Iron in PDB 6z1m: Structure of An Ancestral Glycosidase (Family 1) Bound to Heme

The structure of Structure of An Ancestral Glycosidase (Family 1) Bound to Heme, PDB code: 6z1m was solved by J.A.Gavira, V.A.Risso, J.M.Sanchez-Ruiz, G.Gamiz-Arco, L.Gutierrez-Rus, B.Ibarra-Molero, Y.Oshino, D.Petrovic, A.Romero-Rivera, B.Seelig, S.C.L.Kamerlin, E.A.Gaucher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.32 / 2.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.934, 89.496, 141.120, 90.00, 94.21, 90.00
R / Rfree (%)	17.5 / 22.1

The structure of Structure of An Ancestral Glycosidase (Family 1) Bound to Heme also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Iron atom in the Structure of An Ancestral Glycosidase (Family 1) Bound to Heme (pdb code 6z1m). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Structure of An Ancestral Glycosidase (Family 1) Bound to Heme, PDB code: 6z1m:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Structure of An Ancestral Glycosidase (Family 1) Bound to Heme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of An Ancestral Glycosidase (Family 1) Bound to Heme within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:50.4 occ:1.00 FE A:HEM502 0.0 50.4 1.0 NB A:HEM502 2.0 50.9 1.0 NC A:HEM502 2.0 44.9 1.0 ND A:HEM502 2.1 47.8 1.0 NA A:HEM502 2.1 41.9 1.0 OH A:TYR264 2.3 56.7 1.0 C1C A:HEM502 3.0 54.4 1.0 CZ A:TYR264 3.0 57.0 1.0 C4B A:HEM502 3.0 48.4 1.0 C4C A:HEM502 3.0 52.0 1.0 C1D A:HEM502 3.1 47.7 1.0 C1A A:HEM502 3.1 47.6 1.0 C1B A:HEM502 3.1 48.1 1.0 C4D A:HEM502 3.1 50.3 1.0 C4A A:HEM502 3.1 41.4 1.0 CHC A:HEM502 3.4 51.0 1.0 CHD A:HEM502 3.4 52.3 1.0 CHA A:HEM502 3.5 49.8 1.0 CHB A:HEM502 3.5 42.6 1.0 CE2 A:TYR264 3.5 52.3 1.0 CD2 A:LEU226 3.8 43.4 1.0 CE1 A:TYR264 3.9 52.0 1.0 O A:HOH602 4.2 50.5 1.0 C2C A:HEM502 4.2 58.0 1.0 C3C A:HEM502 4.2 56.3 1.0 C3B A:HEM502 4.2 48.7 1.0 C2B A:HEM502 4.3 47.9 1.0 C2D A:HEM502 4.3 56.5 1.0 C3D A:HEM502 4.3 58.2 1.0 C2A A:HEM502 4.3 48.0 1.0 C3A A:HEM502 4.3 41.4 1.0 CD1 A:LEU226 4.4 56.4 1.0 CD2 A:TYR264 4.7 54.1 1.0 CD1 A:PHE255 4.7 43.2 1.0 CG A:LEU226 4.7 44.5 1.0 CD1 A:TYR264 5.0 56.5 1.0

Iron binding site 2 out of 3 in the Structure of An Ancestral Glycosidase (Family 1) Bound to Heme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of An Ancestral Glycosidase (Family 1) Bound to Heme within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:52.6 occ:1.00 FE B:HEM501 0.0 52.6 1.0 NB B:HEM501 2.0 36.9 1.0 ND B:HEM501 2.0 48.0 1.0 NA B:HEM501 2.0 39.9 1.0 NC B:HEM501 2.1 46.3 1.0 OH B:TYR264 2.3 49.6 1.0 C4B B:HEM501 3.0 38.6 1.0 C4D B:HEM501 3.0 42.9 1.0 C1C B:HEM501 3.0 46.9 1.0 C1A B:HEM501 3.0 43.5 1.0 C1B B:HEM501 3.1 39.1 1.0 C1D B:HEM501 3.1 51.4 1.0 C4A B:HEM501 3.1 41.5 1.0 C4C B:HEM501 3.1 51.1 1.0 CZ B:TYR264 3.2 50.0 1.0 CHC B:HEM501 3.4 45.0 1.0 CHA B:HEM501 3.4 37.8 1.0 CHB B:HEM501 3.5 45.3 1.0 CHD B:HEM501 3.5 55.1 1.0 CD2 B:LEU226 3.8 40.7 1.0 CE1 B:TYR264 3.9 46.8 1.0 CE2 B:TYR264 3.9 50.0 1.0 C3B B:HEM501 4.2 39.9 1.0 C3D B:HEM501 4.3 48.4 1.0 C2B B:HEM501 4.3 37.9 1.0 C2C B:HEM501 4.3 43.1 1.0 C2A B:HEM501 4.3 52.8 1.0 C2D B:HEM501 4.3 44.5 1.0 C3C B:HEM501 4.3 45.7 1.0 C3A B:HEM501 4.3 43.6 1.0 CD1 B:PHE255 4.5 57.4 1.0 CD1 B:LEU226 4.8 59.9 1.0 CE1 B:PHE255 5.0 52.5 1.0 CG B:LEU226 5.0 48.7 1.0

Iron binding site 3 out of 3 in the Structure of An Ancestral Glycosidase (Family 1) Bound to Heme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of An Ancestral Glycosidase (Family 1) Bound to Heme within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe502 b:48.1 occ:1.00 FE C:HEM502 0.0 48.1 1.0 ND C:HEM502 2.0 36.3 1.0 NC C:HEM502 2.0 41.6 1.0 NA C:HEM502 2.0 35.7 1.0 NB C:HEM502 2.1 43.6 1.0 OH C:TYR264 2.4 71.8 1.0 C1C C:HEM502 3.0 45.4 1.0 C1A C:HEM502 3.0 40.6 1.0 C4D C:HEM502 3.0 38.8 1.0 C4B C:HEM502 3.0 45.0 1.0 C1D C:HEM502 3.1 42.5 1.0 C4C C:HEM502 3.1 50.9 1.0 C4A C:HEM502 3.1 40.6 1.0 C1B C:HEM502 3.1 47.2 1.0 CD2 C:LEU226 3.1 56.2 1.0 CZ C:TYR264 3.3 56.7 1.0 CHC C:HEM502 3.4 46.8 1.0 CHA C:HEM502 3.4 37.4 1.0 CHD C:HEM502 3.4 47.6 1.0 CHB C:HEM502 3.5 45.9 1.0 CE1 C:TYR264 3.8 55.7 1.0 O C:HOH601 3.8 46.8 1.0 CE2 C:TYR264 4.2 54.4 1.0 C2C C:HEM502 4.2 50.4 1.0 C3C C:HEM502 4.3 55.5 1.0 C3D C:HEM502 4.3 49.2 1.0 C2A C:HEM502 4.3 47.2 1.0 C2D C:HEM502 4.3 47.6 1.0 C3B C:HEM502 4.3 40.8 1.0 C2B C:HEM502 4.3 45.3 1.0 C3A C:HEM502 4.3 44.0 1.0 CG C:LEU226 4.4 53.6 1.0 CD1 C:LEU226 4.7 61.4 1.0 CD1 C:PHE255 4.9 48.9 1.0

G.Gamiz-Arco, L.Gutierrez-Rus, V.A.Risso, B.Ibarra-Molero, Y.Oshino, D.Petrovic, A.Romero-Rivera, B.Seelig, J.A.Gavira, S.C.L.Kamerlin, E.A.Gaucher, J.M.Sanchez-Ruiz. Novel Heme-Binding Enables Allosteric Modulation in An Ancient Tim-Barrel Glycosidase Biorxiv 2020.
DOI: 10.1101/2020.05.27.118968