Iron in PDB 1dgb: Human Erythrocyte Catalase

All present enzymatic activity of Human Erythrocyte Catalase:
1.11.1.6;

The structure of Human Erythrocyte Catalase, PDB code: 1dgb 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 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	83.497, 139.934, 227.891, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 22.7

The binding sites of Iron atom in the Human Erythrocyte Catalase (pdb code 1dgb). 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: 1dgb:
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:Fe1200 b:57.4 occ:1.00 FE A:HEM1200 0.0 57.4 1.0 OH A:TYR358 1.7 58.6 1.0 ND A:HEM1200 1.8 57.5 1.0 NA A:HEM1200 1.9 57.7 1.0 NB A:HEM1200 1.9 58.0 1.0 NC A:HEM1200 1.9 58.0 1.0 C4D A:HEM1200 2.9 57.3 1.0 CZ A:TYR358 2.9 58.8 1.0 C1A A:HEM1200 2.9 57.3 1.0 C1D A:HEM1200 2.9 57.3 1.0 C1B A:HEM1200 2.9 57.9 1.0 C4A A:HEM1200 2.9 57.7 1.0 C4B A:HEM1200 2.9 58.1 1.0 C1C A:HEM1200 3.0 57.9 1.0 C4C A:HEM1200 3.0 57.7 1.0 CHA A:HEM1200 3.3 57.3 1.0 CHB A:HEM1200 3.3 57.6 1.0 CHC A:HEM1200 3.3 57.9 1.0 CHD A:HEM1200 3.3 57.3 1.0 CE1 A:TYR358 3.6 58.8 1.0 CE2 A:TYR358 3.8 58.7 1.0 NH2 A:ARG354 4.0 58.4 1.0 NE A:ARG354 4.0 58.0 1.0 C2D A:HEM1200 4.1 57.1 1.0 C3D A:HEM1200 4.1 57.1 1.0 C2B A:HEM1200 4.1 57.9 1.0 C2A A:HEM1200 4.1 56.9 1.0 C3A A:HEM1200 4.1 57.2 1.0 C3B A:HEM1200 4.1 58.1 1.0 O A:HOH1396 4.1 85.9 1.0 C3C A:HEM1200 4.2 57.4 1.0 C2C A:HEM1200 4.2 57.5 1.0 CZ A:ARG354 4.4 58.1 1.0 CZ A:PHE161 4.6 58.5 1.0 NE2 A:HIS75 4.7 60.9 1.0 CD2 A:HIS75 4.8 60.7 1.0 CG2 A:VAL74 4.8 60.7 1.0 CD1 A:TYR358 4.9 58.5 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:Fe1201 b:59.1 occ:1.00 FE B:HEM1201 0.0 59.1 1.0 OH B:TYR358 1.8 56.6 1.0 NB B:HEM1201 1.8 58.0 1.0 NA B:HEM1201 1.9 57.8 1.0 ND B:HEM1201 1.9 57.6 1.0 NC B:HEM1201 2.0 57.8 1.0 CZ B:TYR358 2.8 56.6 1.0 C1B B:HEM1201 2.9 58.1 1.0 C4B B:HEM1201 2.9 58.1 1.0 C4A B:HEM1201 2.9 57.9 1.0 C1A B:HEM1201 2.9 57.8 1.0 C4D B:HEM1201 2.9 57.8 1.0 C1D B:HEM1201 3.0 57.4 1.0 C1C B:HEM1201 3.0 57.8 1.0 C4C B:HEM1201 3.0 57.5 1.0 CHB B:HEM1201 3.3 58.2 1.0 CHA B:HEM1201 3.3 58.0 1.0 CHC B:HEM1201 3.3 58.3 1.0 CHD B:HEM1201 3.4 57.7 1.0 CE1 B:TYR358 3.6 56.6 1.0 CE2 B:TYR358 3.7 56.7 1.0 NE B:ARG354 4.0 59.1 1.0 NH2 B:ARG354 4.0 59.7 1.0 C3B B:HEM1201 4.1 58.1 1.0 C2B B:HEM1201 4.1 58.3 1.0 C3A B:HEM1201 4.1 57.7 1.0 C2A B:HEM1201 4.1 57.4 1.0 C2D B:HEM1201 4.1 57.4 1.0 C3D B:HEM1201 4.2 57.6 1.0 C2C B:HEM1201 4.2 57.5 1.0 C3C B:HEM1201 4.2 57.5 1.0 O B:HOH1382 4.3 56.2 1.0 CZ B:ARG354 4.3 59.4 1.0 CZ B:PHE161 4.5 59.4 1.0 NE2 B:HIS75 4.6 56.2 1.0 CD2 B:HIS75 4.7 56.3 1.0 CG2 B:VAL74 4.8 57.5 1.0 CD1 B:TYR358 4.9 56.7 1.0 CD B:ARG354 4.9 58.5 1.0 CD2 B:TYR358 5.0 56.6 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:Fe1202 b:60.5 occ:1.00 FE C:HEM1202 0.0 60.5 1.0 OH C:TYR358 1.7 54.9 1.0 NA C:HEM1202 1.8 60.2 1.0 ND C:HEM1202 1.8 60.4 1.0 NB C:HEM1202 2.0 60.9 1.0 NC C:HEM1202 2.0 60.6 1.0 C1A C:HEM1202 2.8 59.9 1.0 C1D C:HEM1202 2.8 60.4 1.0 C4D C:HEM1202 2.8 60.0 1.0 C4A C:HEM1202 2.8 60.1 1.0 CZ C:TYR358 2.9 55.0 1.0 C4C C:HEM1202 2.9 60.9 1.0 C1B C:HEM1202 3.0 60.9 1.0 C4B C:HEM1202 3.1 60.9 1.0 C1C C:HEM1202 3.1 60.6 1.0 CHA C:HEM1202 3.2 60.1 1.0 CHD C:HEM1202 3.2 60.6 1.0 CHB C:HEM1202 3.3 60.5 1.0 CHC C:HEM1202 3.6 60.8 1.0 CE1 C:TYR358 3.6 54.9 1.0 CE2 C:TYR358 3.8 55.1 1.0 O C:HOH1328 3.9 59.9 1.0 NH2 C:ARG354 4.0 53.7 1.0 C2D C:HEM1202 4.0 60.1 1.0 C2A C:HEM1202 4.0 59.4 1.0 C3A C:HEM1202 4.0 59.7 1.0 NE C:ARG354 4.1 54.4 1.0 C3D C:HEM1202 4.1 60.0 1.0 C3C C:HEM1202 4.2 60.9 1.0 C2B C:HEM1202 4.2 60.8 1.0 C2C C:HEM1202 4.3 60.7 1.0 C3B C:HEM1202 4.3 61.1 1.0 CZ C:ARG354 4.4 54.4 1.0 NE2 C:HIS75 4.5 60.1 1.0 CZ C:PHE161 4.5 56.8 1.0 CG2 C:VAL74 4.7 58.5 1.0 CD2 C:HIS75 4.7 60.0 1.0 CD1 C:TYR358 4.9 54.9 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:Fe1203 b:57.0 occ:1.00 FE D:HEM1203 0.0 57.0 1.0 ND D:HEM1203 1.8 56.2 1.0 OH D:TYR358 1.8 53.0 1.0 NA D:HEM1203 1.9 56.3 1.0 NB D:HEM1203 1.9 56.4 1.0 NC D:HEM1203 1.9 56.7 1.0 C1D D:HEM1203 2.8 56.2 1.0 C4A D:HEM1203 2.9 56.2 1.0 C4C D:HEM1203 2.9 56.7 1.0 C1B D:HEM1203 2.9 56.5 1.0 C4D D:HEM1203 2.9 56.2 1.0 CZ D:TYR358 2.9 53.0 1.0 C1A D:HEM1203 2.9 56.1 1.0 C1C D:HEM1203 3.0 56.7 1.0 C4B D:HEM1203 3.1 56.5 1.0 CHD D:HEM1203 3.2 56.5 1.0 CHB D:HEM1203 3.2 56.5 1.0 CHA D:HEM1203 3.3 56.3 1.0 CHC D:HEM1203 3.5 56.8 1.0 CE1 D:TYR358 3.5 53.0 1.0 O D:HOH1223 3.6 60.9 1.0 CE2 D:TYR358 3.9 53.1 1.0 NH2 D:ARG354 3.9 55.7 1.0 NE D:ARG354 4.0 55.8 1.0 C2D D:HEM1203 4.1 56.1 1.0 C3A D:HEM1203 4.1 55.8 1.0 C3D D:HEM1203 4.1 56.0 1.0 C3C D:HEM1203 4.1 56.7 1.0 C2B D:HEM1203 4.1 56.7 1.0 C2A D:HEM1203 4.2 55.8 1.0 C2C D:HEM1203 4.2 56.6 1.0 C3B D:HEM1203 4.2 56.3 1.0 CZ D:ARG354 4.4 55.5 1.0 CZ D:PHE161 4.7 58.6 1.0 NE2 D:HIS75 4.7 54.1 1.0 CG2 D:VAL74 4.8 56.5 1.0 CD2 D:HIS75 4.9 54.3 1.0 CD1 D:TYR358 4.9 53.4 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