Iron in PDB 8yy7: Crystal Structure of Ptmb in Complex with Cyclo-(L-Trp-L-Trp) and Hypoxanthine

The structure of Crystal Structure of Ptmb in Complex with Cyclo-(L-Trp-L-Trp) and Hypoxanthine, PDB code: 8yy7 was solved by Z.Y.Zhang, X.D.Qu, B.R.Duan, G.Z.Wei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.61 / 2.10
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	84.97, 84.97, 136.22, 90, 90, 90
R / Rfree (%)	19.5 / 22.4

The binding sites of Iron atom in the Crystal Structure of Ptmb in Complex with Cyclo-(L-Trp-L-Trp) and Hypoxanthine (pdb code 8yy7). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Ptmb in Complex with Cyclo-(L-Trp-L-Trp) and Hypoxanthine, PDB code: 8yy7:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Ptmb in Complex with Cyclo-(L-Trp-L-Trp) and Hypoxanthine


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 Ptmb in Complex with Cyclo-(L-Trp-L-Trp) and Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe503 b:28.8 occ:1.00 FE A:HEM503 0.0 28.8 1.0 NB A:HEM503 2.0 23.8 1.0 NA A:HEM503 2.1 24.4 1.0 NC A:HEM503 2.2 26.0 1.0 ND A:HEM503 2.2 26.8 1.0 SG A:CYS361 2.7 19.8 1.0 C1B A:HEM503 3.0 23.3 1.0 C4B A:HEM503 3.0 22.7 1.0 O A:HOH780 3.0 26.9 1.0 C4A A:HEM503 3.0 24.9 1.0 C1C A:HEM503 3.1 25.1 1.0 C1A A:HEM503 3.1 23.0 1.0 C4D A:HEM503 3.2 24.0 1.0 C1D A:HEM503 3.2 22.2 1.0 C4C A:HEM503 3.2 27.3 1.0 CB A:CYS361 3.3 20.4 1.0 CHC A:HEM503 3.3 22.8 1.0 CHB A:HEM503 3.4 22.2 1.0 CHA A:HEM503 3.5 23.1 1.0 CHD A:HEM503 3.6 21.0 1.0 C8 A:HPA502 4.2 24.9 1.0 C3B A:HEM503 4.2 22.3 1.0 C2B A:HEM503 4.3 23.2 1.0 CA A:CYS361 4.3 19.7 1.0 C3A A:HEM503 4.3 25.2 1.0 C2A A:HEM503 4.3 22.8 1.0 C2C A:HEM503 4.4 21.7 1.0 C3C A:HEM503 4.4 25.2 1.0 C3D A:HEM503 4.4 24.8 1.0 C2D A:HEM503 4.5 26.1 1.0 N A:UYM501 4.8 28.5 1.0 CD A:PRO362 5.0 19.9 1.0 N9 A:HPA502 5.0 26.9 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Ptmb in Complex with Cyclo-(L-Trp-L-Trp) and Hypoxanthine


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 Ptmb in Complex with Cyclo-(L-Trp-L-Trp) and Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe503 b:30.8 occ:1.00 FE B:HEM503 0.0 30.8 1.0 ND B:HEM503 2.0 28.9 1.0 NA B:HEM503 2.1 28.8 1.0 NC B:HEM503 2.1 24.8 1.0 NB B:HEM503 2.2 29.5 1.0 O B:HOH765 2.7 31.4 1.0 C4D B:HEM503 3.0 30.4 1.0 C1D B:HEM503 3.0 29.9 1.0 C1A B:HEM503 3.1 32.6 1.0 SG B:CYS361 3.1 23.8 1.0 C4C B:HEM503 3.1 26.3 1.0 C4A B:HEM503 3.1 30.3 1.0 C1C B:HEM503 3.1 28.5 1.0 C1B B:HEM503 3.2 23.4 1.0 C4B B:HEM503 3.2 27.1 1.0 CHA B:HEM503 3.4 27.8 1.0 CHD B:HEM503 3.4 27.5 1.0 CHB B:HEM503 3.5 27.1 1.0 CHC B:HEM503 3.5 22.2 1.0 C8 B:HPA502 3.7 30.9 1.0 CB B:CYS361 3.8 25.6 1.0 C3D B:HEM503 4.3 33.0 1.0 C2D B:HEM503 4.3 32.8 1.0 C2A B:HEM503 4.3 27.9 1.0 C3C B:HEM503 4.3 29.7 1.0 C3A B:HEM503 4.3 29.2 1.0 C2C B:HEM503 4.4 23.4 1.0 N B:UYM501 4.4 34.4 1.0 C3B B:HEM503 4.4 24.8 1.0 C2B B:HEM503 4.4 23.6 1.0 N9 B:HPA502 4.6 30.9 1.0 CA B:CYS361 4.6 27.4 1.0 N7 B:HPA502 4.7 30.7 1.0 OG B:SER254 4.8 19.7 1.0 C4 B:UYM501 4.8 33.5 1.0

G.Z.Wei, B.R.Duan, T.P.Zhou, W.Tian, C.Sun, Z.Lin, Z.Deng, B.Wang, Z.Y.Zhang, X.D.Qu. A Nucleobase-Driven P450 Peroxidase System Enables Regio- and Stereo-Specific Formation of C─C and C─N Bonds Proc.Natl.Acad.Sci.Usa 2024.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.2412890121