Iron in PDB 5gkn: Catalase Structure Determined By Electron Crystallography of Thin 3D Crystals

All present enzymatic activity of Catalase Structure Determined By Electron Crystallography of Thin 3D Crystals:
1.11.1.6;

The binding sites of Iron atom in the Catalase Structure Determined By Electron Crystallography of Thin 3D Crystals (pdb code 5gkn). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Catalase Structure Determined By Electron Crystallography of Thin 3D Crystals, PDB code: 5gkn:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Catalase Structure Determined By Electron Crystallography of Thin 3D Crystals


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Catalase Structure Determined By Electron Crystallography of Thin 3D Crystals within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:66.1 occ:1.00 FE A:HEM601 0.0 66.1 1.0 OH A:TYR357 1.8 24.1 1.0 ND A:HEM601 1.9 30.0 1.0 NA A:HEM601 2.0 35.1 1.0 NC A:HEM601 2.1 37.6 1.0 NB A:HEM601 2.1 32.1 1.0 C1D A:HEM601 2.9 22.6 1.0 C4D A:HEM601 2.9 28.0 1.0 C1A A:HEM601 3.0 23.1 1.0 C4A A:HEM601 3.0 22.0 1.0 CZ A:TYR357 3.0 27.5 1.0 C4C A:HEM601 3.0 38.6 1.0 C1B A:HEM601 3.1 35.2 1.0 C4B A:HEM601 3.1 25.5 1.0 C1C A:HEM601 3.1 33.2 1.0 CHD A:HEM601 3.3 26.3 1.0 CHA A:HEM601 3.4 16.0 1.0 CHB A:HEM601 3.4 25.0 1.0 CHC A:HEM601 3.6 27.6 1.0 CE2 A:TYR357 3.8 24.4 1.0 CE1 A:TYR357 3.9 26.9 1.0 C2D A:HEM601 4.1 17.6 1.0 C3D A:HEM601 4.1 29.7 1.0 C3A A:HEM601 4.2 24.4 1.0 C2A A:HEM601 4.2 26.5 1.0 C3C A:HEM601 4.3 41.0 1.0 NH2 A:ARG353 4.3 36.6 1.0 C2C A:HEM601 4.3 31.4 1.0 C2B A:HEM601 4.3 16.6 1.0 NE A:ARG353 4.4 19.9 1.0 C3B A:HEM601 4.4 14.4 1.0 CZ A:PHE160 4.5 11.9 1.0 CZ A:ARG353 4.6 30.2 1.0 CG2 A:VAL73 4.6 17.9 1.0 CD2 A:HIS74 4.8 19.6 1.0 NE2 A:HIS74 4.9 10.4 1.0

Iron binding site 2 out of 4 in the Catalase Structure Determined By Electron Crystallography of Thin 3D Crystals


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Catalase Structure Determined By Electron Crystallography of Thin 3D Crystals within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:46.5 occ:1.00 FE B:HEM601 0.0 46.5 1.0 ND B:HEM601 1.9 31.7 1.0 NA B:HEM601 2.0 31.1 1.0 OH B:TYR357 2.0 27.8 1.0 NB B:HEM601 2.1 29.7 1.0 NC B:HEM601 2.1 31.8 1.0 C1D B:HEM601 2.9 19.6 1.0 C4D B:HEM601 2.9 28.2 1.0 C1A B:HEM601 2.9 26.0 1.0 C4A B:HEM601 3.0 35.0 1.0 C1B B:HEM601 3.0 21.3 1.0 C4C B:HEM601 3.0 29.4 1.0 CZ B:TYR357 3.1 24.6 1.0 C4B B:HEM601 3.1 32.4 1.0 C1C B:HEM601 3.2 14.8 1.0 CHD B:HEM601 3.3 23.4 1.0 CHA B:HEM601 3.4 20.6 1.0 CHB B:HEM601 3.4 24.6 1.0 CHC B:HEM601 3.6 13.3 1.0 CE2 B:TYR357 3.8 27.8 1.0 CE1 B:TYR357 4.0 33.0 1.0 C2D B:HEM601 4.1 21.9 1.0 C3D B:HEM601 4.1 30.7 1.0 C2A B:HEM601 4.1 15.8 1.0 C3A B:HEM601 4.2 33.4 1.0 NE B:ARG353 4.3 13.2 1.0 C2B B:HEM601 4.3 26.9 1.0 C3C B:HEM601 4.3 21.4 1.0 C2C B:HEM601 4.4 14.6 1.0 C3B B:HEM601 4.4 31.4 1.0 NH2 B:ARG353 4.4 19.4 1.0 CZ B:PHE160 4.5 21.9 1.0 CG2 B:VAL73 4.5 13.0 1.0 CZ B:ARG353 4.6 17.0 1.0 NE2 B:HIS74 4.7 26.4 1.0 CD2 B:HIS74 4.7 39.0 1.0

Iron binding site 3 out of 4 in the Catalase Structure Determined By Electron Crystallography of Thin 3D Crystals


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Catalase Structure Determined By Electron Crystallography of Thin 3D Crystals within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe601 b:96.6 occ:1.00 FE C:HEM601 0.0 96.6 1.0 ND C:HEM601 1.9 20.2 1.0 NA C:HEM601 2.0 31.5 1.0 NC C:HEM601 2.1 23.5 1.0 NB C:HEM601 2.1 30.2 1.0 OH C:TYR357 2.2 20.6 1.0 C1D C:HEM601 2.9 20.9 1.0 C4D C:HEM601 2.9 23.0 1.0 C1A C:HEM601 3.0 22.3 1.0 C4A C:HEM601 3.0 26.8 1.0 C4C C:HEM601 3.0 27.8 1.0 C1B C:HEM601 3.1 19.3 1.0 C4B C:HEM601 3.1 29.4 1.0 C1C C:HEM601 3.1 22.5 1.0 CZ C:TYR357 3.2 18.9 1.0 CHD C:HEM601 3.3 22.6 1.0 CHA C:HEM601 3.4 22.8 1.0 CHB C:HEM601 3.4 24.1 1.0 CHC C:HEM601 3.6 24.8 1.0 CE1 C:TYR357 3.9 22.3 1.0 C2D C:HEM601 4.1 23.9 1.0 C3D C:HEM601 4.1 29.6 1.0 C2A C:HEM601 4.1 21.7 1.0 C3A C:HEM601 4.2 16.5 1.0 CE2 C:TYR357 4.2 13.9 1.0 NH2 C:ARG353 4.3 12.0 1.0 C3C C:HEM601 4.3 51.7 1.0 C2C C:HEM601 4.3 49.4 1.0 C2B C:HEM601 4.3 16.9 1.0 NE C:ARG353 4.4 25.6 1.0 C3B C:HEM601 4.4 18.4 1.0 CZ C:PHE160 4.5 23.9 1.0 NE2 C:HIS74 4.6 31.5 1.0 CD2 C:HIS74 4.6 21.1 1.0 CZ C:ARG353 4.6 17.9 1.0 CE1 C:PHE160 5.0 19.9 1.0

Iron binding site 4 out of 4 in the Catalase Structure Determined By Electron Crystallography of Thin 3D Crystals


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Catalase Structure Determined By Electron Crystallography of Thin 3D Crystals within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe601 b:47.1 occ:1.00 FE D:HEM601 0.0 47.1 1.0 ND D:HEM601 1.9 29.8 1.0 OH D:TYR357 1.9 22.5 1.0 NA D:HEM601 2.0 32.8 1.0 NC D:HEM601 2.1 40.5 1.0 NB D:HEM601 2.1 38.9 1.0 C1D D:HEM601 2.9 28.8 1.0 C4D D:HEM601 2.9 30.1 1.0 C1A D:HEM601 3.0 26.4 1.0 C4A D:HEM601 3.0 21.4 1.0 C4C D:HEM601 3.0 40.6 1.0 C1B D:HEM601 3.1 23.5 1.0 CZ D:TYR357 3.1 15.0 1.0 C4B D:HEM601 3.1 23.4 1.0 C1C D:HEM601 3.2 25.9 1.0 CHD D:HEM601 3.3 25.0 1.0 CHA D:HEM601 3.4 13.9 1.0 CHB D:HEM601 3.5 14.8 1.0 CHC D:HEM601 3.6 11.4 1.0 CE2 D:TYR357 3.8 12.6 1.0 CE1 D:TYR357 4.1 14.7 1.0 C2D D:HEM601 4.1 31.3 1.0 C3D D:HEM601 4.1 40.2 1.0 C2A D:HEM601 4.2 19.1 1.0 C3A D:HEM601 4.2 19.8 1.0 NH2 D:ARG353 4.2 19.5 1.0 NE D:ARG353 4.3 27.4 1.0 C3C D:HEM601 4.3 36.3 1.0 C2B D:HEM601 4.3 22.1 1.0 C2C D:HEM601 4.3 32.5 1.0 C3B D:HEM601 4.4 25.0 1.0 CG2 D:VAL73 4.5 18.8 1.0 CZ D:PHE160 4.5 28.9 1.0 CZ D:ARG353 4.6 30.0 1.0 CD2 D:HIS74 4.7 25.6 1.0 NE2 D:HIS74 4.7 23.8 1.0

K.Yonekura, M.Maki-Yonekura. Refinement of Cryo-Em Structures Using Scattering Factors of Charged Atoms J.Appl.Crystallogr. V. 49 1517 2016.
ISSN: ESSN 1600-5767
DOI: 10.1107/S1600576716011274