Iron in PDB 3rgp: Structural and Kinetic Analysis of the Beef Liver Catalase Complexed with Nitric Oxide

All present enzymatic activity of Structural and Kinetic Analysis of the Beef Liver Catalase Complexed with Nitric Oxide:
1.11.1.6;

The structure of Structural and Kinetic Analysis of the Beef Liver Catalase Complexed with Nitric Oxide, PDB code: 3rgp was solved by N.Purwar, M.Schmidt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.30 / 1.88
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.110, 139.940, 228.020, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 21.4

The binding sites of Iron atom in the Structural and Kinetic Analysis of the Beef Liver Catalase Complexed with Nitric Oxide (pdb code 3rgp). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structural and Kinetic Analysis of the Beef Liver Catalase Complexed with Nitric Oxide, PDB code: 3rgp:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structural and Kinetic Analysis of the Beef Liver Catalase Complexed with Nitric Oxide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structural and Kinetic Analysis of the Beef Liver Catalase Complexed with Nitric Oxide within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1 b:14.5 occ:1.00 FE A:HEM1 0.0 14.5 1.0 N A:NO502 1.8 25.1 1.0 NB A:HEM1 1.9 16.6 1.0 NA A:HEM1 2.0 13.6 1.0 NC A:HEM1 2.0 18.5 1.0 ND A:HEM1 2.0 13.4 1.0 OH A:TYR357 2.0 13.7 1.0 O A:NO502 2.9 26.3 1.0 C1B A:HEM1 3.0 15.9 1.0 C4B A:HEM1 3.0 14.2 1.0 C4A A:HEM1 3.0 13.9 1.0 C4C A:HEM1 3.0 17.3 1.0 C1C A:HEM1 3.0 17.6 1.0 C1D A:HEM1 3.0 14.2 1.0 C1A A:HEM1 3.0 12.9 1.0 C4D A:HEM1 3.0 13.1 1.0 CZ A:TYR357 3.1 13.8 1.0 CHB A:HEM1 3.4 15.1 1.0 CHD A:HEM1 3.4 14.1 1.0 CHC A:HEM1 3.4 15.9 1.0 CHA A:HEM1 3.4 12.0 1.0 CE2 A:TYR357 3.7 12.9 1.0 CE1 A:TYR357 4.0 14.2 1.0 O A:HOH864 4.1 33.2 1.0 NE A:ARG353 4.2 14.2 1.0 NH2 A:ARG353 4.2 12.5 1.0 C2B A:HEM1 4.2 13.9 1.0 C3B A:HEM1 4.2 14.0 1.0 C3D A:HEM1 4.3 13.7 1.0 C3C A:HEM1 4.3 18.8 1.0 C2C A:HEM1 4.3 19.4 1.0 C3A A:HEM1 4.3 13.7 1.0 C2D A:HEM1 4.3 13.8 1.0 C2A A:HEM1 4.3 12.2 1.0 CZ A:PHE160 4.4 14.6 1.0 CZ A:ARG353 4.6 14.6 1.0 CG2 A:VAL73 4.6 16.8 1.0 NE2 A:HIS74 4.7 17.2 1.0 CD2 A:HIS74 4.7 19.6 1.0 CE1 A:PHE160 5.0 14.8 1.0

Iron binding site 2 out of 4 in the Structural and Kinetic Analysis of the Beef Liver Catalase Complexed with Nitric Oxide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structural and Kinetic Analysis of the Beef Liver Catalase Complexed with Nitric Oxide within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1 b:17.0 occ:1.00 FE B:HEM1 0.0 17.0 1.0 N B:NO502 1.7 27.1 1.0 NB B:HEM1 1.9 17.6 1.0 NA B:HEM1 2.0 16.6 1.0 ND B:HEM1 2.0 16.9 1.0 OH B:TYR357 2.0 18.7 1.0 NC B:HEM1 2.0 21.4 1.0 O B:NO502 2.9 30.8 1.0 C1B B:HEM1 3.0 18.0 1.0 C4B B:HEM1 3.0 18.9 1.0 C4A B:HEM1 3.0 15.8 1.0 C4D B:HEM1 3.0 18.0 1.0 C1A B:HEM1 3.0 15.2 1.0 C1D B:HEM1 3.0 17.9 1.0 C1C B:HEM1 3.0 21.6 1.0 C4C B:HEM1 3.1 21.6 1.0 CZ B:TYR357 3.1 16.0 1.0 CHB B:HEM1 3.4 15.6 1.0 CHA B:HEM1 3.4 18.7 1.0 CHC B:HEM1 3.4 20.0 1.0 CHD B:HEM1 3.4 19.9 1.0 CE2 B:TYR357 3.7 14.9 1.0 CE1 B:TYR357 4.0 13.9 1.0 O B:HOH977 4.1 38.3 1.0 C2B B:HEM1 4.2 17.2 1.0 C3B B:HEM1 4.2 18.4 1.0 NE B:ARG353 4.2 12.6 1.0 C3D B:HEM1 4.2 17.6 1.0 NH2 B:ARG353 4.2 13.3 1.0 C2A B:HEM1 4.3 14.3 1.0 C3A B:HEM1 4.3 16.0 1.0 C2D B:HEM1 4.3 18.5 1.0 C2C B:HEM1 4.3 22.6 1.0 C3C B:HEM1 4.3 22.4 1.0 CZ B:PHE160 4.5 18.9 1.0 NE2 B:HIS74 4.5 17.4 1.0 CD2 B:HIS74 4.6 15.9 1.0 CZ B:ARG353 4.7 14.6 1.0 CG2 B:VAL73 4.7 19.0 1.0

Iron binding site 3 out of 4 in the Structural and Kinetic Analysis of the Beef Liver Catalase Complexed with Nitric Oxide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structural and Kinetic Analysis of the Beef Liver Catalase Complexed with Nitric Oxide within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1 b:17.4 occ:1.00 FE C:HEM1 0.0 17.4 1.0 N C:NO502 1.7 27.8 1.0 OH C:TYR357 2.0 14.4 1.0 ND C:HEM1 2.0 15.9 1.0 NA C:HEM1 2.0 16.6 1.0 NB C:HEM1 2.0 16.6 1.0 NC C:HEM1 2.0 20.9 1.0 O C:NO502 2.8 31.8 1.0 C4D C:HEM1 3.0 16.2 1.0 C1A C:HEM1 3.0 15.4 1.0 C1D C:HEM1 3.0 17.1 1.0 C1B C:HEM1 3.0 17.1 1.0 C4B C:HEM1 3.0 18.8 1.0 C4C C:HEM1 3.0 20.7 1.0 C4A C:HEM1 3.0 16.5 1.0 C1C C:HEM1 3.1 20.8 1.0 CZ C:TYR357 3.1 13.4 1.0 CHA C:HEM1 3.4 15.8 1.0 CHD C:HEM1 3.4 17.0 1.0 CHC C:HEM1 3.4 18.9 1.0 CHB C:HEM1 3.4 16.7 1.0 CE2 C:TYR357 3.8 11.1 1.0 CE1 C:TYR357 4.0 11.8 1.0 NE C:ARG353 4.2 11.2 1.0 NH2 C:ARG353 4.2 16.4 1.0 C3D C:HEM1 4.2 16.0 1.0 O C:HOH1185 4.2 34.5 1.0 C2D C:HEM1 4.2 17.5 1.0 C2A C:HEM1 4.3 15.5 1.0 C2B C:HEM1 4.3 16.4 1.0 C3B C:HEM1 4.3 19.4 1.0 C3A C:HEM1 4.3 17.4 1.0 C3C C:HEM1 4.3 21.9 1.0 C2C C:HEM1 4.3 22.6 1.0 CZ C:PHE160 4.5 15.4 1.0 CZ C:ARG353 4.6 14.0 1.0 CD2 C:HIS74 4.6 13.3 1.0 NE2 C:HIS74 4.7 16.5 1.0 CG2 C:VAL73 4.7 21.3 1.0

Iron binding site 4 out of 4 in the Structural and Kinetic Analysis of the Beef Liver Catalase Complexed with Nitric Oxide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structural and Kinetic Analysis of the Beef Liver Catalase Complexed with Nitric Oxide within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe1 b:15.6 occ:1.00 FE D:HEM1 0.0 15.6 1.0 N D:NO502 1.7 22.6 1.0 NB D:HEM1 2.0 15.7 1.0 OH D:TYR357 2.0 14.3 1.0 ND D:HEM1 2.0 14.2 1.0 NA D:HEM1 2.0 14.4 1.0 NC D:HEM1 2.0 18.7 1.0 O D:NO502 2.8 26.5 1.0 C1D D:HEM1 3.0 14.3 1.0 C1B D:HEM1 3.0 16.6 1.0 C4B D:HEM1 3.0 16.7 1.0 C4C D:HEM1 3.0 18.9 1.0 C1A D:HEM1 3.0 12.6 1.0 C4A D:HEM1 3.0 16.6 1.0 C4D D:HEM1 3.0 14.7 1.0 CZ D:TYR357 3.0 15.1 1.0 C1C D:HEM1 3.0 19.6 1.0 CHD D:HEM1 3.4 14.9 1.0 CHB D:HEM1 3.4 16.2 1.0 CHA D:HEM1 3.4 14.0 1.0 CHC D:HEM1 3.4 17.1 1.0 CE2 D:TYR357 3.8 13.7 1.0 CE1 D:TYR357 3.9 14.0 1.0 NH2 D:ARG353 4.1 16.3 1.0 NE D:ARG353 4.2 14.4 1.0 O D:HOH727 4.2 24.9 1.0 C3D D:HEM1 4.2 14.9 1.0 C2D D:HEM1 4.2 15.4 1.0 C2B D:HEM1 4.3 17.1 1.0 C3B D:HEM1 4.3 17.2 1.0 C3C D:HEM1 4.3 20.8 1.0 C2A D:HEM1 4.3 15.2 1.0 C2C D:HEM1 4.3 19.9 1.0 C3A D:HEM1 4.3 16.1 1.0 CZ D:PHE160 4.4 17.9 1.0 CZ D:ARG353 4.5 18.6 1.0 CD2 D:HIS74 4.7 17.4 1.0 CG2 D:VAL73 4.7 18.1 1.0 NE2 D:HIS74 4.8 21.7 1.0

N.Purwar, J.M.Mcgarry, J.Kostera, A.A.Pacheco, M.Schmidt. Interaction of Nitric Oxide with Catalase: Structural and Kinetic Analysis. Biochemistry V. 50 4491 2011.
ISSN: ISSN 0006-2960
PubMed: 21524057
DOI: 10.1021/BI200130R