and Ripp Peptide 5 Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:55.9 occ:0.83 FE1 B:SF4401 0.0 55.9 0.8 N B:SAH403 2.3 56.9 1.0 S4 B:SF4401 2.3 52.0 0.8 S2 B:SF4401 2.3 52.6 0.8 S3 B:SF4401 2.3 52.8 0.8 O B:SAH403 2.4 58.2 1.0 FE4 B:SF4401 2.8 52.5 0.8 FE2 B:SF4401 2.8 51.4 0.8 FE3 B:SF4401 2.8 51.7 0.8 C B:SAH403 3.0 58.0 1.0 CA B:SAH403 3.1 57.4 1.0 SD B:SAH403 3.6 56.7 1.0 NE2 B:HIS120 3.7 57.4 1.0 CG B:SAH403 3.8 57.6 1.0 S1 B:SF4401 4.0 52.3 0.8 CB B:SAH403 4.0 57.8 1.0 OXT B:SAH403 4.3 58.1 1.0 CD2 B:HIS120 4.5 56.7 1.0 SG B:CYS14 4.6 54.9 1.0 CE1 B:HIS120 4.7 57.0 1.0 O B:GLY59 4.7 52.6 1.0 C2' B:SAH403 4.8 56.2 1.0 C3' B:SAH403 4.9 55.9 1.0 SG B:CYS21 4.9 58.7 1.0 SG B:CYS18 4.9 57.6 1.0

Iron binding site 10 out of 16 in the Crystal Structure of Radical Sam Epimerase Epee From Bacillus Subtilis with [4FE-4S] Clusters, S-Adenosyl-L-Homocysteine and Ripp Peptide 5 Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Radical Sam Epimerase Epee From Bacillus Subtilis with [4FE-4S] Clusters, S-Adenosyl-L-Homocysteine and Ripp Peptide 5 Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:51.4 occ:0.83 FE2 B:SF4401 0.0 51.4 0.8 SG B:CYS21 2.2 58.7 1.0 S3 B:SF4401 2.3 52.8 0.8 S1 B:SF4401 2.3 52.3 0.8 S4 B:SF4401 2.3 52.0 0.8 FE4 B:SF4401 2.7 52.5 0.8 FE3 B:SF4401 2.8 51.7 0.8 FE1 B:SF4401 2.8 55.9 0.8 CB B:CYS21 3.2 57.6 1.0 CB B:SER25 3.9 61.6 1.0 S2 B:SF4401 3.9 52.6 0.8 CA B:CYS21 4.1 58.0 1.0 OG B:SER25 4.1 61.7 1.0 N B:SAH403 4.6 56.9 1.0 CB B:CYS18 4.7 59.5 1.0 N B:SER25 4.7 61.8 1.0 SD B:SAH403 4.8 56.7 1.0 CA B:SER25 4.8 61.9 1.0 SG B:CYS18 4.8 57.6 1.0 SG B:CYS14 4.9 54.9 1.0

X.Kubiak, I.Polsinelli, L.M.G.Chavas, C.D.Fyfe, A.Guillot, L.Fradale, C.Brewee, S.Grimaldi, G.Gerbaud, A.Thureau, P.Legrand, O.Berteau, A.Benjdia. Structural and Mechanistic Basis For Ripp Epimerization By A Radical Sam Enzyme Nat.Chem.Biol. 2023.
ISSN: ESSN 1552-4469
DOI: 10.1038/S41589-023-01493-1