Iron in PDB 2ygx: Structure of the Mixed-Function P450 Mycg in P21 Space Group

The structure of Structure of the Mixed-Function P450 Mycg in P21 Space Group, PDB code: 2ygx was solved by S.Li, P.M.Kells, F.U.Rutaganira, D.H.Sherman, L.M.Podust, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	80.99 / 2.39
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.150, 161.980, 100.110, 90.00, 89.99, 90.00
R / Rfree (%)	18.407 / 24.749

The binding sites of Iron atom in the Structure of the Mixed-Function P450 Mycg in P21 Space Group (pdb code 2ygx). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of the Mixed-Function P450 Mycg in P21 Space Group, PDB code: 2ygx:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of the Mixed-Function P450 Mycg in P21 Space Group


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of the Mixed-Function P450 Mycg in P21 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe450 b:12.4 occ:1.00 FE A:HEM450 0.0 12.4 1.0 NB A:HEM450 2.0 12.6 1.0 NA A:HEM450 2.0 9.8 1.0 ND A:HEM450 2.1 9.1 1.0 NC A:HEM450 2.1 11.7 1.0 SG A:CYS346 2.2 14.9 1.0 O A:HOH2074 2.5 9.7 1.0 C4B A:HEM450 3.0 13.8 1.0 C1A A:HEM450 3.0 11.4 1.0 C1B A:HEM450 3.1 11.2 1.0 C4D A:HEM450 3.1 11.4 1.0 C4A A:HEM450 3.1 10.8 1.0 C1C A:HEM450 3.1 12.1 1.0 C1D A:HEM450 3.1 9.1 1.0 C4C A:HEM450 3.1 11.4 1.0 CHC A:HEM450 3.4 12.9 1.0 CHA A:HEM450 3.4 10.7 1.0 CHB A:HEM450 3.4 10.4 1.0 CB A:CYS346 3.4 13.3 1.0 CHD A:HEM450 3.5 11.6 1.0 CA A:CYS346 4.1 13.9 1.0 O A:ALA234 4.2 20.0 1.0 C3B A:HEM450 4.2 10.2 1.0 C2B A:HEM450 4.3 8.5 1.0 C3A A:HEM450 4.3 11.8 1.0 C2A A:HEM450 4.3 12.1 1.0 C2C A:HEM450 4.3 11.0 1.0 C3C A:HEM450 4.3 11.3 1.0 C3D A:HEM450 4.3 9.1 1.0 C2D A:HEM450 4.3 8.1 1.0 O A:HOH2041 4.6 16.1 1.0 N A:GLY348 4.7 14.0 1.0 C A:CYS346 4.8 14.4 1.0 CB A:ALA234 4.9 19.5 1.0 N A:LEU347 4.9 14.3 1.0

Iron binding site 2 out of 4 in the Structure of the Mixed-Function P450 Mycg in P21 Space Group


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of the Mixed-Function P450 Mycg in P21 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe450 b:12.6 occ:1.00 FE B:HEM450 0.0 12.6 1.0 NC B:HEM450 2.0 10.3 1.0 NB B:HEM450 2.0 12.1 1.0 ND B:HEM450 2.1 10.1 1.0 NA B:HEM450 2.1 11.0 1.0 SG B:CYS346 2.2 13.7 1.0 O B:HOH2066 2.6 21.8 1.0 C4B B:HEM450 3.0 15.1 1.0 C1C B:HEM450 3.0 12.3 1.0 C4C B:HEM450 3.0 10.3 1.0 C1B B:HEM450 3.1 12.5 1.0 C4D B:HEM450 3.1 10.8 1.0 C1A B:HEM450 3.1 11.4 1.0 C4A B:HEM450 3.1 10.2 1.0 C1D B:HEM450 3.1 10.1 1.0 CB B:CYS346 3.3 14.8 1.0 CHC B:HEM450 3.4 12.0 1.0 CHD B:HEM450 3.5 10.1 1.0 CHB B:HEM450 3.5 12.8 1.0 CHA B:HEM450 3.5 10.5 1.0 CA B:CYS346 4.0 14.6 1.0 C3B B:HEM450 4.2 13.8 1.0 C3C B:HEM450 4.3 7.6 1.0 C2C B:HEM450 4.3 11.0 1.0 C2B B:HEM450 4.3 12.6 1.0 C3A B:HEM450 4.3 12.2 1.0 C2A B:HEM450 4.4 12.6 1.0 C3D B:HEM450 4.4 9.9 1.0 O B:ALA234 4.4 18.8 1.0 C2D B:HEM450 4.4 8.0 1.0 O B:HOH2025 4.6 30.3 1.0 C B:CYS346 4.8 15.0 1.0 N B:GLY348 4.8 13.9 1.0 CB B:ALA234 5.0 16.8 1.0

Iron binding site 3 out of 4 in the Structure of the Mixed-Function P450 Mycg in P21 Space Group


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of the Mixed-Function P450 Mycg in P21 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe450 b:10.7 occ:1.00 FE C:HEM450 0.0 10.7 1.0 NA C:HEM450 2.0 10.7 1.0 NB C:HEM450 2.1 12.5 1.0 NC C:HEM450 2.1 11.0 1.0 ND C:HEM450 2.1 9.1 1.0 SG C:CYS346 2.1 17.0 1.0 O C:HOH2073 2.5 8.3 1.0 C1A C:HEM450 3.0 12.1 1.0 C4B C:HEM450 3.1 14.6 1.0 C4D C:HEM450 3.1 10.6 1.0 C1C C:HEM450 3.1 12.6 1.0 C4A C:HEM450 3.1 11.8 1.0 C1B C:HEM450 3.1 12.8 1.0 C4C C:HEM450 3.1 10.3 1.0 C1D C:HEM450 3.1 9.3 1.0 CHA C:HEM450 3.3 10.9 1.0 CB C:CYS346 3.4 14.4 1.0 CHC C:HEM450 3.4 13.2 1.0 CHB C:HEM450 3.5 14.5 1.0 CHD C:HEM450 3.5 12.2 1.0 CA C:CYS346 4.1 14.7 1.0 O C:ALA234 4.2 18.6 1.0 C2A C:HEM450 4.3 12.7 1.0 C3B C:HEM450 4.3 14.4 1.0 C3A C:HEM450 4.3 12.6 1.0 C2C C:HEM450 4.3 11.8 1.0 C2B C:HEM450 4.3 13.4 1.0 C3C C:HEM450 4.3 10.7 1.0 C3D C:HEM450 4.3 8.9 1.0 C2D C:HEM450 4.4 9.4 1.0 O C:HOH2031 4.6 29.6 1.0 N C:GLY348 4.7 14.4 1.0 C C:CYS346 4.8 15.3 1.0 CB C:ALA234 4.9 18.5 1.0 N C:LEU347 5.0 15.6 1.0

Iron binding site 4 out of 4 in the Structure of the Mixed-Function P450 Mycg in P21 Space Group


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of the Mixed-Function P450 Mycg in P21 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe450 b:11.2 occ:1.00 FE D:HEM450 0.0 11.2 1.0 NC D:HEM450 2.0 10.5 1.0 ND D:HEM450 2.0 8.0 1.0 NB D:HEM450 2.0 12.1 1.0 NA D:HEM450 2.1 8.8 1.0 SG D:CYS346 2.2 13.8 1.0 O D:HOH2069 2.8 21.0 1.0 C4C D:HEM450 3.0 8.4 1.0 C1D D:HEM450 3.0 7.1 1.0 C4D D:HEM450 3.0 9.9 1.0 C1C D:HEM450 3.0 10.6 1.0 C4B D:HEM450 3.0 13.2 1.0 C1B D:HEM450 3.1 10.2 1.0 C4A D:HEM450 3.1 8.9 1.0 C1A D:HEM450 3.2 8.1 1.0 CHD D:HEM450 3.3 7.4 1.0 CB D:CYS346 3.4 11.1 1.0 CHC D:HEM450 3.4 10.9 1.0 CHB D:HEM450 3.4 9.7 1.0 CHA D:HEM450 3.5 7.2 1.0 O D:ALA234 4.1 18.6 1.0 CA D:CYS346 4.1 11.1 1.0 C3C D:HEM450 4.2 9.1 1.0 C2C D:HEM450 4.2 9.8 1.0 C3D D:HEM450 4.3 7.8 1.0 C3B D:HEM450 4.3 10.9 1.0 C2D D:HEM450 4.3 6.2 1.0 C2B D:HEM450 4.3 9.0 1.0 C3A D:HEM450 4.4 9.2 1.0 C2A D:HEM450 4.4 10.4 1.0 CB D:ALA234 4.8 16.4 1.0 C D:CYS346 4.9 11.3 1.0 N D:GLY348 4.9 11.6 1.0 C D:ALA234 5.0 17.6 1.0

S.Li, D.R.Tietz, F.U.Rutaganira, P.M.Kells, Y.Anzai, F.Kato, T.C.Pochapsky, D.H.Sherman, L.M.Podust. Substrate Recognition By the Multifunctional Cytochrome P450 Mycg in Mycinamicin Hydroxylation and Epoxidation Reactions. J.Biol.Chem. V. 287 37880 2012.
ISSN: ISSN 0021-9258
PubMed: 22952225
DOI: 10.1074/JBC.M112.410340