Iron in PDB 6v59: Crystal Structure of the Diheme Peroxidase Btha Y463M Variant From Burkholderia Thailandensis E264

The structure of Crystal Structure of the Diheme Peroxidase Btha Y463M Variant From Burkholderia Thailandensis E264, PDB code: 6v59 was solved by S.E.Cohen, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.23 / 1.59
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.970, 87.605, 184.170, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 17.7

The structure of Crystal Structure of the Diheme Peroxidase Btha Y463M Variant From Burkholderia Thailandensis E264 also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	4 atoms

The binding sites of Iron atom in the Crystal Structure of the Diheme Peroxidase Btha Y463M Variant From Burkholderia Thailandensis E264 (pdb code 6v59). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of the Diheme Peroxidase Btha Y463M Variant From Burkholderia Thailandensis E264, PDB code: 6v59:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of the Diheme Peroxidase Btha Y463M Variant From Burkholderia Thailandensis E264


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 the Diheme Peroxidase Btha Y463M Variant From Burkholderia Thailandensis E264 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:13.3 occ:1.00 FE A:HEC601 0.0 13.3 1.0 NA A:HEC601 2.0 11.9 1.0 NC A:HEC601 2.0 12.4 1.0 NB A:HEC601 2.0 12.8 1.0 ND A:HEC601 2.1 13.7 1.0 NE2 A:HIS192 2.2 14.4 1.0 O A:HOH931 2.4 26.7 1.0 C4C A:HEC601 3.1 15.8 1.0 C1C A:HEC601 3.1 12.5 1.0 C1B A:HEC601 3.1 13.6 1.0 C4A A:HEC601 3.1 13.9 1.0 C1A A:HEC601 3.1 14.6 1.0 C4B A:HEC601 3.1 12.5 1.0 C1D A:HEC601 3.1 13.7 1.0 C4D A:HEC601 3.1 14.8 1.0 CD2 A:HIS192 3.1 14.8 1.0 CE1 A:HIS192 3.2 12.4 1.0 HD2 A:HIS192 3.3 17.8 1.0 CHD A:HEC601 3.4 12.8 1.0 HE1 A:HIS192 3.4 14.8 1.0 CHB A:HEC601 3.4 12.6 1.0 CHC A:HEC601 3.5 12.7 1.0 CHA A:HEC601 3.5 17.8 1.0 HE22 A:GLN267 3.7 24.3 1.0 HG3 A:PRO271 3.8 29.7 1.0 O A:HOH751 4.1 31.4 1.0 HB3 A:PRO271 4.2 23.8 1.0 HD11 A:LEU229 4.2 19.3 1.0 NE2 A:GLN267 4.2 20.3 1.0 C2C A:HEC601 4.3 13.9 1.0 C3C A:HEC601 4.3 14.5 1.0 C2B A:HEC601 4.3 13.4 1.0 C3B A:HEC601 4.3 14.4 1.0 C3A A:HEC601 4.3 14.2 1.0 C2A A:HEC601 4.3 15.1 1.0 C2D A:HEC601 4.3 15.6 1.0 ND1 A:HIS192 4.3 15.1 1.0 CG A:HIS192 4.3 14.1 1.0 C3D A:HEC601 4.3 13.2 1.0 HE21 A:GLN267 4.3 24.3 1.0 HD21 A:LEU229 4.4 17.2 1.0 HHD A:HEC601 4.4 15.3 1.0 HHB A:HEC601 4.4 15.2 1.0 HHC A:HEC601 4.4 15.3 1.0 HHA A:HEC601 4.4 21.3 1.0 HB2 A:CYS191 4.6 17.3 1.0 HB1 A:ALA226 4.6 15.6 1.0 CG A:PRO271 4.7 24.7 1.0 CB A:PRO271 4.8 19.8 1.0 HE1 A:PHE256 4.9 28.6 1.0 HD3 A:PRO271 4.9 30.0 1.0

Iron binding site 2 out of 4 in the Crystal Structure of the Diheme Peroxidase Btha Y463M Variant From Burkholderia Thailandensis E264


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 the Diheme Peroxidase Btha Y463M Variant From Burkholderia Thailandensis E264 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:14.4 occ:1.00 FE A:HEC602 0.0 14.4 1.0 NA A:HEC602 2.0 12.8 1.0 NC A:HEC602 2.0 13.9 1.0 NB A:HEC602 2.0 13.8 1.0 ND A:HEC602 2.1 14.2 1.0 NE2 A:HIS371 2.3 15.9 1.0 C4A A:HEC602 3.0 14.2 1.0 C1A A:HEC602 3.0 12.1 1.0 C4C A:HEC602 3.0 13.5 1.0 C1B A:HEC602 3.1 16.3 1.0 C4D A:HEC602 3.1 16.4 1.0 C1C A:HEC602 3.1 14.1 1.0 C4B A:HEC602 3.1 13.4 1.0 C1D A:HEC602 3.1 15.7 1.0 CD2 A:HIS371 3.2 12.7 1.0 CE1 A:HIS371 3.3 16.6 1.0 HD2 A:HIS371 3.3 15.2 1.0 CHA A:HEC602 3.4 14.2 1.0 CHD A:HEC602 3.4 12.5 1.0 CHB A:HEC602 3.4 13.4 1.0 CHC A:HEC602 3.4 13.9 1.0 HE1 A:HIS371 3.4 19.9 1.0 HE2 A:MET463 3.8 23.4 1.0 SD A:MET463 4.1 21.1 1.0 HG3 A:MET463 4.1 21.8 1.0 C3A A:HEC602 4.3 13.0 1.0 HE1 A:MET463 4.3 23.4 1.0 CE A:MET463 4.3 19.5 1.0 C2A A:HEC602 4.3 13.7 1.0 C2C A:HEC602 4.3 13.6 1.0 C3C A:HEC602 4.3 13.5 1.0 C2B A:HEC602 4.3 14.6 1.0 C3B A:HEC602 4.3 14.3 1.0 C3D A:HEC602 4.3 14.3 1.0 HD13 A:ILE393 4.3 19.7 1.0 C2D A:HEC602 4.3 13.7 1.0 CG A:HIS371 4.4 14.8 1.0 ND1 A:HIS371 4.4 15.3 1.0 HG23 A:THR435 4.4 19.6 1.0 HHD A:HEC602 4.4 15.0 1.0 HHA A:HEC602 4.4 17.0 1.0 HHB A:HEC602 4.4 16.1 1.0 HHC A:HEC602 4.4 16.7 1.0 HD21 A:LEU438 4.6 17.5 1.0 HD11 A:LEU438 4.7 19.0 1.0 CG A:MET463 4.7 18.2 1.0 HD2 A:PRO436 4.7 19.2 1.0 HE1 A:MET448 4.9 21.0 1.0 HB2 A:CYS370 5.0 17.6 1.0

Iron binding site 3 out of 4 in the Crystal Structure of the Diheme Peroxidase Btha Y463M Variant From Burkholderia Thailandensis E264


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Diheme Peroxidase Btha Y463M Variant From Burkholderia Thailandensis E264 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:13.2 occ:1.00 FE B:HEC601 0.0 13.2 1.0 ND B:HEC601 2.0 12.9 1.0 NC B:HEC601 2.0 12.5 1.0 NA B:HEC601 2.1 13.8 1.0 NB B:HEC601 2.1 11.8 1.0 NE2 B:HIS192 2.2 13.6 1.0 C4D B:HEC601 3.0 14.1 1.0 C1D B:HEC601 3.0 11.6 1.0 C1C B:HEC601 3.1 12.5 1.0 C1A B:HEC601 3.1 14.0 1.0 C4C B:HEC601 3.1 14.8 1.0 C4B B:HEC601 3.1 13.3 1.0 C4A B:HEC601 3.1 13.4 1.0 C1B B:HEC601 3.1 11.8 1.0 CD2 B:HIS192 3.2 14.4 1.0 CE1 B:HIS192 3.3 12.0 1.0 HD2 B:HIS192 3.3 17.3 1.0 CHA B:HEC601 3.4 13.1 1.0 CHD B:HEC601 3.4 13.2 1.0 CHC B:HEC601 3.4 12.2 1.0 HE1 B:HIS192 3.4 14.4 1.0 CHB B:HEC601 3.5 12.7 1.0 HE22 B:GLN267 3.5 21.8 1.0 HG3 B:PRO271 3.6 22.7 1.0 NE2 B:GLN267 4.1 18.1 1.0 HB3 B:PRO271 4.2 23.8 1.0 HE21 B:GLN267 4.2 21.8 1.0 C2D B:HEC601 4.3 14.9 1.0 C2C B:HEC601 4.3 13.2 1.0 C3D B:HEC601 4.3 14.7 1.0 C3C B:HEC601 4.3 15.6 1.0 C3A B:HEC601 4.3 14.3 1.0 C2B B:HEC601 4.3 14.3 1.0 C3B B:HEC601 4.3 12.6 1.0 HD21 B:LEU229 4.3 18.2 1.0 C2A B:HEC601 4.3 13.5 1.0 CG B:HIS192 4.3 13.5 1.0 ND1 B:HIS192 4.3 13.3 1.0 HD11 B:LEU229 4.3 18.9 1.0 HHA B:HEC601 4.4 15.7 1.0 HHD B:HEC601 4.4 15.8 1.0 HHB B:HEC601 4.4 15.3 1.0 HHC B:HEC601 4.4 14.7 1.0 CG B:PRO271 4.5 18.9 1.0 HB1 B:ALA226 4.5 16.7 1.0 HB2 B:CYS191 4.6 17.9 1.0 CB B:PRO271 4.8 19.9 1.0 HD3 B:PRO271 4.8 22.7 1.0 HE1 B:PHE256 5.0 23.6 1.0 HB2 B:ALA226 5.0 16.7 1.0

Iron binding site 4 out of 4 in the Crystal Structure of the Diheme Peroxidase Btha Y463M Variant From Burkholderia Thailandensis E264


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the Diheme Peroxidase Btha Y463M Variant From Burkholderia Thailandensis E264 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe602 b:15.3 occ:1.00 FE B:HEC602 0.0 15.3 1.0 NC B:HEC602 2.0 16.3 1.0 NA B:HEC602 2.0 17.2 1.0 NB B:HEC602 2.0 13.4 1.0 ND B:HEC602 2.1 14.7 1.0 NE2 B:HIS371 2.3 16.4 1.0 C4C B:HEC602 3.1 15.2 1.0 C1A B:HEC602 3.1 14.7 1.0 C1C B:HEC602 3.1 16.7 1.0 C4B B:HEC602 3.1 16.1 1.0 C1B B:HEC602 3.1 15.1 1.0 C4A B:HEC602 3.1 14.3 1.0 C4D B:HEC602 3.1 14.4 1.0 C1D B:HEC602 3.1 15.7 1.0 CD2 B:HIS371 3.2 18.1 1.0 HD2 B:HIS371 3.3 21.8 1.0 CE1 B:HIS371 3.3 15.3 1.0 CHD B:HEC602 3.4 16.7 1.0 CHC B:HEC602 3.4 16.5 1.0 CHA B:HEC602 3.4 15.1 1.0 CHB B:HEC602 3.5 14.7 1.0 HE1 B:HIS371 3.5 18.4 1.0 HE2 B:MET463 3.6 26.2 1.0 HG3 B:MET463 4.0 23.5 1.0 SD B:MET463 4.0 23.0 1.0 CE B:MET463 4.1 21.9 1.0 HE1 B:MET463 4.1 26.2 1.0 C3C B:HEC602 4.3 13.6 1.0 C2C B:HEC602 4.3 15.6 1.0 C2A B:HEC602 4.3 14.6 1.0 C3A B:HEC602 4.3 13.3 1.0 C2B B:HEC602 4.3 14.6 1.0 C3B B:HEC602 4.3 15.1 1.0 C3D B:HEC602 4.3 13.4 1.0 C2D B:HEC602 4.3 14.6 1.0 CG B:HIS371 4.4 14.5 1.0 ND1 B:HIS371 4.4 14.2 1.0 HD13 B:ILE393 4.4 20.4 1.0 HHD B:HEC602 4.4 20.1 1.0 HG23 B:THR435 4.4 19.4 1.0 HHC B:HEC602 4.4 19.8 1.0 HHA B:HEC602 4.4 18.1 1.0 HHB B:HEC602 4.4 17.7 1.0 CG B:MET463 4.6 19.6 1.0 HD21 B:LEU438 4.6 17.3 1.0 HD11 B:LEU438 4.6 19.1 1.0 HD2 B:PRO436 4.8 17.6 1.0 HE1 B:MET448 4.9 23.1 1.0 HB2 B:CYS370 5.0 18.2 1.0

K.Rizzolo, A.C.Weitz, S.E.Cohen, C.L.Drennan, M.P.Hendrich, S.J.Elliott. A Stable Ferryl Porphyrin at the Active Site of Y463M Btha. J.Am.Chem.Soc. V. 142 11978 2020.
ISSN: ESSN 1520-5126
PubMed: 32564595
DOI: 10.1021/JACS.0C04023