Iron in PDB 5y17: Catpo Mutant - E316F

All present enzymatic activity of Catpo Mutant - E316F:
1.11.1.6;

The structure of Catpo Mutant - E316F, PDB code: 5y17 was solved by Y.Karakus Yuzugullu, G.Goc, S.Balci, A.R.Pearson, B.Yorke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	100.51 / 2.30
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	125.733, 120.870, 183.804, 90.00, 101.97, 90.00
R / Rfree (%)	17.8 / 22

The structure of Catpo Mutant - E316F also contains other interesting chemical elements:

Calcium

(Ca)

10 atoms

The binding sites of Iron atom in the Catpo Mutant - E316F (pdb code 5y17). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Catpo Mutant - E316F, PDB code: 5y17:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Catpo Mutant - E316F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Catpo Mutant - E316F within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe701 b:23.7 occ:1.00 FE A:HDD701 0.0 23.7 1.0 ND A:HDD701 2.0 22.6 1.0 OH A:TYR369 2.0 23.0 1.0 NC A:HDD701 2.1 22.0 1.0 NA A:HDD701 2.1 23.1 1.0 NB A:HDD701 2.1 23.2 1.0 C1D A:HDD701 3.0 22.4 1.0 C4C A:HDD701 3.0 21.3 1.0 C4D A:HDD701 3.0 22.0 1.0 CZ A:TYR369 3.0 23.2 1.0 C1A A:HDD701 3.1 22.7 1.0 C4A A:HDD701 3.1 22.4 1.0 C1B A:HDD701 3.1 22.2 1.0 C4B A:HDD701 3.1 22.1 1.0 C1C A:HDD701 3.1 21.7 1.0 CHD A:HDD701 3.3 20.7 1.0 CHA A:HDD701 3.4 22.8 1.0 CHB A:HDD701 3.4 22.7 1.0 CHC A:HDD701 3.5 21.2 1.0 CE2 A:TYR369 3.8 22.2 1.0 CE1 A:TYR369 3.8 23.4 1.0 NE A:ARG365 4.2 22.6 1.0 C3C A:HDD701 4.2 21.1 1.0 NH2 A:ARG365 4.3 19.9 1.0 C2D A:HDD701 4.3 23.1 1.0 C3A A:HDD701 4.3 23.1 1.0 C3D A:HDD701 4.4 23.2 1.0 O A:HOH810 4.4 22.9 1.0 C2C A:HDD701 4.4 21.2 1.0 C2A A:HDD701 4.4 22.1 1.0 C3B A:HDD701 4.4 22.4 1.0 C2B A:HDD701 4.4 21.7 1.0 CG2 A:VAL81 4.5 19.9 1.0 CZ A:PHE168 4.6 23.6 1.0 CZ A:ARG365 4.7 22.5 1.0 NE2 A:HIS82 4.7 20.2 1.0 CD2 A:HIS82 4.7 19.9 1.0

Iron binding site 2 out of 4 in the Catpo Mutant - E316F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Catpo Mutant - E316F within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe701 b:24.5 occ:1.00 FE B:HDD701 0.0 24.5 1.0 ND B:HDD701 1.9 22.9 1.0 OH B:TYR369 2.0 24.8 1.0 NC B:HDD701 2.0 22.7 1.0 NA B:HDD701 2.1 22.3 1.0 NB B:HDD701 2.1 23.1 1.0 C1D B:HDD701 2.9 24.7 1.0 C4C B:HDD701 2.9 23.2 1.0 C4D B:HDD701 3.0 24.0 1.0 C1A B:HDD701 3.0 22.7 1.0 C4A B:HDD701 3.1 22.6 1.0 CZ B:TYR369 3.1 23.0 1.0 C4B B:HDD701 3.1 23.3 1.0 C1C B:HDD701 3.1 23.7 1.0 C1B B:HDD701 3.1 23.6 1.0 CHD B:HDD701 3.3 24.1 1.0 CHA B:HDD701 3.4 23.6 1.0 CHB B:HDD701 3.5 22.9 1.0 CHC B:HDD701 3.5 22.9 1.0 CE2 B:TYR369 3.8 22.1 1.0 CE1 B:TYR369 3.9 22.3 1.0 NE B:ARG365 4.1 22.0 1.0 NH2 B:ARG365 4.2 21.3 1.0 O B:HOH937 4.3 24.6 1.0 C3C B:HDD701 4.3 23.6 1.0 C2D B:HDD701 4.3 23.1 1.0 C3D B:HDD701 4.3 23.4 1.0 C2A B:HDD701 4.3 23.2 1.0 C3A B:HDD701 4.4 23.6 1.0 C3B B:HDD701 4.4 23.2 1.0 C2C B:HDD701 4.4 23.6 1.0 C2B B:HDD701 4.5 23.4 1.0 CG2 B:VAL81 4.5 24.0 1.0 CZ B:PHE168 4.5 26.1 1.0 CZ B:ARG365 4.6 22.2 1.0 NE2 B:HIS82 4.7 21.4 1.0 CD2 B:HIS82 4.7 20.8 1.0 CE2 B:PHE168 4.9 27.1 1.0

Iron binding site 3 out of 4 in the Catpo Mutant - E316F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Catpo Mutant - E316F within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe701 b:26.1 occ:1.00 FE C:HDD701 0.0 26.1 1.0 OH C:TYR369 1.9 25.6 1.0 ND C:HDD701 2.0 25.2 1.0 NC C:HDD701 2.1 26.7 1.0 NB C:HDD701 2.1 26.0 1.0 NA C:HDD701 2.1 25.2 1.0 CZ C:TYR369 3.0 27.1 1.0 C1D C:HDD701 3.0 25.2 1.0 C4D C:HDD701 3.0 24.5 1.0 C4C C:HDD701 3.1 26.2 1.0 C4B C:HDD701 3.1 26.9 1.0 C1C C:HDD701 3.1 25.8 1.0 C1A C:HDD701 3.1 24.8 1.0 C1B C:HDD701 3.1 26.6 1.0 C4A C:HDD701 3.1 25.0 1.0 CHA C:HDD701 3.4 24.1 1.0 CHD C:HDD701 3.4 25.7 1.0 CHC C:HDD701 3.4 26.6 1.0 CHB C:HDD701 3.5 25.7 1.0 CE1 C:TYR369 3.8 27.1 1.0 CE2 C:TYR369 3.8 24.9 1.0 NE C:ARG365 4.1 27.0 1.0 O C:HOH952 4.1 23.2 1.0 NH2 C:ARG365 4.2 24.1 1.0 C2D C:HDD701 4.3 25.2 1.0 C3C C:HDD701 4.3 25.9 1.0 C3D C:HDD701 4.4 25.1 1.0 C3B C:HDD701 4.4 27.9 1.0 C2C C:HDD701 4.4 25.7 1.0 C3A C:HDD701 4.4 25.1 1.0 C2B C:HDD701 4.4 27.5 1.0 C2A C:HDD701 4.4 23.4 1.0 CG2 C:VAL81 4.6 26.1 1.0 CZ C:ARG365 4.6 25.4 1.0 CZ C:PHE168 4.6 24.1 1.0 NE2 C:HIS82 4.7 24.9 1.0 CD2 C:HIS82 4.8 24.6 1.0 CE2 C:PHE168 4.9 24.5 1.0 CD C:ARG365 5.0 29.3 1.0

Iron binding site 4 out of 4 in the Catpo Mutant - E316F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Catpo Mutant - E316F within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe701 b:25.6 occ:1.00 FE D:HDD701 0.0 25.6 1.0 OH D:TYR369 2.0 23.0 1.0 ND D:HDD701 2.0 25.4 1.0 NA D:HDD701 2.1 25.8 1.0 NB D:HDD701 2.1 27.0 1.0 NC D:HDD701 2.1 27.8 1.0 CZ D:TYR369 3.0 24.2 1.0 C1A D:HDD701 3.0 25.8 1.0 C4D D:HDD701 3.0 25.4 1.0 C1D D:HDD701 3.0 24.8 1.0 C4B D:HDD701 3.1 27.8 1.0 C1B D:HDD701 3.1 27.8 1.0 C4C D:HDD701 3.1 27.0 1.0 C4A D:HDD701 3.1 25.8 1.0 C1C D:HDD701 3.1 28.5 1.0 CHA D:HDD701 3.4 25.6 1.0 CHD D:HDD701 3.4 25.6 1.0 CHB D:HDD701 3.4 27.2 1.0 CHC D:HDD701 3.4 29.0 1.0 CE2 D:TYR369 3.8 24.8 1.0 CE1 D:TYR369 3.8 25.2 1.0 NE D:ARG365 4.1 28.1 1.0 NH2 D:ARG365 4.2 28.0 1.0 C2A D:HDD701 4.3 24.8 1.0 C3C D:HDD701 4.3 27.9 1.0 C3B D:HDD701 4.3 27.9 1.0 C2B D:HDD701 4.4 27.7 1.0 C3D D:HDD701 4.4 24.6 1.0 C3A D:HDD701 4.4 24.6 1.0 C2D D:HDD701 4.4 25.7 1.0 CG2 D:VAL81 4.4 24.7 1.0 C2C D:HDD701 4.4 29.1 1.0 O D:HOH991 4.6 21.2 1.0 CZ D:ARG365 4.6 27.4 1.0 CZ D:PHE168 4.6 25.3 1.0 NE2 D:HIS82 4.8 25.1 1.0 CD2 D:HIS82 4.8 22.8 1.0 CE2 D:PHE168 5.0 25.2 1.0

Y.Yuzugullu Karakus, G.Goc, S.Balci, B.A.Yorke, C.H.Trinh, M.J.Mcpherson, A.R.Pearson. Identification of the Site of Oxidase Substrate Binding in Scytalidium Thermophilum Catalase. Acta Crystallogr D Struct V. 74 979 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 30289408
DOI: 10.1107/S2059798318010628