Iron in PDB 1dgf: Human Erythrocyte Catalase

All present enzymatic activity of Human Erythrocyte Catalase:
1.11.1.6;

The structure of Human Erythrocyte Catalase, PDB code: 1dgf was solved by C.D.Putnam, A.S.Arvai, Y.Bourne, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	83.717, 142.505, 232.066, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 19.2

The binding sites of Iron atom in the Human Erythrocyte Catalase (pdb code 1dgf). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Human Erythrocyte Catalase, PDB code: 1dgf:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Human Erythrocyte Catalase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Human Erythrocyte Catalase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe3000 b:12.6 occ:1.00 FE A:HEM3000 0.0 12.6 1.0 OH A:TYR358 1.9 11.8 1.0 ND A:HEM3000 2.0 11.2 1.0 NB A:HEM3000 2.0 11.1 1.0 NA A:HEM3000 2.0 11.0 1.0 NC A:HEM3000 2.0 11.4 1.0 C4D A:HEM3000 3.0 10.5 1.0 C1B A:HEM3000 3.0 10.7 1.0 C1D A:HEM3000 3.0 10.8 1.0 C4B A:HEM3000 3.0 10.5 1.0 CZ A:TYR358 3.0 10.8 1.0 C4A A:HEM3000 3.0 9.9 1.0 C4C A:HEM3000 3.0 10.9 1.0 C1A A:HEM3000 3.0 10.3 1.0 C1C A:HEM3000 3.0 11.5 1.0 CHA A:HEM3000 3.4 10.8 1.0 CHB A:HEM3000 3.4 10.5 1.0 CHD A:HEM3000 3.4 11.8 1.0 CHC A:HEM3000 3.4 11.5 1.0 CE1 A:TYR358 3.8 10.6 1.0 CE2 A:TYR358 3.9 10.9 1.0 NE A:ARG354 4.1 10.8 1.0 NH2 A:ARG354 4.1 10.1 1.0 O A:HOH5141 4.2 16.5 1.0 C3D A:HEM3000 4.2 11.3 1.0 C2D A:HEM3000 4.3 11.5 1.0 C2B A:HEM3000 4.3 10.8 1.0 C3B A:HEM3000 4.3 10.6 1.0 C3A A:HEM3000 4.3 10.2 1.0 C2C A:HEM3000 4.3 11.1 1.0 C3C A:HEM3000 4.3 11.3 1.0 C2A A:HEM3000 4.3 10.6 1.0 CZ A:ARG354 4.5 10.6 1.0 CZ A:PHE161 4.5 10.0 1.0 CG2 A:VAL74 4.6 10.9 1.0 NE2 A:HIS75 4.7 11.4 1.0 CD2 A:HIS75 4.7 12.0 1.0

Iron binding site 2 out of 4 in the Human Erythrocyte Catalase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Human Erythrocyte Catalase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe3001 b:10.8 occ:1.00 FE B:HEM3001 0.0 10.8 1.0 OH B:TYR358 1.9 10.7 1.0 ND B:HEM3001 2.0 10.5 1.0 NA B:HEM3001 2.0 9.4 1.0 NB B:HEM3001 2.0 10.1 1.0 NC B:HEM3001 2.0 10.1 1.0 C4A B:HEM3001 3.0 9.5 1.0 C1B B:HEM3001 3.0 9.7 1.0 C4D B:HEM3001 3.0 9.4 1.0 CZ B:TYR358 3.0 9.2 1.0 C1D B:HEM3001 3.0 10.2 1.0 C1A B:HEM3001 3.0 9.7 1.0 C4C B:HEM3001 3.0 9.8 1.0 C4B B:HEM3001 3.0 9.7 1.0 C1C B:HEM3001 3.1 9.4 1.0 CHB B:HEM3001 3.4 9.7 1.0 CHD B:HEM3001 3.4 10.2 1.0 CHA B:HEM3001 3.4 9.6 1.0 CHC B:HEM3001 3.4 9.0 1.0 CE1 B:TYR358 3.8 9.4 1.0 CE2 B:TYR358 3.9 9.2 1.0 O B:HOH5120 4.1 16.4 1.0 NE B:ARG354 4.1 10.9 1.0 NH2 B:ARG354 4.2 10.1 1.0 C3D B:HEM3001 4.2 9.3 1.0 C2D B:HEM3001 4.3 9.8 1.0 C3A B:HEM3001 4.3 9.6 1.0 C2B B:HEM3001 4.3 9.7 1.0 C3C B:HEM3001 4.3 10.1 1.0 C2A B:HEM3001 4.3 10.1 1.0 C3B B:HEM3001 4.3 9.8 1.0 C2C B:HEM3001 4.3 9.2 1.0 CZ B:PHE161 4.5 10.0 1.0 CZ B:ARG354 4.6 11.8 1.0 CG2 B:VAL74 4.6 9.7 1.0 NE2 B:HIS75 4.6 10.8 1.0 CD2 B:HIS75 4.7 10.7 1.0

Iron binding site 3 out of 4 in the Human Erythrocyte Catalase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Human Erythrocyte Catalase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe3002 b:10.7 occ:1.00 FE C:HEM3002 0.0 10.7 1.0 OH C:TYR358 2.0 10.7 1.0 ND C:HEM3002 2.0 10.4 1.0 NB C:HEM3002 2.0 10.8 1.0 NC C:HEM3002 2.0 11.2 1.0 NA C:HEM3002 2.0 10.2 1.0 C4D C:HEM3002 3.0 9.8 1.0 C1D C:HEM3002 3.0 9.7 1.0 CZ C:TYR358 3.0 9.8 1.0 C1B C:HEM3002 3.0 9.8 1.0 C1C C:HEM3002 3.0 10.9 1.0 C4B C:HEM3002 3.0 10.0 1.0 C1A C:HEM3002 3.0 9.5 1.0 C4C C:HEM3002 3.0 9.8 1.0 C4A C:HEM3002 3.1 9.0 1.0 CHA C:HEM3002 3.4 9.9 1.0 CHD C:HEM3002 3.4 9.5 1.0 CHB C:HEM3002 3.4 9.5 1.0 CHC C:HEM3002 3.4 10.0 1.0 CE1 C:TYR358 3.8 9.8 1.0 CE2 C:TYR358 3.9 10.2 1.0 NE C:ARG354 4.1 11.1 1.0 O C:HOH5183 4.1 16.5 1.0 NH2 C:ARG354 4.1 10.9 1.0 C3D C:HEM3002 4.2 9.6 1.0 C2D C:HEM3002 4.3 9.9 1.0 C2C C:HEM3002 4.3 10.6 1.0 C2B C:HEM3002 4.3 9.2 1.0 C3C C:HEM3002 4.3 10.1 1.0 C3B C:HEM3002 4.3 9.7 1.0 C3A C:HEM3002 4.3 9.2 1.0 C2A C:HEM3002 4.3 9.3 1.0 CZ C:ARG354 4.5 11.5 1.0 CZ C:PHE161 4.6 10.0 1.0 NE2 C:HIS75 4.6 12.8 1.0 CG2 C:VAL74 4.6 10.7 1.0 CD2 C:HIS75 4.7 12.5 1.0

Iron binding site 4 out of 4 in the Human Erythrocyte Catalase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Human Erythrocyte Catalase within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe3003 b:12.7 occ:1.00 FE D:HEM3003 0.0 12.7 1.0 ND D:HEM3003 2.0 10.9 1.0 NB D:HEM3003 2.0 10.7 1.0 NA D:HEM3003 2.0 10.0 1.0 NC D:HEM3003 2.0 10.5 1.0 OH D:TYR358 2.0 10.5 1.0 C1D D:HEM3003 3.0 10.2 1.0 C4D D:HEM3003 3.0 10.0 1.0 C4C D:HEM3003 3.0 10.1 1.0 C4B D:HEM3003 3.0 10.2 1.0 C1A D:HEM3003 3.0 9.6 1.0 C1B D:HEM3003 3.0 10.3 1.0 C4A D:HEM3003 3.0 9.5 1.0 C1C D:HEM3003 3.1 10.5 1.0 CZ D:TYR358 3.1 10.0 1.0 CHD D:HEM3003 3.4 9.1 1.0 CHA D:HEM3003 3.4 8.9 1.0 CHB D:HEM3003 3.4 9.2 1.0 CHC D:HEM3003 3.4 10.1 1.0 CE1 D:TYR358 3.8 9.5 1.0 CE2 D:TYR358 4.0 9.6 1.0 O D:HOH5175 4.1 17.3 1.0 NE D:ARG354 4.1 10.7 1.0 NH2 D:ARG354 4.1 11.4 1.0 C3D D:HEM3003 4.3 9.2 1.0 C2D D:HEM3003 4.3 9.4 1.0 C2A D:HEM3003 4.3 9.3 1.0 C3C D:HEM3003 4.3 9.7 1.0 C2B D:HEM3003 4.3 10.2 1.0 C3A D:HEM3003 4.3 8.9 1.0 C2C D:HEM3003 4.3 9.4 1.0 C3B D:HEM3003 4.3 10.5 1.0 CZ D:ARG354 4.5 11.4 1.0 CZ D:PHE161 4.6 9.6 1.0 CG2 D:VAL74 4.6 10.1 1.0 NE2 D:HIS75 4.7 10.1 1.0 CD2 D:HIS75 4.7 10.6 1.0

C.D.Putnam, A.S.Arvai, Y.Bourne, J.A.Tainer. Active and Inhibited Human Catalase Structures: Ligand and Nadph Binding and Catalytic Mechanism. J.Mol.Biol. V. 296 295 2000.
ISSN: ISSN 0022-2836
PubMed: 10656833
DOI: 10.1006/JMBI.1999.3458