Iron in PDB 6p78: Queuine Lyase From Clostridium Spiroforme Bound to Sam and Queuine

The structure of Queuine Lyase From Clostridium Spiroforme Bound to Sam and Queuine, PDB code: 6p78 was solved by S.C.Almo, T.L.Grove, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.80 / 1.73
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	57.606, 57.606, 152.414, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 20

The binding sites of Iron atom in the Queuine Lyase From Clostridium Spiroforme Bound to Sam and Queuine (pdb code 6p78). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Queuine Lyase From Clostridium Spiroforme Bound to Sam and Queuine, PDB code: 6p78:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Queuine Lyase From Clostridium Spiroforme Bound to Sam and Queuine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Queuine Lyase From Clostridium Spiroforme Bound to Sam and Queuine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:20.1 occ:1.00 FE1 A:SF4501 0.0 20.1 1.0 S2 A:SF4501 2.2 23.6 1.0 S3 A:SF4501 2.3 24.3 1.0 S4 A:SF4501 2.3 23.9 1.0 SG A:CYS23 2.4 24.7 1.0 FE4 A:SF4501 2.6 21.6 1.0 FE3 A:SF4501 2.7 21.4 1.0 FE2 A:SF4501 2.7 23.7 1.0 CB A:CYS23 3.4 23.7 1.0 S1 A:SF4501 3.9 20.8 1.0 CG2 A:ILE34 3.9 40.6 1.0 N A:GLY26 4.0 25.9 1.0 N A:SAM503 4.1 31.1 1.0 CA A:GLY26 4.3 29.4 1.0 O A:HOH628 4.7 30.1 1.0 SG A:CYS31 4.8 26.9 1.0 SG A:CYS28 4.8 24.1 1.0 CA A:CYS23 4.8 26.3 1.0 CA A:GLY68 4.8 30.5 1.0 OXT A:SAM503 4.9 27.2 1.0

Iron binding site 2 out of 4 in the Queuine Lyase From Clostridium Spiroforme Bound to Sam and Queuine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Queuine Lyase From Clostridium Spiroforme Bound to Sam and Queuine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:23.7 occ:1.00 FE2 A:SF4501 0.0 23.7 1.0 S4 A:SF4501 2.3 23.9 1.0 S1 A:SF4501 2.3 20.8 1.0 S3 A:SF4501 2.4 24.3 1.0 N A:SAM503 2.4 31.1 1.0 OXT A:SAM503 2.5 27.2 1.0 FE3 A:SF4501 2.7 21.4 1.0 FE1 A:SF4501 2.7 20.1 1.0 FE4 A:SF4501 2.8 21.6 1.0 C A:SAM503 3.2 26.1 1.0 CA A:SAM503 3.3 29.1 1.0 SD A:SAM503 3.5 61.2 1.0 S2 A:SF4501 4.0 23.6 1.0 CG A:SAM503 4.0 53.0 1.0 CB A:SAM503 4.0 39.0 1.0 NZ A:LYS136 4.0 22.6 1.0 CE A:SAM503 4.1 53.9 1.0 O A:SAM503 4.4 25.2 1.0 SG A:CYS23 4.6 24.7 1.0 SG A:CYS28 4.7 24.1 1.0 CD2 A:HIS98 4.9 25.8 1.0 SG A:CYS31 5.0 26.9 1.0

Iron binding site 3 out of 4 in the Queuine Lyase From Clostridium Spiroforme Bound to Sam and Queuine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Queuine Lyase From Clostridium Spiroforme Bound to Sam and Queuine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:21.4 occ:1.00 FE3 A:SF4501 0.0 21.4 1.0 S4 A:SF4501 2.2 23.9 1.0 SG A:CYS28 2.3 24.1 1.0 S2 A:SF4501 2.3 23.6 1.0 S1 A:SF4501 2.3 20.8 1.0 FE4 A:SF4501 2.6 21.6 1.0 FE1 A:SF4501 2.7 20.1 1.0 FE2 A:SF4501 2.7 23.7 1.0 CB A:CYS28 3.1 24.6 1.0 S3 A:SF4501 3.8 24.3 1.0 NZ A:LYS136 3.9 22.6 1.0 OXT A:SAM503 4.1 27.2 1.0 N A:CYS28 4.2 26.2 1.0 CD1 A:TRP25 4.3 25.3 1.0 CA A:CYS28 4.3 25.9 1.0 CB A:CYS31 4.4 22.5 1.0 CE A:LYS136 4.5 22.4 1.0 SG A:CYS31 4.6 26.9 1.0 SG A:CYS23 4.8 24.7 1.0 N A:SAM503 4.9 31.1 1.0 N A:GLY26 5.0 25.9 1.0 CD A:LYS136 5.0 19.7 1.0

Iron binding site 4 out of 4 in the Queuine Lyase From Clostridium Spiroforme Bound to Sam and Queuine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Queuine Lyase From Clostridium Spiroforme Bound to Sam and Queuine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:21.6 occ:1.00 FE4 A:SF4501 0.0 21.6 1.0 S3 A:SF4501 2.3 24.3 1.0 S2 A:SF4501 2.3 23.6 1.0 S1 A:SF4501 2.3 20.8 1.0 SG A:CYS31 2.4 26.9 1.0 FE3 A:SF4501 2.6 21.4 1.0 FE1 A:SF4501 2.6 20.1 1.0 FE2 A:SF4501 2.8 23.7 1.0 CB A:CYS31 3.2 22.5 1.0 S4 A:SF4501 3.8 23.9 1.0 CG2 A:ILE34 4.0 40.6 1.0 CA A:CYS31 4.6 24.7 1.0 CB A:CYS28 4.7 24.6 1.0 SG A:CYS28 4.7 24.1 1.0 SD A:SAM503 4.7 61.2 1.0 N A:SAM503 4.9 31.1 1.0 SG A:CYS23 5.0 24.7 1.0

Y.Yuan, R.Zallot, T.L.Grove, D.J.Payan, I.Martin-Verstraete, S.Sepic, S.Balamkundu, R.Neelakandan, V.K.Gadi, C.F.Liu, M.A.Swairjo, P.C.Dedon, S.C.Almo, J.A.Gerlt, V.De Crecy-Lagard. Discovery of Novel Bacterial Queuine Salvage Enzymes and Pathways in Human Pathogens. Proc.Natl.Acad.Sci.Usa V. 116 19126 2019.
ISSN: ESSN 1091-6490
PubMed: 31481610
DOI: 10.1073/PNAS.1909604116