Iron in PDB 2zdo: Crystal Structure of Isdg-N7A in Complex with Hemin

All present enzymatic activity of Crystal Structure of Isdg-N7A in Complex with Hemin:
1.14.99.3;

The structure of Crystal Structure of Isdg-N7A in Complex with Hemin, PDB code: 2zdo was solved by W.C.Lee, M.L.Reniere, E.P.Skaar, M.E.P.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.80 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.585, 58.631, 59.692, 77.57, 74.39, 75.15
R / Rfree (%)	19.8 / 23.4

The binding sites of Iron atom in the Crystal Structure of Isdg-N7A in Complex with Hemin (pdb code 2zdo). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Isdg-N7A in Complex with Hemin, PDB code: 2zdo:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Isdg-N7A in Complex with Hemin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Isdg-N7A in Complex with Hemin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe200 b:22.4 occ:1.00 FE A:HEM200 0.0 22.4 1.0 NA A:HEM200 2.0 21.8 1.0 ND A:HEM200 2.0 20.4 1.0 NC A:HEM200 2.0 21.8 1.0 NB A:HEM200 2.1 22.9 1.0 NE2 A:HIS77 2.2 23.1 1.0 C1A A:HEM200 3.0 22.6 1.0 C4D A:HEM200 3.0 18.7 1.0 C4A A:HEM200 3.0 22.5 1.0 C1D A:HEM200 3.0 18.3 1.0 C4C A:HEM200 3.0 21.3 1.0 C4B A:HEM200 3.0 24.1 1.0 C1C A:HEM200 3.0 24.1 1.0 C1B A:HEM200 3.1 23.2 1.0 CD2 A:HIS77 3.1 23.3 1.0 CE1 A:HIS77 3.2 22.1 1.0 CHA A:HEM200 3.3 21.3 1.0 CHC A:HEM200 3.4 23.0 1.0 CHD A:HEM200 3.4 21.1 1.0 CHB A:HEM200 3.4 22.3 1.0 CD1 A:ILE54 3.8 21.4 1.0 C2A A:HEM200 4.2 23.5 1.0 C3A A:HEM200 4.2 22.6 1.0 C3D A:HEM200 4.2 18.0 1.0 C2D A:HEM200 4.2 15.9 1.0 C3C A:HEM200 4.3 23.9 1.0 C3B A:HEM200 4.3 25.2 1.0 CG A:HIS77 4.3 24.9 1.0 C2C A:HEM200 4.3 24.2 1.0 C2B A:HEM200 4.3 24.2 1.0 ND1 A:HIS77 4.3 23.3 1.0 CE1 A:PHE23 4.7 22.3 1.0 CZ A:PHE23 4.9 24.5 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Isdg-N7A in Complex with Hemin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Isdg-N7A in Complex with Hemin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe200 b:20.7 occ:1.00 FE B:HEM200 0.0 20.7 1.0 NA B:HEM200 2.0 22.2 1.0 NB B:HEM200 2.0 22.4 1.0 ND B:HEM200 2.1 18.7 1.0 NC B:HEM200 2.1 23.1 1.0 NE2 B:HIS77 2.2 21.9 1.0 C4B B:HEM200 3.0 24.0 1.0 C1A B:HEM200 3.0 21.3 1.0 C4A B:HEM200 3.0 22.9 1.0 C4D B:HEM200 3.0 17.3 1.0 C1B B:HEM200 3.0 23.5 1.0 C1D B:HEM200 3.1 19.3 1.0 C1C B:HEM200 3.1 24.3 1.0 C4C B:HEM200 3.1 21.1 1.0 CD2 B:HIS77 3.1 23.6 1.0 CE1 B:HIS77 3.3 21.3 1.0 CHA B:HEM200 3.3 20.8 1.0 CHC B:HEM200 3.3 23.2 1.0 CHB B:HEM200 3.4 23.8 1.0 CHD B:HEM200 3.4 20.7 1.0 CD1 B:ILE54 3.9 21.5 1.0 C3B B:HEM200 4.2 25.5 1.0 C2A B:HEM200 4.2 23.6 1.0 C3A B:HEM200 4.2 23.4 1.0 C2B B:HEM200 4.2 24.2 1.0 C3D B:HEM200 4.3 16.9 1.0 C2D B:HEM200 4.3 16.6 1.0 CG B:HIS77 4.3 23.6 1.0 C3C B:HEM200 4.3 24.4 1.0 C2C B:HEM200 4.3 24.0 1.0 ND1 B:HIS77 4.4 22.7 1.0 CE1 B:PHE23 4.8 22.7 1.0 CZ B:PHE23 5.0 21.8 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Isdg-N7A in Complex with Hemin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Isdg-N7A in Complex with Hemin within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe200 b:24.9 occ:1.00 FE C:HEM200 0.0 24.9 1.0 NA C:HEM200 2.0 24.7 1.0 NC C:HEM200 2.0 24.9 1.0 ND C:HEM200 2.0 23.6 1.0 NB C:HEM200 2.0 26.0 1.0 NE2 C:HIS77 2.2 27.5 1.0 C1A C:HEM200 3.0 25.9 1.0 C1C C:HEM200 3.0 27.2 1.0 C4B C:HEM200 3.0 27.1 1.0 C4D C:HEM200 3.0 22.9 1.0 C4A C:HEM200 3.0 26.2 1.0 C4C C:HEM200 3.0 24.2 1.0 C1D C:HEM200 3.0 21.5 1.0 C1B C:HEM200 3.1 26.7 1.0 CD2 C:HIS77 3.1 28.4 1.0 CE1 C:HIS77 3.2 26.7 1.0 CHC C:HEM200 3.3 26.1 1.0 CHA C:HEM200 3.3 24.3 1.0 CHD C:HEM200 3.4 23.4 1.0 CHB C:HEM200 3.4 27.2 1.0 CD1 C:ILE54 3.9 22.3 1.0 C2A C:HEM200 4.2 27.5 1.0 C3A C:HEM200 4.2 27.2 1.0 C3C C:HEM200 4.2 26.6 1.0 C2C C:HEM200 4.2 26.9 1.0 C3B C:HEM200 4.2 27.4 1.0 C2D C:HEM200 4.2 18.7 1.0 C3D C:HEM200 4.2 19.0 1.0 ND1 C:HIS77 4.3 27.4 1.0 C2B C:HEM200 4.3 27.1 1.0 CG C:HIS77 4.3 29.8 1.0 CE1 C:PHE23 4.9 24.9 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Isdg-N7A in Complex with Hemin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Isdg-N7A in Complex with Hemin within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe200 b:26.9 occ:1.00 FE D:HEM200 0.0 26.9 1.0 NC D:HEM200 2.0 27.7 1.0 NA D:HEM200 2.0 28.2 1.0 ND D:HEM200 2.1 24.5 1.0 NB D:HEM200 2.1 28.5 1.0 NE2 D:HIS77 2.2 24.9 1.0 C1C D:HEM200 3.0 29.9 1.0 C1A D:HEM200 3.0 28.6 1.0 C4C D:HEM200 3.0 26.9 1.0 C4B D:HEM200 3.0 30.5 1.0 C4A D:HEM200 3.0 28.6 1.0 C4D D:HEM200 3.0 23.6 1.0 C1D D:HEM200 3.1 22.9 1.0 C1B D:HEM200 3.1 29.6 1.0 CD2 D:HIS77 3.1 27.5 1.0 CE1 D:HIS77 3.2 25.5 1.0 CHC D:HEM200 3.3 29.2 1.0 CHA D:HEM200 3.3 26.1 1.0 CHD D:HEM200 3.4 25.6 1.0 CHB D:HEM200 3.4 29.1 1.0 CD1 D:ILE54 3.7 20.9 1.0 C2C D:HEM200 4.2 30.1 1.0 C3C D:HEM200 4.2 28.3 1.0 C2A D:HEM200 4.2 30.0 1.0 C3A D:HEM200 4.2 29.4 1.0 C3B D:HEM200 4.3 32.0 1.0 CG D:HIS77 4.3 27.4 1.0 C3D D:HEM200 4.3 21.0 1.0 C2D D:HEM200 4.3 21.9 1.0 C2B D:HEM200 4.3 30.1 1.0 ND1 D:HIS77 4.3 26.8 1.0 CE1 D:PHE23 4.8 26.8 1.0

W.C.Lee, M.L.Reniere, E.P.Skaar, M.E.P.Murphy. Ruffling of Metalloporphyrins Bound to Isdg and Isdi, Two Heme-Degrading Enzymes in Staphylococcus Aureus J.Biol.Chem. V. 283 30957 2008.
ISSN: ISSN 0021-9258
PubMed: 18713745
DOI: 10.1074/JBC.M709486200