Iron in PDB 6jnt: Catalase Structure Determined By Eefd (Dataset 1)

All present enzymatic activity of Catalase Structure Determined By Eefd (Dataset 1):
1.11.1.6;

The binding sites of Iron atom in the Catalase Structure Determined By Eefd (Dataset 1) (pdb code 6jnt). 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 Eefd (Dataset 1), PDB code: 6jnt:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Catalase Structure Determined By Eefd (Dataset 1)


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 Eefd (Dataset 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:25.2 occ:1.00 FE A:HEM601 0.0 25.2 1.0 NC A:HEM601 2.0 27.3 1.0 ND A:HEM601 2.0 25.2 1.0 NA A:HEM601 2.1 20.8 1.0 NB A:HEM601 2.1 22.0 1.0 OH A:TYR357 2.3 7.1 1.0 C1C A:HEM601 3.0 26.8 1.0 C4C A:HEM601 3.0 30.3 1.0 C4D A:HEM601 3.1 24.6 1.0 C1D A:HEM601 3.1 24.6 1.0 C1A A:HEM601 3.1 18.6 1.0 C4B A:HEM601 3.1 19.1 1.0 C4A A:HEM601 3.1 18.6 1.0 C1B A:HEM601 3.1 21.7 1.0 CHC A:HEM601 3.4 21.3 1.0 CHA A:HEM601 3.4 22.9 1.0 CHD A:HEM601 3.4 27.4 1.0 CZ A:TYR357 3.4 7.1 1.0 CHB A:HEM601 3.5 22.3 1.0 HZ A:PHE160 3.6 8.4 1.0 HG21 A:VAL73 3.7 8.3 1.0 HE2 A:TYR357 3.9 8.5 1.0 HD2 A:HIS74 4.0 13.9 1.0 HE2 A:HIS74 4.0 13.5 1.0 CE2 A:TYR357 4.1 7.1 1.0 HE A:ARG353 4.1 8.7 1.0 HH21 A:ARG353 4.1 8.7 1.0 CZ A:PHE160 4.2 7.0 1.0 C2C A:HEM601 4.2 31.3 1.0 C3C A:HEM601 4.3 34.1 1.0 C3D A:HEM601 4.3 20.6 1.0 C2D A:HEM601 4.3 19.2 1.0 C2A A:HEM601 4.3 10.7 1.0 C3A A:HEM601 4.3 11.1 1.0 C3B A:HEM601 4.3 14.5 1.0 C2B A:HEM601 4.3 14.9 1.0 HHC A:HEM601 4.3 25.5 1.0 CE1 A:TYR357 4.4 7.1 1.0 HHA A:HEM601 4.4 27.5 1.0 HE1 A:TYR357 4.4 8.5 1.0 HG23 A:VAL73 4.4 8.3 1.0 HHD A:HEM601 4.4 32.8 1.0 CG2 A:VAL73 4.4 6.9 1.0 NE2 A:HIS74 4.4 11.2 1.0 CD2 A:HIS74 4.4 11.6 1.0 HHB A:HEM601 4.4 26.7 1.0 NE A:ARG353 4.6 7.2 1.0 NH2 A:ARG353 4.6 7.2 1.0 HE1 A:PHE160 4.7 8.5 1.0 HG22 A:VAL73 4.7 8.3 1.0 CE1 A:PHE160 4.8 7.1 1.0 HE2 A:PHE160 4.9 8.4 1.0 CE2 A:PHE160 4.9 7.0 1.0 HG2 A:ARG353 4.9 8.7 1.0 CZ A:ARG353 4.9 7.2 1.0

Iron binding site 2 out of 4 in the Catalase Structure Determined By Eefd (Dataset 1)


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 Eefd (Dataset 1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:20.9 occ:1.00 FE B:HEM601 0.0 20.9 1.0 NC B:HEM601 2.0 23.5 1.0 NB B:HEM601 2.0 22.1 1.0 ND B:HEM601 2.1 20.4 1.0 NA B:HEM601 2.1 15.1 1.0 OH B:TYR357 2.4 7.7 1.0 C4C B:HEM601 3.0 27.5 1.0 C1C B:HEM601 3.0 24.2 1.0 C4B B:HEM601 3.1 25.5 1.0 C1B B:HEM601 3.1 21.2 1.0 C1D B:HEM601 3.1 21.6 1.0 C4A B:HEM601 3.1 11.2 1.0 C4D B:HEM601 3.1 18.9 1.0 C1A B:HEM601 3.1 13.9 1.0 CHC B:HEM601 3.4 23.4 1.0 CHD B:HEM601 3.4 24.3 1.0 CHB B:HEM601 3.5 14.4 1.0 HZ B:PHE160 3.5 9.3 1.0 CZ B:TYR357 3.5 7.6 1.0 CHA B:HEM601 3.5 18.1 1.0 HG21 B:VAL73 3.5 19.8 1.0 HE2 B:TYR357 4.0 9.1 1.0 CZ B:PHE160 4.1 7.7 1.0 HG23 B:VAL73 4.1 19.8 1.0 CE2 B:TYR357 4.2 7.6 1.0 HD2 B:HIS74 4.2 41.7 1.0 CG2 B:VAL73 4.2 16.5 1.0 C2C B:HEM601 4.2 26.9 1.0 C3C B:HEM601 4.2 33.3 1.0 C3B B:HEM601 4.3 29.6 1.0 C2B B:HEM601 4.3 27.8 1.0 C2D B:HEM601 4.3 18.9 1.0 HHC B:HEM601 4.3 28.1 1.0 C3A B:HEM601 4.3 7.5 1.0 C3D B:HEM601 4.3 15.0 1.0 HE B:ARG353 4.3 26.6 1.0 C2A B:HEM601 4.4 7.5 1.0 HE1 B:TYR357 4.4 9.2 1.0 CE1 B:TYR357 4.4 7.6 1.0 HHD B:HEM601 4.4 29.2 1.0 NE2 B:HIS74 4.4 34.8 1.0 HHB B:HEM601 4.4 17.3 1.0 HHA B:HEM601 4.5 21.8 1.0 HH21 B:ARG353 4.5 32.3 1.0 CD2 B:HIS74 4.5 34.8 1.0 HG22 B:VAL73 4.6 19.8 1.0 HE1 B:PHE160 4.7 9.3 1.0 HE2 B:PHE160 4.7 9.2 1.0 NE B:ARG353 4.7 22.1 1.0 CE1 B:PHE160 4.7 7.8 1.0 CE2 B:PHE160 4.7 7.7 1.0 NH2 B:ARG353 4.8 26.9 1.0 CZ B:ARG353 4.9 25.1 1.0 HG2 B:ARG353 5.0 17.9 1.0

Iron binding site 3 out of 4 in the Catalase Structure Determined By Eefd (Dataset 1)


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 Eefd (Dataset 1) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe601 b:27.4 occ:1.00 FE C:HEM601 0.0 27.4 1.0 NC C:HEM601 2.0 29.4 1.0 ND C:HEM601 2.0 26.3 1.0 NB C:HEM601 2.1 30.1 1.0 NA C:HEM601 2.1 27.1 1.0 OH C:TYR357 2.4 8.2 1.0 C1C C:HEM601 3.0 31.1 1.0 C4C C:HEM601 3.0 29.1 1.0 C1D C:HEM601 3.1 25.2 1.0 C4B C:HEM601 3.1 32.1 1.0 C4D C:HEM601 3.1 25.3 1.0 C1A C:HEM601 3.1 25.3 1.0 C1B C:HEM601 3.1 27.8 1.0 C4A C:HEM601 3.1 25.0 1.0 CHC C:HEM601 3.4 33.4 1.0 CHD C:HEM601 3.4 27.9 1.0 CHA C:HEM601 3.4 26.4 1.0 CZ C:TYR357 3.4 8.1 1.0 CHB C:HEM601 3.5 27.2 1.0 HZ C:PHE160 3.6 33.5 1.0 HE1 C:TYR357 3.9 9.7 1.0 HE2 C:HIS74 3.9 9.8 1.0 HH21 C:ARG353 3.9 10.1 1.0 HE C:ARG353 3.9 10.1 1.0 HD2 C:HIS74 4.0 9.7 1.0 CE1 C:TYR357 4.1 8.1 1.0 CZ C:PHE160 4.2 27.9 1.0 C2C C:HEM601 4.2 30.6 1.0 C3C C:HEM601 4.2 29.9 1.0 C2D C:HEM601 4.3 23.0 1.0 C3D C:HEM601 4.3 23.8 1.0 HHC C:HEM601 4.3 40.1 1.0 C3B C:HEM601 4.3 32.0 1.0 C2B C:HEM601 4.3 27.1 1.0 C2A C:HEM601 4.3 20.0 1.0 C3A C:HEM601 4.3 19.8 1.0 NE2 C:HIS74 4.4 8.1 1.0 CE2 C:TYR357 4.4 8.1 1.0 HHD C:HEM601 4.4 33.5 1.0 NH2 C:ARG353 4.4 8.4 1.0 HHA C:HEM601 4.4 31.7 1.0 HE2 C:TYR357 4.4 9.8 1.0 CD2 C:HIS74 4.4 8.1 1.0 NE C:ARG353 4.5 8.4 1.0 HHB C:HEM601 4.5 32.6 1.0 HE1 C:PHE160 4.6 32.5 1.0 HB C:VAL73 4.7 17.4 1.0 CZ C:ARG353 4.8 8.4 1.0 CE1 C:PHE160 4.8 27.1 1.0 HG11 C:VAL73 4.8 19.2 1.0 HH22 C:ARG353 4.9 10.1 1.0 HE2 C:PHE160 4.9 35.6 1.0 CE2 C:PHE160 4.9 29.7 1.0

Iron binding site 4 out of 4 in the Catalase Structure Determined By Eefd (Dataset 1)


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 Eefd (Dataset 1) within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe601 b:21.1 occ:1.00 FE D:HEM601 0.0 21.1 1.0 NC D:HEM601 2.0 24.1 1.0 ND D:HEM601 2.0 20.9 1.0 NB D:HEM601 2.1 21.4 1.0 NA D:HEM601 2.1 21.9 1.0 OH D:TYR357 2.3 7.7 1.0 C1C D:HEM601 3.0 25.2 1.0 C4C D:HEM601 3.0 28.1 1.0 C4B D:HEM601 3.1 22.6 1.0 C4D D:HEM601 3.1 20.4 1.0 C1A D:HEM601 3.1 25.1 1.0 C1D D:HEM601 3.1 22.6 1.0 C1B D:HEM601 3.1 21.3 1.0 C4A D:HEM601 3.1 21.2 1.0 CHC D:HEM601 3.4 22.0 1.0 CHA D:HEM601 3.4 23.5 1.0 CHD D:HEM601 3.4 27.0 1.0 CZ D:TYR357 3.4 7.6 1.0 CHB D:HEM601 3.5 19.6 1.0 HG21 D:VAL73 3.6 9.0 1.0 HZ D:PHE160 3.7 17.0 1.0 HH21 D:ARG353 3.7 29.5 1.0 HE D:ARG353 3.8 16.7 1.0 HE2 D:TYR357 3.9 9.1 1.0 HG23 D:VAL73 4.0 9.0 1.0 CE2 D:TYR357 4.1 7.5 1.0 HE2 D:HIS74 4.1 17.2 1.0 HD2 D:HIS74 4.2 17.3 1.0 CZ D:PHE160 4.2 14.2 1.0 CG2 D:VAL73 4.2 7.5 1.0 C2C D:HEM601 4.2 29.5 1.0 C3C D:HEM601 4.2 30.8 1.0 C3D D:HEM601 4.3 15.8 1.0 C3B D:HEM601 4.3 23.8 1.0 C2A D:HEM601 4.3 26.0 1.0 C2D D:HEM601 4.3 17.8 1.0 C2B D:HEM601 4.3 22.2 1.0 HHC D:HEM601 4.3 26.4 1.0 C3A D:HEM601 4.3 22.9 1.0 NH2 D:ARG353 4.3 24.6 1.0 CE1 D:TYR357 4.3 7.7 1.0 HE1 D:TYR357 4.3 9.2 1.0 HHA D:HEM601 4.4 28.2 1.0 HHD D:HEM601 4.4 32.4 1.0 NE D:ARG353 4.4 13.9 1.0 HHB D:HEM601 4.5 23.6 1.0 NE2 D:HIS74 4.5 14.3 1.0 CD2 D:HIS74 4.5 14.4 1.0 HG22 D:VAL73 4.6 9.0 1.0 HE1 D:PHE160 4.7 17.0 1.0 CZ D:ARG353 4.8 20.6 1.0 CE1 D:PHE160 4.8 14.2 1.0 HH22 D:ARG353 4.9 29.5 1.0 HE2 D:PHE160 4.9 16.7 1.0 CE2 D:PHE160 4.9 13.9 1.0 HG2 D:ARG353 5.0 13.2 1.0

K.Yonekura, T.Ishikawa, S.Maki-Yonekura. A New Cryo-Em System For Electron 3D Crystallography By Eefd. J.Struct.Biol. V. 206 243 2019.
ISSN: ESSN 1095-8657
PubMed: 30928615
DOI: 10.1016/J.JSB.2019.03.009