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

The structure of Crystal Structure of Ptmb in Complex with Cyclo-(L-Trp-L-Trp) and Adenine, PDB code: 8yyp 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)	25.01 / 2.60
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	84.453, 84.453, 133.377, 90, 90, 90
R / Rfree (%)	20.6 / 25.7

The binding sites of Iron atom in the Crystal Structure of Ptmb in Complex with Cyclo-(L-Trp-L-Trp) and Adenine (pdb code 8yyp). 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 Adenine, PDB code: 8yyp:
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 Adenine


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 Adenine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:40.2 occ:1.00 FE A:HEM502 0.0 40.2 1.0 NC A:HEM502 2.0 34.1 1.0 ND A:HEM502 2.1 37.9 1.0 NB A:HEM502 2.1 32.5 1.0 NA A:HEM502 2.1 28.9 1.0 SG A:CYS361 2.4 40.9 1.0 C1C A:HEM502 2.9 34.4 1.0 C4B A:HEM502 3.0 33.9 1.0 C1A A:HEM502 3.0 30.5 1.0 C4D A:HEM502 3.0 33.7 1.0 C4C A:HEM502 3.1 34.4 1.0 C4A A:HEM502 3.1 31.0 1.0 C1D A:HEM502 3.1 37.5 1.0 C1B A:HEM502 3.1 33.2 1.0 CHC A:HEM502 3.2 34.2 1.0 CB A:CYS361 3.3 40.1 1.0 CHA A:HEM502 3.4 35.6 1.0 CHD A:HEM502 3.5 33.1 1.0 CHB A:HEM502 3.5 31.8 1.0 C2C A:HEM502 4.2 33.8 1.0 C3C A:HEM502 4.2 35.2 1.0 CA A:CYS361 4.2 42.2 1.0 C3B A:HEM502 4.2 37.4 1.0 C2A A:HEM502 4.2 29.6 1.0 C3A A:HEM502 4.3 32.2 1.0 C3D A:HEM502 4.3 37.5 1.0 C2D A:HEM502 4.3 37.2 1.0 C2B A:HEM502 4.3 36.2 1.0 C8 A:ADE501 4.6 73.9 1.0 CD A:PRO362 4.8 46.4 1.0 N9 A:ADE501 4.8 73.0 1.0

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


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 Adenine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:29.3 occ:1.00 FE B:HEM502 0.0 29.3 1.0 NA B:HEM502 1.9 25.4 1.0 ND B:HEM502 2.0 25.5 1.0 NB B:HEM502 2.0 24.5 1.0 NC B:HEM502 2.1 26.0 1.0 SG B:CYS361 2.4 28.0 1.0 C4A B:HEM502 3.0 25.9 1.0 C1A B:HEM502 3.0 25.5 1.0 C1B B:HEM502 3.0 26.5 1.0 C4D B:HEM502 3.0 28.6 1.0 C4B B:HEM502 3.1 26.2 1.0 C1D B:HEM502 3.1 26.7 1.0 C1C B:HEM502 3.1 27.4 1.0 C4C B:HEM502 3.2 27.3 1.0 CB B:CYS361 3.2 31.8 1.0 O B:HOH607 3.3 46.6 1.0 CHB B:HEM502 3.3 25.4 1.0 CHA B:HEM502 3.3 27.3 1.0 CHC B:HEM502 3.5 28.1 1.0 CHD B:HEM502 3.5 26.8 1.0 CA B:CYS361 4.1 32.2 1.0 C2A B:HEM502 4.2 26.3 1.0 C3A B:HEM502 4.2 25.7 1.0 C3B B:HEM502 4.3 27.7 1.0 C2B B:HEM502 4.3 28.5 1.0 C3D B:HEM502 4.3 29.8 1.0 C2D B:HEM502 4.3 28.6 1.0 C3C B:HEM502 4.3 28.0 1.0 C2C B:HEM502 4.4 29.1 1.0 N36 B:UYM503 4.6 72.8 1.0 C8 B:ADE501 4.7 56.3 1.0 CD B:PRO362 4.9 30.5 1.0 OG B:SER254 5.0 34.3 1.0 N9 B:ADE501 5.0 50.0 1.0

G.Wei, B.Duan, T.P.Zhou, W.Tian, C.Sun, Z.Lin, Z.Deng, B.Wang, Z.Zhang, X.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 V. 121 90121 2024.
ISSN: ESSN 1091-6490
PubMed: 39508763
DOI: 10.1073/PNAS.2412890121