Iron in PDB 6fd2: Radical Sam 1,2-Diol Dehydratase APRD4 in Complex with Its Substrate Paromamine

The structure of Radical Sam 1,2-Diol Dehydratase APRD4 in Complex with Its Substrate Paromamine, PDB code: 6fd2 was solved by W.Q.Liu, P.Amara, J.M.Mouesca, X.Ji, O.Renoux, L.Martin, C.Zhang, Q.Zhang, Y.Nicolet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.08 / 2.55
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	121.820, 121.820, 233.780, 90.00, 90.00, 120.00
R / Rfree (%)	22.8 / 26.3

The binding sites of Iron atom in the Radical Sam 1,2-Diol Dehydratase APRD4 in Complex with Its Substrate Paromamine (pdb code 6fd2). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Radical Sam 1,2-Diol Dehydratase APRD4 in Complex with Its Substrate Paromamine, PDB code: 6fd2:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Radical Sam 1,2-Diol Dehydratase APRD4 in Complex with Its Substrate Paromamine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Radical Sam 1,2-Diol Dehydratase APRD4 in Complex with Its Substrate Paromamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:65.9 occ:1.00 FE1 B:SF4502 0.0 65.9 1.0 S4 B:SF4502 2.3 80.1 1.0 S2 B:SF4502 2.3 95.9 1.0 S3 B:SF4502 2.3 89.2 1.0 SG B:CYS214 2.6 67.8 1.0 FE3 B:SF4502 2.7 67.7 1.0 FE4 B:SF4502 2.7 63.6 1.0 FE2 B:SF4502 2.7 58.1 1.0 CB B:CYS214 2.9 72.7 1.0 S1 B:SF4502 3.9 75.9 1.0 CA B:CYS214 4.4 63.3 1.0 C5' B:5AD504 4.5 0.1 1.0 CD B:PRO217 4.5 60.0 1.0 O B:MET503 4.6 97.0 1.0 CB B:TYR216 4.6 62.5 1.0 N B:MET503 4.7 76.0 1.0 O B:CYS210 4.7 57.2 1.0 C3' B:5AD504 4.9 69.2 1.0 CD1 B:TYR216 4.9 54.6 1.0 C B:CYS214 5.0 62.1 1.0 CG B:PRO217 5.0 67.9 1.0

Iron binding site 2 out of 8 in the Radical Sam 1,2-Diol Dehydratase APRD4 in Complex with Its Substrate Paromamine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Radical Sam 1,2-Diol Dehydratase APRD4 in Complex with Its Substrate Paromamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:58.1 occ:1.00 FE2 B:SF4502 0.0 58.1 1.0 S4 B:SF4502 2.3 80.1 1.0 S3 B:SF4502 2.3 89.2 1.0 S1 B:SF4502 2.3 75.9 1.0 SG B:CYS206 2.5 56.6 1.0 FE4 B:SF4502 2.7 63.6 1.0 FE1 B:SF4502 2.7 65.9 1.0 FE3 B:SF4502 2.8 67.7 1.0 CB B:CYS206 3.3 46.3 1.0 S2 B:SF4502 3.9 95.9 1.0 N B:MET503 4.3 76.0 1.0 CG B:PRO217 4.4 67.9 1.0 CG2 B:VAL253 4.5 45.5 1.0 CD B:PRO217 4.6 60.0 1.0 CB B:TYR208 4.6 62.7 1.0 O B:MET503 4.7 97.0 1.0 CA B:CYS206 4.7 51.1 1.0 CB B:PRO252 4.8 59.1 1.0 CD2 B:TYR208 4.9 83.0 1.0 SG B:CYS214 4.9 67.8 1.0

Iron binding site 3 out of 8 in the Radical Sam 1,2-Diol Dehydratase APRD4 in Complex with Its Substrate Paromamine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Radical Sam 1,2-Diol Dehydratase APRD4 in Complex with Its Substrate Paromamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:67.7 occ:1.00 FE3 B:SF4502 0.0 67.7 1.0 S2 B:SF4502 2.3 95.9 1.0 S4 B:SF4502 2.3 80.1 1.0 S1 B:SF4502 2.3 75.9 1.0 SG B:CYS210 2.6 79.2 1.0 FE1 B:SF4502 2.7 65.9 1.0 FE2 B:SF4502 2.8 58.1 1.0 FE4 B:SF4502 2.8 63.6 1.0 CB B:CYS210 3.3 80.7 1.0 NZ B:LYS320 3.7 66.3 1.0 O B:MET503 3.8 97.0 1.0 S3 B:SF4502 3.9 89.2 1.0 CA B:CYS210 4.2 62.7 1.0 NH2 B:ARG282 4.2 83.5 1.0 CB B:TYR208 4.3 62.7 1.0 C B:CYS210 4.3 59.1 1.0 N B:CYS210 4.5 59.4 1.0 O B:CYS210 4.5 57.2 1.0 SG B:CYS206 4.5 56.6 1.0 N B:ARG211 4.7 55.5 1.0 CB B:CYS214 4.8 72.7 1.0 CE B:LYS320 4.9 51.9 1.0 N B:MET503 5.0 76.0 1.0

Iron binding site 4 out of 8 in the Radical Sam 1,2-Diol Dehydratase APRD4 in Complex with Its Substrate Paromamine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Radical Sam 1,2-Diol Dehydratase APRD4 in Complex with Its Substrate Paromamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:63.6 occ:1.00 FE4 B:SF4502 0.0 63.6 1.0 O B:MET503 2.3 97.0 1.0 N B:MET503 2.3 76.0 1.0 S3 B:SF4502 2.3 89.2 1.0 S2 B:SF4502 2.3 95.9 1.0 S1 B:SF4502 2.3 75.9 1.0 FE1 B:SF4502 2.7 65.9 1.0 FE2 B:SF4502 2.7 58.1 1.0 FE3 B:SF4502 2.8 67.7 1.0 C B:MET503 3.1 83.4 1.0 CA B:MET503 3.2 63.6 1.0 S4 B:SF4502 3.9 80.1 1.0 CB B:MET503 4.2 68.9 1.0 NZ B:LYS320 4.2 66.3 1.0 OXT B:MET503 4.3 89.4 1.0 O B:PRO252 4.6 57.0 1.0 SG B:CYS206 4.9 56.6 1.0 C5' B:5AD504 4.9 0.1 1.0 CG2 B:VAL253 4.9 45.5 1.0 CG B:ARG282 4.9 72.0 1.0 O3' B:5AD504 4.9 79.4 1.0 C3' B:5AD504 5.0 69.2 1.0

Iron binding site 5 out of 8 in the Radical Sam 1,2-Diol Dehydratase APRD4 in Complex with Its Substrate Paromamine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Radical Sam 1,2-Diol Dehydratase APRD4 in Complex with Its Substrate Paromamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:67.5 occ:1.00 FE1 A:SF4502 0.0 67.5 1.0 S3 A:SF4502 2.3 79.3 1.0 S4 A:SF4502 2.3 64.3 1.0 S2 A:SF4502 2.3 90.5 1.0 SG A:CYS214 2.6 85.0 1.0 FE2 A:SF4502 2.6 65.2 1.0 FE4 A:SF4502 2.7 58.4 1.0 FE3 A:SF4502 2.7 58.4 1.0 CB A:CYS214 3.1 72.7 1.0 S1 A:SF4502 3.8 69.4 1.0 N A:MET503 4.4 49.6 1.0 CD A:PRO217 4.5 67.3 1.0 CB A:TYR216 4.5 61.0 1.0 C5' A:5AD504 4.5 81.6 1.0 CA A:CYS214 4.6 80.7 1.0 O A:MET503 4.7 55.9 1.0 CD1 A:TYR216 4.7 61.9 1.0 CG A:PRO217 5.0 70.9 1.0

Iron binding site 6 out of 8 in the Radical Sam 1,2-Diol Dehydratase APRD4 in Complex with Its Substrate Paromamine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Radical Sam 1,2-Diol Dehydratase APRD4 in Complex with Its Substrate Paromamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:65.2 occ:1.00 FE2 A:SF4502 0.0 65.2 1.0 S4 A:SF4502 2.3 64.3 1.0 S1 A:SF4502 2.3 69.4 1.0 S3 A:SF4502 2.3 79.3 1.0 FE1 A:SF4502 2.6 67.5 1.0 SG A:CYS206 2.6 77.6 1.0 FE3 A:SF4502 2.7 58.4 1.0 FE4 A:SF4502 2.7 58.4 1.0 CB A:CYS206 3.5 66.0 1.0 S2 A:SF4502 3.8 90.5 1.0 CG2 A:VAL253 4.5 50.1 1.0 CG A:PRO217 4.5 70.9 1.0 CB A:TYR208 4.5 56.9 1.0 N A:MET503 4.5 49.6 1.0 CD A:PRO217 4.7 67.3 1.0 CD2 A:TYR208 4.7 53.2 1.0 O A:MET503 4.7 55.9 1.0 SG A:CYS214 4.9 85.0 1.0 CB A:PRO252 4.9 49.0 1.0 CA A:CYS206 4.9 68.0 1.0

Iron binding site 7 out of 8 in the Radical Sam 1,2-Diol Dehydratase APRD4 in Complex with Its Substrate Paromamine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Radical Sam 1,2-Diol Dehydratase APRD4 in Complex with Its Substrate Paromamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:58.4 occ:1.00 FE3 A:SF4502 0.0 58.4 1.0 S4 A:SF4502 2.3 64.3 1.0 S1 A:SF4502 2.3 69.4 1.0 S2 A:SF4502 2.3 90.5 1.0 SG A:CYS210 2.7 73.8 1.0 FE2 A:SF4502 2.7 65.2 1.0 FE1 A:SF4502 2.7 67.5 1.0 FE4 A:SF4502 2.8 58.4 1.0 CB A:CYS210 3.4 77.3 1.0 O A:MET503 3.9 55.9 1.0 NZ A:LYS320 3.9 62.1 1.0 S3 A:SF4502 4.0 79.3 1.0 CB A:TYR208 4.3 56.9 1.0 CA A:CYS210 4.3 65.4 1.0 NH2 A:ARG282 4.4 51.2 1.0 C A:CYS210 4.4 70.2 1.0 N A:CYS210 4.6 69.0 1.0 O A:CYS210 4.6 80.5 1.0 CB A:CYS214 4.6 72.7 1.0 N A:ARG211 4.8 77.1 1.0 SG A:CYS206 4.9 77.6 1.0 CD A:LYS320 4.9 64.1 1.0

Iron binding site 8 out of 8 in the Radical Sam 1,2-Diol Dehydratase APRD4 in Complex with Its Substrate Paromamine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Radical Sam 1,2-Diol Dehydratase APRD4 in Complex with Its Substrate Paromamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:58.4 occ:1.00 FE4 A:SF4502 0.0 58.4 1.0 O A:MET503 2.2 55.9 1.0 N A:MET503 2.3 49.6 1.0 S2 A:SF4502 2.3 90.5 1.0 S3 A:SF4502 2.3 79.3 1.0 S1 A:SF4502 2.3 69.4 1.0 FE1 A:SF4502 2.7 67.5 1.0 FE2 A:SF4502 2.7 65.2 1.0 FE3 A:SF4502 2.8 58.4 1.0 C A:MET503 3.1 59.1 1.0 CA A:MET503 3.2 53.9 1.0 S4 A:SF4502 3.9 64.3 1.0 NZ A:LYS320 4.1 62.1 1.0 OXT A:MET503 4.2 57.5 1.0 CB A:MET503 4.4 62.5 1.0 O A:PRO252 4.8 72.7 1.0 CG2 A:VAL253 4.8 50.1 1.0 CG A:ARG282 4.8 49.5 1.0 C5' A:5AD504 4.9 81.6 1.0

W.Q.Liu, P.Amara, J.M.Mouesca, X.Ji, O.Renoux, L.Martin, C.Zhang, Q.Zhang, Y.Nicolet. 1,2-Diol Dehydration By the Radical Sam Enzyme APRD4: A Matter of Proton Circulation and Substrate Flexibility. J. Am. Chem. Soc. V. 140 1365 2018.
ISSN: ESSN 1520-5126
PubMed: 29300094
DOI: 10.1021/JACS.7B10501