Iron in PDB 5xy4: Catpo Mutant - V536W

All present enzymatic activity of Catpo Mutant - V536W:
1.11.1.6;

The structure of Catpo Mutant - V536W, PDB code: 5xy4 was solved by Y.Yuzugullu Karakus, 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)	90.46 / 1.80
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	125.420, 120.743, 184.653, 90.00, 102.05, 90.00
R / Rfree (%)	15.8 / 19.3

The structure of Catpo Mutant - V536W also contains other interesting chemical elements:

Calcium

(Ca)

10 atoms

The binding sites of Iron atom in the Catpo Mutant - V536W (pdb code 5xy4). 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 - V536W, PDB code: 5xy4:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Catpo Mutant - V536W


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Catpo Mutant - V536W within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe701 b:18.1 occ:1.00 FE A:HDD701 0.0 18.1 1.0 OH A:TYR369 1.9 20.1 1.0 ND A:HDD701 2.0 17.8 1.0 NA A:HDD701 2.0 17.7 1.0 NC A:HDD701 2.1 17.9 1.0 NB A:HDD701 2.1 19.8 1.0 CZ A:TYR369 2.9 17.3 1.0 C4C A:HDD701 3.0 17.4 1.0 C1D A:HDD701 3.0 18.9 1.0 C1A A:HDD701 3.0 18.2 1.0 C4A A:HDD701 3.0 18.4 1.0 C4D A:HDD701 3.0 19.1 1.0 C1C A:HDD701 3.1 18.4 1.0 C1B A:HDD701 3.1 18.0 1.0 C4B A:HDD701 3.1 18.6 1.0 CHB A:HDD701 3.4 19.1 1.0 CHD A:HDD701 3.4 17.1 1.0 CHA A:HDD701 3.4 18.2 1.0 CHC A:HDD701 3.5 18.5 1.0 CE2 A:TYR369 3.7 17.0 1.0 CE1 A:TYR369 3.8 17.7 1.0 NE A:ARG365 4.0 17.0 1.0 NH2 A:ARG365 4.2 16.7 1.0 C3C A:HDD701 4.3 18.0 1.0 C3A A:HDD701 4.3 18.5 1.0 C2A A:HDD701 4.3 17.9 1.0 C3B A:HDD701 4.3 18.9 1.0 C2B A:HDD701 4.3 18.8 1.0 C2D A:HDD701 4.4 19.2 1.0 O A:HOH1321 4.4 31.5 1.0 C2C A:HDD701 4.4 18.0 1.0 C3D A:HDD701 4.4 19.5 1.0 CZ A:ARG365 4.5 16.0 1.0 CG2 A:VAL81 4.6 17.4 1.0 CZ A:PHE168 4.6 21.9 1.0 NE2 A:HIS82 4.7 19.4 1.0 CD2 A:HIS82 4.8 17.5 1.0 CD2 A:TYR369 5.0 16.6 1.0 CD A:ARG365 5.0 17.8 1.0

Iron binding site 2 out of 4 in the Catpo Mutant - V536W


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Catpo Mutant - V536W within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe701 b:19.5 occ:1.00 FE B:HDD701 0.0 19.5 1.0 OH B:TYR369 2.0 20.3 1.0 ND B:HDD701 2.0 19.9 1.0 NC B:HDD701 2.0 18.1 1.0 NB B:HDD701 2.0 18.9 1.0 NA B:HDD701 2.0 18.9 1.0 CZ B:TYR369 3.0 19.4 1.0 C1A B:HDD701 3.0 18.8 1.0 C4D B:HDD701 3.0 18.9 1.0 C4A B:HDD701 3.0 18.9 1.0 C1B B:HDD701 3.0 18.9 1.0 C1D B:HDD701 3.1 18.9 1.0 C4C B:HDD701 3.1 18.9 1.0 C4B B:HDD701 3.1 19.9 1.0 C1C B:HDD701 3.1 18.5 1.0 CHA B:HDD701 3.4 20.6 1.0 CHB B:HDD701 3.4 18.3 1.0 CHD B:HDD701 3.5 18.1 1.0 CHC B:HDD701 3.5 19.1 1.0 CE2 B:TYR369 3.7 19.5 1.0 CE1 B:TYR369 3.8 18.6 1.0 NE B:ARG365 4.1 19.4 1.0 NH2 B:ARG365 4.1 18.9 1.0 C2A B:HDD701 4.3 18.4 1.0 C3B B:HDD701 4.3 19.1 1.0 C3D B:HDD701 4.3 19.5 1.0 C3A B:HDD701 4.3 17.7 1.0 C3C B:HDD701 4.3 18.6 1.0 C2B B:HDD701 4.3 19.7 1.0 C2D B:HDD701 4.4 19.0 1.0 C2C B:HDD701 4.4 19.2 1.0 CG2 B:VAL81 4.5 17.2 1.0 CZ B:ARG365 4.6 19.7 1.0 CZ B:PHE168 4.6 20.5 1.0 NE2 B:HIS82 4.6 17.5 1.0 CD2 B:HIS82 4.7 17.8 1.0 CD2 B:TYR369 4.9 20.2 1.0

Iron binding site 3 out of 4 in the Catpo Mutant - V536W


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Catpo Mutant - V536W within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe701 b:19.4 occ:1.00 FE C:HDD701 0.0 19.4 1.0 ND C:HDD701 2.0 18.0 1.0 OH C:TYR369 2.0 16.9 1.0 NB C:HDD701 2.1 19.7 1.0 NA C:HDD701 2.1 18.2 1.0 NC C:HDD701 2.1 19.1 1.0 C1D C:HDD701 3.0 19.9 1.0 C4D C:HDD701 3.0 18.4 1.0 CZ C:TYR369 3.0 18.1 1.0 C4C C:HDD701 3.0 19.1 1.0 C4A C:HDD701 3.0 18.0 1.0 C1A C:HDD701 3.0 18.1 1.0 C4B C:HDD701 3.1 19.9 1.0 C1B C:HDD701 3.1 19.7 1.0 C1C C:HDD701 3.1 19.4 1.0 CHD C:HDD701 3.4 18.8 1.0 CHA C:HDD701 3.4 17.1 1.0 CHB C:HDD701 3.4 19.3 1.0 CHC C:HDD701 3.5 19.7 1.0 CE2 C:TYR369 3.8 18.6 1.0 CE1 C:TYR369 3.8 17.9 1.0 NE C:ARG365 4.1 20.6 1.0 NH2 C:ARG365 4.3 21.1 1.0 C3C C:HDD701 4.3 20.1 1.0 C3D C:HDD701 4.3 19.6 1.0 C2D C:HDD701 4.3 20.4 1.0 C3A C:HDD701 4.3 18.2 1.0 C3B C:HDD701 4.3 20.5 1.0 C2A C:HDD701 4.3 17.7 1.0 C2B C:HDD701 4.4 20.5 1.0 C2C C:HDD701 4.4 19.4 1.0 CG2 C:VAL81 4.5 19.6 1.0 CZ C:PHE168 4.6 21.1 1.0 CZ C:ARG365 4.6 21.4 1.0 NE2 C:HIS82 4.7 19.7 1.0 CD2 C:HIS82 4.7 17.7 1.0 O1D C:HDD701 5.0 21.1 1.0

Iron binding site 4 out of 4 in the Catpo Mutant - V536W


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Catpo Mutant - V536W within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe701 b:19.8 occ:1.00 FE D:HDD701 0.0 19.8 1.0 OH D:TYR369 2.0 21.7 1.0 ND D:HDD701 2.0 18.6 1.0 NA D:HDD701 2.0 18.5 1.0 NC D:HDD701 2.0 19.3 1.0 NB D:HDD701 2.1 21.1 1.0 C4A D:HDD701 3.0 18.3 1.0 C1D D:HDD701 3.0 19.4 1.0 CZ D:TYR369 3.0 21.6 1.0 C4C D:HDD701 3.0 19.3 1.0 C1A D:HDD701 3.0 18.2 1.0 C4D D:HDD701 3.0 18.5 1.0 C1B D:HDD701 3.1 19.9 1.0 C1C D:HDD701 3.1 20.6 1.0 C4B D:HDD701 3.1 20.6 1.0 CHD D:HDD701 3.4 20.1 1.0 CHA D:HDD701 3.4 18.4 1.0 CHB D:HDD701 3.4 19.4 1.0 CHC D:HDD701 3.5 20.1 1.0 CE2 D:TYR369 3.7 22.1 1.0 CE1 D:TYR369 3.8 23.4 1.0 NE D:ARG365 4.2 21.9 1.0 NH2 D:ARG365 4.2 17.6 1.0 C3C D:HDD701 4.3 20.4 1.0 C3A D:HDD701 4.3 18.4 1.0 C2A D:HDD701 4.3 17.4 1.0 C2C D:HDD701 4.3 20.0 1.0 C2D D:HDD701 4.3 20.8 1.0 C3D D:HDD701 4.4 19.5 1.0 C3B D:HDD701 4.4 20.5 1.0 O D:HOH905 4.4 29.6 1.0 C2B D:HDD701 4.4 20.3 1.0 CG2 D:VAL81 4.5 18.5 1.0 CZ D:PHE168 4.6 20.7 1.0 CZ D:ARG365 4.7 20.3 1.0 NE2 D:HIS82 4.7 19.5 1.0 CD2 D:HIS82 4.7 19.4 1.0 CD2 D:TYR369 5.0 21.6 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