Iron in PDB 8dsg: P411-Pfa Carbene Transferase

All present enzymatic activity of P411-Pfa Carbene Transferase:
1.14.14.1; 1.6.2.4;

The structure of P411-Pfa Carbene Transferase, PDB code: 8dsg was solved by A.O.Maggiolo, N.J.Porter, J.Zhang, F.H.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.60 / 1.87
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	105.254, 172.462, 225.623, 90, 90, 90
R / Rfree (%)	18.7 / 21.8

The binding sites of Iron atom in the P411-Pfa Carbene Transferase (pdb code 8dsg). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the P411-Pfa Carbene Transferase, PDB code: 8dsg:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the P411-Pfa Carbene Transferase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of P411-Pfa Carbene Transferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:15.3 occ:1.00 FE A:HEM501 0.0 15.3 1.0 ND A:HEM501 1.9 14.2 1.0 NA A:HEM501 2.0 13.8 1.0 OG A:SER400 2.0 15.6 1.0 NC A:HEM501 2.1 14.4 1.0 NB A:HEM501 2.1 14.3 1.0 C1D A:HEM501 2.9 14.4 1.0 C4D A:HEM501 2.9 14.2 1.0 C1A A:HEM501 3.0 13.8 1.0 CB A:SER400 3.0 14.9 1.0 C4C A:HEM501 3.1 14.5 1.0 C4A A:HEM501 3.1 13.6 1.0 C1B A:HEM501 3.1 14.0 1.0 C4B A:HEM501 3.1 14.2 1.0 C1C A:HEM501 3.1 14.4 1.0 CHA A:HEM501 3.4 13.8 1.0 CHD A:HEM501 3.4 14.3 1.0 CHB A:HEM501 3.5 13.6 1.0 CHC A:HEM501 3.5 14.3 1.0 CA A:SER400 3.8 15.1 1.0 C2D A:HEM501 4.2 14.4 1.0 C3D A:HEM501 4.2 14.3 1.0 C2A A:HEM501 4.2 13.6 1.0 C3A A:HEM501 4.2 13.5 1.0 C3C A:HEM501 4.3 14.5 1.0 C2C A:HEM501 4.3 14.4 1.0 C2B A:HEM501 4.3 13.8 1.0 C3B A:HEM501 4.4 13.8 1.0 C A:SER400 4.8 15.0 1.0 CD A:PRO401 4.8 15.8 1.0 N A:GLY402 4.8 15.9 1.0 N A:SER400 4.9 14.8 1.0

Iron binding site 2 out of 4 in the P411-Pfa Carbene Transferase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of P411-Pfa Carbene Transferase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:15.0 occ:1.00 FE B:HEM501 0.0 15.0 1.0 ND B:HEM501 1.9 13.5 1.0 NA B:HEM501 2.0 13.1 1.0 OG B:SER400 2.1 14.3 1.0 NC B:HEM501 2.1 13.7 1.0 NB B:HEM501 2.1 13.4 1.0 C4D B:HEM501 2.9 13.4 1.0 C1D B:HEM501 2.9 13.4 1.0 C1A B:HEM501 3.0 13.1 1.0 CB B:SER400 3.0 13.8 1.0 C4C B:HEM501 3.0 13.8 1.0 C4B B:HEM501 3.1 13.4 1.0 C4A B:HEM501 3.1 12.9 1.0 C1B B:HEM501 3.1 13.1 1.0 C1C B:HEM501 3.1 13.5 1.0 CHA B:HEM501 3.4 13.1 1.0 CHD B:HEM501 3.4 13.6 1.0 CHB B:HEM501 3.5 12.8 1.0 CHC B:HEM501 3.5 13.5 1.0 CA B:SER400 3.9 13.7 1.0 C2D B:HEM501 4.2 13.3 1.0 C3D B:HEM501 4.2 13.2 1.0 C2A B:HEM501 4.2 12.7 1.0 C3A B:HEM501 4.2 12.6 1.0 C3C B:HEM501 4.3 13.8 1.0 C2C B:HEM501 4.3 13.6 1.0 C2B B:HEM501 4.3 13.2 1.0 C3B B:HEM501 4.3 13.1 1.0 CD B:PRO401 4.8 14.3 1.0 C B:SER400 4.8 13.9 1.0 N B:GLY402 4.8 14.7 1.0 N B:SER400 5.0 13.6 1.0

Iron binding site 3 out of 4 in the P411-Pfa Carbene Transferase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of P411-Pfa Carbene Transferase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1102 b:21.5 occ:1.00 FE C:HEM1102 0.0 21.5 1.0 ND C:HEM1102 1.9 19.9 1.0 NA C:HEM1102 2.0 19.4 1.0 OG C:SER400 2.0 20.7 1.0 NC C:HEM1102 2.1 20.2 1.0 NB C:HEM1102 2.1 19.8 1.0 C4D C:HEM1102 2.9 19.9 1.0 C1D C:HEM1102 2.9 19.8 1.0 C1A C:HEM1102 3.0 19.4 1.0 CB C:SER400 3.0 20.1 1.0 C4C C:HEM1102 3.1 20.0 1.0 C4A C:HEM1102 3.1 19.1 1.0 C1B C:HEM1102 3.1 19.3 1.0 C4B C:HEM1102 3.1 19.6 1.0 C1C C:HEM1102 3.1 20.2 1.0 CHA C:HEM1102 3.4 19.5 1.0 CHD C:HEM1102 3.4 20.2 1.0 CHB C:HEM1102 3.5 19.1 1.0 CHC C:HEM1102 3.5 20.0 1.0 CA C:SER400 3.9 19.9 1.0 C3D C:HEM1102 4.2 20.0 1.0 C2D C:HEM1102 4.2 20.0 1.0 C2A C:HEM1102 4.2 18.9 1.0 C3A C:HEM1102 4.2 18.6 1.0 C3C C:HEM1102 4.3 20.3 1.0 C2C C:HEM1102 4.3 20.1 1.0 C2B C:HEM1102 4.3 19.2 1.0 C3B C:HEM1102 4.4 19.6 1.0 C C:SER400 4.8 19.7 1.0 CD C:PRO401 4.9 20.2 1.0 N C:GLY402 4.9 21.7 1.0 N C:SER400 4.9 19.9 1.0

Iron binding site 4 out of 4 in the P411-Pfa Carbene Transferase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of P411-Pfa Carbene Transferase within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:14.7 occ:1.00 FE D:HEM501 0.0 14.7 1.0 ND D:HEM501 1.9 13.0 1.0 NA D:HEM501 2.0 12.8 1.0 OG D:SER400 2.0 14.6 1.0 NC D:HEM501 2.1 13.3 1.0 NB D:HEM501 2.1 13.0 1.0 C1D D:HEM501 2.9 13.1 1.0 C4D D:HEM501 2.9 13.1 1.0 C1A D:HEM501 3.0 12.9 1.0 C4C D:HEM501 3.0 13.2 1.0 C4A D:HEM501 3.1 12.7 1.0 CB D:SER400 3.1 15.0 1.0 C4B D:HEM501 3.1 12.9 1.0 C1B D:HEM501 3.1 12.9 1.0 C1C D:HEM501 3.1 13.2 1.0 CHD D:HEM501 3.4 13.0 1.0 CHA D:HEM501 3.4 12.8 1.0 CHB D:HEM501 3.5 12.6 1.0 CHC D:HEM501 3.5 13.1 1.0 CA D:SER400 3.9 15.2 1.0 C2D D:HEM501 4.2 13.0 1.0 C3D D:HEM501 4.2 13.0 1.0 C2A D:HEM501 4.2 12.8 1.0 C3A D:HEM501 4.2 12.6 1.0 C3C D:HEM501 4.3 13.4 1.0 C2C D:HEM501 4.3 13.1 1.0 C2B D:HEM501 4.3 12.6 1.0 C3B D:HEM501 4.3 12.6 1.0 CD D:PRO401 4.8 16.3 1.0 C D:SER400 4.8 15.6 1.0 N D:GLY402 4.8 17.6 1.0 N D:SER400 5.0 15.1 1.0

J.Zhang, A.O.Maggiolo, E.Alfonzo, R.Mao, N.J.Porter, N.M.Abney, F.H.Arnold. Chemodivergent C(SP3)-H and C(SP2)-H Cyanomethylation Using Engineered Carbene Transferases Nat Catal V. 6 152 2023.
ISSN: ESSN 2520-1158
DOI: 10.1038/S41929-022-00908-X