Iron in PDB 5ex6: Structure of P450 Stah From Glycopeptide Antibiotic A47934 Biosynthesis

The structure of Structure of P450 Stah From Glycopeptide Antibiotic A47934 Biosynthesis, PDB code: 5ex6 was solved by M.J.Cryle, V.Ulrich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.40 / 2.40
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	109.520, 109.520, 187.700, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 24.7

The binding sites of Iron atom in the Structure of P450 Stah From Glycopeptide Antibiotic A47934 Biosynthesis (pdb code 5ex6). 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 P450 Stah From Glycopeptide Antibiotic A47934 Biosynthesis, PDB code: 5ex6:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Structure of P450 Stah From Glycopeptide Antibiotic A47934 Biosynthesis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of P450 Stah From Glycopeptide Antibiotic A47934 Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe502 b:24.8 occ:1.00 FE C:HEM502 0.0 24.8 1.0 NC C:HEM502 2.1 25.5 1.0 NB C:HEM502 2.1 25.2 1.0 ND C:HEM502 2.1 24.5 1.0 NA C:HEM502 2.1 24.7 1.0 SG C:CYS347 2.2 22.8 1.0 O C:HOH607 2.4 26.0 1.0 C4C C:HEM502 3.0 25.8 1.0 C1D C:HEM502 3.1 25.2 1.0 C1B C:HEM502 3.1 26.8 1.0 C4B C:HEM502 3.1 26.6 1.0 C1C C:HEM502 3.1 26.1 1.0 C4A C:HEM502 3.1 25.1 1.0 C4D C:HEM502 3.1 24.7 1.0 C1A C:HEM502 3.1 24.1 1.0 CB C:CYS347 3.4 24.4 1.0 CHD C:HEM502 3.4 26.7 1.0 CHB C:HEM502 3.4 26.1 1.0 CHC C:HEM502 3.5 26.4 1.0 CHA C:HEM502 3.5 24.4 1.0 CA C:CYS347 4.1 24.6 1.0 C3C C:HEM502 4.3 26.1 1.0 O C:ALA236 4.3 34.3 1.0 C2C C:HEM502 4.3 26.7 1.0 C3B C:HEM502 4.3 26.6 1.0 C2B C:HEM502 4.3 26.2 1.0 C2D C:HEM502 4.3 24.0 1.0 C3A C:HEM502 4.3 24.9 1.0 C3D C:HEM502 4.3 23.5 1.0 C2A C:HEM502 4.3 23.8 1.0 ND2 C:ASN240 4.5 26.9 1.0 O1 C:EDO501 4.6 41.7 1.0 C C:CYS347 4.8 25.5 1.0 N C:LEU348 4.9 25.9 1.0 C1 C:EDO501 4.9 41.8 1.0 N C:GLY349 4.9 26.6 1.0

Iron binding site 2 out of 3 in the Structure of P450 Stah From Glycopeptide Antibiotic A47934 Biosynthesis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of P450 Stah From Glycopeptide Antibiotic A47934 Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe504 b:24.2 occ:1.00 FE A:HEM504 0.0 24.2 1.0 O A:HOH615 2.0 51.2 1.0 NA A:HEM504 2.0 24.2 1.0 NC A:HEM504 2.1 24.0 1.0 NB A:HEM504 2.1 24.9 1.0 ND A:HEM504 2.1 24.0 1.0 SG A:CYS347 2.3 26.8 1.0 C4A A:HEM504 3.0 25.1 1.0 C4C A:HEM504 3.1 25.4 1.0 C1C A:HEM504 3.1 25.2 1.0 C1B A:HEM504 3.1 25.1 1.0 C1A A:HEM504 3.1 24.9 1.0 C1D A:HEM504 3.1 24.7 1.0 C4B A:HEM504 3.1 24.5 1.0 C4D A:HEM504 3.1 24.8 1.0 CHB A:HEM504 3.4 25.6 1.0 CHD A:HEM504 3.4 24.7 1.0 CHC A:HEM504 3.4 25.2 1.0 CHA A:HEM504 3.5 24.7 1.0 CB A:CYS347 3.5 26.3 1.0 O A:ALA236 4.1 29.5 1.0 CA A:CYS347 4.2 26.9 1.0 O1 A:EDO502 4.3 42.6 1.0 C3A A:HEM504 4.3 25.7 1.0 C3C A:HEM504 4.3 26.2 1.0 C2C A:HEM504 4.3 25.5 1.0 C2A A:HEM504 4.3 25.7 1.0 C2B A:HEM504 4.3 24.9 1.0 C3B A:HEM504 4.3 25.1 1.0 C2D A:HEM504 4.3 25.0 1.0 C3D A:HEM504 4.3 25.1 1.0 ND2 A:ASN240 4.7 23.7 1.0 CB A:ALA236 4.8 31.1 1.0 C A:CYS347 4.9 27.5 1.0 N A:GLY349 4.9 27.3 1.0 N A:LEU348 4.9 28.0 1.0 C A:ALA236 4.9 30.6 1.0

Iron binding site 3 out of 3 in the Structure of P450 Stah From Glycopeptide Antibiotic A47934 Biosynthesis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of P450 Stah From Glycopeptide Antibiotic A47934 Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe503 b:25.6 occ:1.00 FE B:HEM503 0.0 25.6 1.0 O B:HOH601 2.0 37.7 1.0 NC B:HEM503 2.0 23.8 1.0 NA B:HEM503 2.0 24.7 1.0 NB B:HEM503 2.1 24.7 1.0 ND B:HEM503 2.1 24.8 1.0 SG B:CYS347 2.3 27.9 1.0 C1C B:HEM503 3.0 24.8 1.0 C1A B:HEM503 3.0 26.4 1.0 C4D B:HEM503 3.0 24.7 1.0 C4B B:HEM503 3.1 24.6 1.0 C4C B:HEM503 3.1 25.1 1.0 C4A B:HEM503 3.1 26.1 1.0 C1D B:HEM503 3.1 25.1 1.0 C1B B:HEM503 3.2 25.1 1.0 CHA B:HEM503 3.4 25.7 1.0 CHC B:HEM503 3.4 24.1 1.0 CB B:CYS347 3.5 26.9 1.0 CHD B:HEM503 3.5 25.1 1.0 CHB B:HEM503 3.5 25.9 1.0 O2 B:GOL502 3.6 49.0 1.0 CA B:CYS347 4.2 27.2 1.0 C2C B:HEM503 4.2 24.8 1.0 O B:ALA236 4.3 31.8 1.0 C2A B:HEM503 4.3 27.5 1.0 C3C B:HEM503 4.3 24.3 1.0 C3A B:HEM503 4.3 26.6 1.0 C3D B:HEM503 4.3 25.6 1.0 C3B B:HEM503 4.3 25.3 1.0 C2B B:HEM503 4.4 24.8 1.0 C2D B:HEM503 4.4 25.1 1.0 ND2 B:ASN240 4.5 29.9 1.0 C2 B:GOL502 4.8 48.3 1.0 C B:CYS347 4.9 26.8 1.0 N B:GLY349 4.9 27.7 1.0 N B:LEU348 5.0 27.5 1.0

V.Ulrich, M.Peschke, C.Brieke, M.J.Cryle. More Than Just Recruitment: the X-Domain Influences Catalysis of the First Phenolic Coupling Reaction in A47934 Biosynthesis By Cytochrome P450 Stah. Mol Biosyst V. 12 2992 2016.
ISSN: ESSN 1742-2051
PubMed: 27477788
DOI: 10.1039/C6MB00373G