Iron in PDB 8yz8: Crystal Structure of Ptmb in Complex with Adenine

The structure of Crystal Structure of Ptmb in Complex with Adenine, PDB code: 8yz8 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)	30.27 / 2.86
Space group	I 41
Cell size a, b, c (Å), α, β, γ (°)	145.406, 145.406, 129.178, 90, 90, 90
R / Rfree (%)	20.8 / 27.1

The binding sites of Iron atom in the Crystal Structure of Ptmb in Complex with Adenine (pdb code 8yz8). 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 Adenine, PDB code: 8yz8:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Ptmb in Complex with 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 Adenine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:53.9 occ:1.00 FE A:HEM501 0.0 53.9 1.0 NB A:HEM501 1.8 39.8 1.0 NA A:HEM501 2.0 44.3 1.0 NC A:HEM501 2.1 40.6 1.0 ND A:HEM501 2.3 53.1 1.0 C1B A:HEM501 2.8 38.7 1.0 C4B A:HEM501 2.8 40.8 1.0 SG A:CYS361 2.9 44.4 1.0 C1C A:HEM501 2.9 41.8 1.0 C4A A:HEM501 3.0 46.1 1.0 C1A A:HEM501 3.1 44.9 1.0 C4C A:HEM501 3.2 37.8 1.0 CHC A:HEM501 3.2 39.6 1.0 CHB A:HEM501 3.2 43.3 1.0 C1D A:HEM501 3.3 46.9 1.0 C4D A:HEM501 3.3 49.1 1.0 CHD A:HEM501 3.6 39.9 1.0 CHA A:HEM501 3.6 49.4 1.0 CB A:CYS361 3.7 44.0 1.0 N9 A:ADE502 3.9 58.9 1.0 C3B A:HEM501 4.0 39.7 1.0 C2B A:HEM501 4.0 35.3 1.0 C8 A:ADE502 4.0 59.7 1.0 C3A A:HEM501 4.2 48.0 1.0 C2C A:HEM501 4.2 40.5 1.0 OG A:SER254 4.3 44.3 1.0 C2A A:HEM501 4.3 46.2 1.0 C3C A:HEM501 4.3 36.0 1.0 C2D A:HEM501 4.5 44.3 1.0 C3D A:HEM501 4.5 51.0 1.0 CB A:SER254 4.6 39.8 1.0 CA A:CYS361 4.7 45.6 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Ptmb in Complex with 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 Adenine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:44.8 occ:1.00 FE B:HEM501 0.0 44.8 1.0 NA B:HEM501 1.5 40.8 1.0 NB B:HEM501 1.9 39.6 1.0 ND B:HEM501 2.4 51.3 1.0 C4A B:HEM501 2.5 44.2 1.0 NC B:HEM501 2.5 34.8 1.0 C1A B:HEM501 2.6 45.5 1.0 C1B B:HEM501 2.7 35.9 1.0 SG B:CYS361 2.9 50.1 1.0 CHB B:HEM501 2.9 42.3 1.0 C4B B:HEM501 3.1 38.9 1.0 C4D B:HEM501 3.1 49.2 1.0 CHA B:HEM501 3.2 47.3 1.0 C1C B:HEM501 3.4 39.8 1.0 C1D B:HEM501 3.4 42.1 1.0 CB B:CYS361 3.5 46.1 1.0 C4C B:HEM501 3.6 37.9 1.0 CHC B:HEM501 3.6 38.8 1.0 C3A B:HEM501 3.7 46.7 1.0 C2A B:HEM501 3.7 46.9 1.0 N9 B:ADE502 3.8 53.0 1.0 CHD B:HEM501 3.9 37.6 1.0 C8 B:ADE502 4.0 57.9 1.0 C2B B:HEM501 4.0 39.5 1.0 C3B B:HEM501 4.1 41.7 1.0 C3D B:HEM501 4.4 48.6 1.0 CA B:CYS361 4.4 47.2 1.0 OG B:SER254 4.5 43.5 1.0 C2D B:HEM501 4.6 44.4 1.0 C2C B:HEM501 4.7 38.3 1.0 C3C B:HEM501 4.7 37.6 1.0 CB B:SER254 5.0 36.3 1.0 CD1 B:PHE354 5.0 40.4 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