Iron in PDB 9ebm: Piperazate Synthase (Pips) in Complex with Haem and N5-Oh-L-Ornithine

The structure of Piperazate Synthase (Pips) in Complex with Haem and N5-Oh-L-Ornithine, PDB code: 9ebm was solved by M.A.Higgins, K.S.Ryan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	79.83 / 1.92
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	67.002, 67.002, 479.001, 90, 90, 120
R / Rfree (%)	17.4 / 21.2

The binding sites of Iron atom in the Piperazate Synthase (Pips) in Complex with Haem and N5-Oh-L-Ornithine (pdb code 9ebm). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Piperazate Synthase (Pips) in Complex with Haem and N5-Oh-L-Ornithine, PDB code: 9ebm:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Piperazate Synthase (Pips) in Complex with Haem and N5-Oh-L-Ornithine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Piperazate Synthase (Pips) in Complex with Haem and N5-Oh-L-Ornithine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:29.7 occ:1.00 FE B:HEM501 0.0 29.7 1.0 NB B:HEM501 2.0 27.9 1.0 ND B:HEM501 2.0 30.6 1.0 NE B:ONH502 2.0 41.9 1.0 NC B:HEM501 2.1 32.2 1.0 NE2 B:HIS66 2.1 29.6 1.0 NA B:HEM501 2.1 24.8 1.0 OZ B:ONH502 2.9 64.9 1.0 C1B B:HEM501 3.0 31.6 1.0 C1D B:HEM501 3.0 36.7 1.0 CE1 B:HIS66 3.0 30.6 1.0 C4C B:HEM501 3.1 27.7 1.0 C4D B:HEM501 3.1 33.4 1.0 C4B B:HEM501 3.1 33.1 1.0 C4A B:HEM501 3.1 23.2 1.0 C1C B:HEM501 3.1 30.4 1.0 C1A B:HEM501 3.2 25.0 1.0 CD2 B:HIS66 3.2 31.6 1.0 CD B:ONH502 3.3 41.5 1.0 CHD B:HEM501 3.3 34.0 1.0 CHB B:HEM501 3.4 26.0 1.0 CHC B:HEM501 3.5 31.5 1.0 CHA B:HEM501 3.5 23.2 1.0 C2B B:HEM501 4.2 27.3 1.0 ND1 B:HIS66 4.2 26.7 1.0 C2D B:HEM501 4.2 33.7 1.0 C3B B:HEM501 4.3 34.5 1.0 C3D B:HEM501 4.3 32.3 1.0 C3C B:HEM501 4.3 30.5 1.0 CG B:HIS66 4.3 27.0 1.0 C2C B:HEM501 4.3 33.2 1.0 C3A B:HEM501 4.4 25.1 1.0 C2A B:HEM501 4.4 26.8 1.0 CG B:ONH502 4.4 45.4 1.0 CB B:ONH502 4.9 50.2 1.0

Iron binding site 2 out of 2 in the Piperazate Synthase (Pips) in Complex with Haem and N5-Oh-L-Ornithine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Piperazate Synthase (Pips) in Complex with Haem and N5-Oh-L-Ornithine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:24.6 occ:1.00 FE A:HEM301 0.0 24.6 1.0 NE A:ONH304 2.0 41.0 1.0 NB A:HEM301 2.0 23.4 1.0 NA A:HEM301 2.1 21.5 1.0 ND A:HEM301 2.1 21.5 1.0 NC A:HEM301 2.1 23.6 1.0 NE2 A:HIS66 2.1 22.1 1.0 OZ A:ONH304 2.6 59.2 1.0 C4B A:HEM301 3.0 31.7 1.0 C1B A:HEM301 3.1 29.7 1.0 C4A A:HEM301 3.1 25.4 1.0 C1A A:HEM301 3.1 29.1 1.0 CE1 A:HIS66 3.1 28.0 1.0 C1C A:HEM301 3.1 30.3 1.0 C4D A:HEM301 3.1 29.3 1.0 C1D A:HEM301 3.1 26.2 1.0 C4C A:HEM301 3.1 29.1 1.0 CD2 A:HIS66 3.2 27.5 1.0 CHC A:HEM301 3.4 28.3 1.0 CD A:ONH304 3.4 47.3 1.0 CHA A:HEM301 3.4 25.9 1.0 CHB A:HEM301 3.5 25.1 1.0 CHD A:HEM301 3.5 23.5 1.0 ND1 A:HIS66 4.2 27.2 1.0 C3B A:HEM301 4.2 23.7 1.0 C2B A:HEM301 4.3 27.0 1.0 C3A A:HEM301 4.3 25.8 1.0 C2A A:HEM301 4.3 21.4 1.0 CG A:HIS66 4.3 24.3 1.0 C3D A:HEM301 4.3 35.4 1.0 C2D A:HEM301 4.3 34.0 1.0 C2C A:HEM301 4.3 27.1 1.0 C3C A:HEM301 4.3 30.9 1.0 CG A:ONH304 4.4 43.2 1.0 O A:HOH402 4.5 72.1 1.0 CB A:ONH304 4.7 46.5 1.0

M.A.Higgins, X.Shi, J.Soler, J.B.Harland, T.Parkkila, N.Lehnert, M.Garcia-Borras, Y.L.Du, K.S.Ryan. Structure and Mechanism of Haem-Dependent Nitrogen-Nitrogen Bond Formation in Piperazate Synthase To Be Published.