Iron in PDB 9ebk: Piperazate Synthase (Pips) in Complex with Haem

The structure of Piperazate Synthase (Pips) in Complex with Haem, PDB code: 9ebk 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)	79.78 / 2.08
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	66.51, 66.51, 478.694, 90, 90, 120
R / Rfree (%)	18.8 / 22.8

The binding sites of Iron atom in the Piperazate Synthase (Pips) in Complex with Haem (pdb code 9ebk). 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, PDB code: 9ebk:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Piperazate Synthase (Pips) in Complex with Haem


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:34.3 occ:1.00 FE B:HEM501 0.0 34.3 1.0 ND B:HEM501 1.9 30.0 1.0 NB B:HEM501 2.0 33.7 1.0 NC B:HEM501 2.1 35.9 1.0 NA B:HEM501 2.1 36.2 1.0 NE2 B:HIS66 2.3 31.6 1.0 NE2 A:HIS223 2.5 73.2 1.0 C1D B:HEM501 2.9 35.2 1.0 C4D B:HEM501 3.0 37.4 1.0 C1B B:HEM501 3.0 34.8 1.0 C4C B:HEM501 3.0 32.7 1.0 C4B B:HEM501 3.1 40.1 1.0 C4A B:HEM501 3.1 31.1 1.0 C1C B:HEM501 3.1 36.0 1.0 C1A B:HEM501 3.1 35.3 1.0 CE1 B:HIS66 3.2 32.0 1.0 CE1 A:HIS223 3.2 76.9 1.0 CD2 B:HIS66 3.2 33.8 1.0 CHD B:HEM501 3.3 30.9 1.0 CHB B:HEM501 3.4 29.5 1.0 CHA B:HEM501 3.5 31.9 1.0 CHC B:HEM501 3.5 39.2 1.0 CD2 A:HIS223 3.6 77.1 1.0 C2D B:HEM501 4.2 33.7 1.0 C3D B:HEM501 4.2 26.9 1.0 C2B B:HEM501 4.3 35.5 1.0 C3B B:HEM501 4.3 36.6 1.0 C3C B:HEM501 4.3 36.9 1.0 C2C B:HEM501 4.3 32.6 1.0 C3A B:HEM501 4.3 34.2 1.0 C2A B:HEM501 4.3 30.3 1.0 ND1 B:HIS66 4.4 33.0 1.0 CG B:HIS66 4.4 33.5 1.0 ND1 A:HIS223 4.4 75.0 1.0 CG A:HIS223 4.6 81.7 1.0

Iron binding site 2 out of 2 in the Piperazate Synthase (Pips) in Complex with Haem


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:31.2 occ:1.00 FE A:HEM301 0.0 31.2 1.0 ND A:HEM301 2.0 33.0 1.0 NC A:HEM301 2.1 37.4 1.0 NB A:HEM301 2.1 29.4 1.0 NA A:HEM301 2.1 27.5 1.0 NE2 A:HIS66 2.2 26.0 1.0 NE2 B:HIS223 2.4 60.5 1.0 C1D A:HEM301 3.1 42.1 1.0 C4D A:HEM301 3.1 37.6 1.0 C1C A:HEM301 3.1 37.6 1.0 C4C A:HEM301 3.1 40.4 1.0 C1B A:HEM301 3.1 38.2 1.0 C4B A:HEM301 3.1 40.6 1.0 C4A A:HEM301 3.1 33.7 1.0 C1A A:HEM301 3.1 34.4 1.0 CE1 B:HIS223 3.2 58.5 1.0 CE1 A:HIS66 3.2 28.7 1.0 CD2 A:HIS66 3.2 29.0 1.0 CHD A:HEM301 3.4 37.5 1.0 CHA A:HEM301 3.4 35.7 1.0 CHC A:HEM301 3.5 34.0 1.0 CHB A:HEM301 3.5 32.6 1.0 CD2 B:HIS223 3.5 63.1 1.0 C3D A:HEM301 4.3 39.5 1.0 C2D A:HEM301 4.3 40.1 1.0 C2C A:HEM301 4.3 36.5 1.0 C3C A:HEM301 4.3 39.6 1.0 ND1 A:HIS66 4.3 28.4 1.0 C2B A:HEM301 4.3 34.5 1.0 C3B A:HEM301 4.3 41.9 1.0 C3A A:HEM301 4.4 36.0 1.0 ND1 B:HIS223 4.4 58.2 1.0 C2A A:HEM301 4.4 34.2 1.0 CG A:HIS66 4.4 25.6 1.0 CG B:HIS223 4.5 64.1 1.0 CE1 B:HIS222 4.7 59.1 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.