Iron in PDB 4b7f: Structure of A Liganded Bacterial Catalase

All present enzymatic activity of Structure of A Liganded Bacterial Catalase:
1.11.1.6;

The structure of Structure of A Liganded Bacterial Catalase, PDB code: 4b7f was solved by A.Gumiero, M.Walsh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	100.580 / 1.76
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	151.510, 151.510, 156.620, 90.00, 90.00, 120.00
R / Rfree (%)	15.79 / 19.42

The structure of Structure of A Liganded Bacterial Catalase also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Iron atom in the Structure of A Liganded Bacterial Catalase (pdb code 4b7f). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of A Liganded Bacterial Catalase, PDB code: 4b7f:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of A Liganded Bacterial Catalase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of A Liganded Bacterial Catalase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe3000 b:11.1 occ:1.00 FE A:HEM3000 0.0 11.1 1.0 N A:NO1519 1.5 20.0 1.0 NB A:HEM3000 2.0 10.0 1.0 NC A:HEM3000 2.0 12.6 1.0 OH A:TYR353 2.0 11.5 1.0 NA A:HEM3000 2.0 9.3 1.0 ND A:HEM3000 2.0 10.9 1.0 O A:NO1519 2.6 20.0 1.0 C4C A:HEM3000 3.0 13.8 1.0 C1B A:HEM3000 3.0 10.8 1.0 C4B A:HEM3000 3.0 12.4 1.0 C1D A:HEM3000 3.0 13.3 1.0 CZ A:TYR353 3.0 12.6 1.0 C1C A:HEM3000 3.0 13.3 1.0 C4A A:HEM3000 3.0 10.5 1.0 C4D A:HEM3000 3.1 10.6 1.0 C1A A:HEM3000 3.1 11.3 1.0 CHD A:HEM3000 3.4 10.6 1.0 CHC A:HEM3000 3.4 11.2 1.0 CHB A:HEM3000 3.4 8.5 1.0 CHA A:HEM3000 3.5 11.0 1.0 CE2 A:TYR353 3.8 11.6 1.0 CE1 A:TYR353 3.9 12.2 1.0 NE A:ARG349 4.1 11.4 1.0 C3C A:HEM3000 4.2 12.7 1.0 C2C A:HEM3000 4.2 10.8 1.0 C2B A:HEM3000 4.2 10.2 1.0 C3B A:HEM3000 4.2 9.2 1.0 C3A A:HEM3000 4.3 9.0 1.0 C2D A:HEM3000 4.3 7.8 1.0 NH2 A:ARG349 4.3 10.3 1.0 C2A A:HEM3000 4.3 12.3 1.0 C3D A:HEM3000 4.3 10.1 1.0 O A:HOH2074 4.3 15.3 1.0 NE2 A:HIS71 4.4 12.3 1.0 CD2 A:HIS71 4.5 9.2 1.0 CZ A:PHE156 4.5 11.6 1.0 CZ A:ARG349 4.6 11.5 1.0 CE1 A:PHE156 4.8 13.4 1.0 CD A:PRO70 5.0 10.8 1.0

Iron binding site 2 out of 4 in the Structure of A Liganded Bacterial Catalase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of A Liganded Bacterial Catalase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe3001 b:12.9 occ:1.00 FE B:HEM3001 0.0 12.9 1.0 N B:NO1520 1.6 20.0 1.0 OH B:TYR353 2.0 11.3 1.0 NB B:HEM3001 2.0 13.7 1.0 NA B:HEM3001 2.0 10.4 1.0 ND B:HEM3001 2.0 10.3 1.0 NC B:HEM3001 2.1 13.9 1.0 O B:NO1520 2.7 20.0 1.0 CZ B:TYR353 3.0 13.0 1.0 C4B B:HEM3001 3.0 15.1 1.0 C1C B:HEM3001 3.1 13.5 1.0 C4A B:HEM3001 3.1 10.8 1.0 C4D B:HEM3001 3.1 14.0 1.0 C1A B:HEM3001 3.1 12.1 1.0 C1B B:HEM3001 3.1 15.1 1.0 C1D B:HEM3001 3.1 11.9 1.0 C4C B:HEM3001 3.1 15.4 1.0 CHC B:HEM3001 3.4 12.5 1.0 CHA B:HEM3001 3.4 13.2 1.0 CHB B:HEM3001 3.4 10.3 1.0 CHD B:HEM3001 3.4 14.6 1.0 CE2 B:TYR353 3.8 10.4 1.0 CE1 B:TYR353 3.8 10.3 1.0 NE B:ARG349 4.1 11.8 1.0 C3A B:HEM3001 4.3 10.0 1.0 C3B B:HEM3001 4.3 13.1 1.0 C2A B:HEM3001 4.3 8.0 1.0 C2C B:HEM3001 4.3 16.8 1.0 C2B B:HEM3001 4.3 12.7 1.0 C3D B:HEM3001 4.3 9.6 1.0 C3C B:HEM3001 4.3 14.0 1.0 C2D B:HEM3001 4.3 10.8 1.0 NH2 B:ARG349 4.4 10.9 1.0 NE2 B:HIS71 4.4 12.6 1.0 CZ B:PHE156 4.4 10.4 1.0 O B:HOH2039 4.4 17.4 1.0 CD2 B:HIS71 4.5 11.9 1.0 CZ B:ARG349 4.6 12.1 1.0 CD B:PRO70 4.8 12.6 1.0 CE1 B:PHE156 4.9 16.3 1.0 CD B:ARG349 5.0 12.1 1.0

Iron binding site 3 out of 4 in the Structure of A Liganded Bacterial Catalase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of A Liganded Bacterial Catalase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe3002 b:11.2 occ:1.00 FE C:HEM3002 0.0 11.2 1.0 N C:NO1519 1.6 20.0 1.0 OH C:TYR353 2.0 10.6 1.0 NC C:HEM3002 2.0 10.2 1.0 NA C:HEM3002 2.0 10.3 1.0 NB C:HEM3002 2.0 13.5 1.0 ND C:HEM3002 2.0 10.7 1.0 O C:NO1519 2.6 20.0 1.0 C4B C:HEM3002 3.0 11.8 1.0 C1C C:HEM3002 3.0 11.3 1.0 CZ C:TYR353 3.0 10.8 1.0 C1A C:HEM3002 3.0 11.9 1.0 C4D C:HEM3002 3.0 11.2 1.0 C4C C:HEM3002 3.1 13.3 1.0 C4A C:HEM3002 3.1 12.5 1.0 C1D C:HEM3002 3.1 10.2 1.0 C1B C:HEM3002 3.1 10.6 1.0 CHC C:HEM3002 3.4 10.5 1.0 CHA C:HEM3002 3.4 8.1 1.0 CHD C:HEM3002 3.5 11.5 1.0 CHB C:HEM3002 3.5 9.9 1.0 CE2 C:TYR353 3.8 11.3 1.0 CE1 C:TYR353 3.9 10.9 1.0 NE C:ARG349 4.1 7.9 1.0 C2C C:HEM3002 4.2 11.4 1.0 C2A C:HEM3002 4.2 9.8 1.0 C3A C:HEM3002 4.3 10.3 1.0 C3B C:HEM3002 4.3 10.9 1.0 C3D C:HEM3002 4.3 9.1 1.0 C3C C:HEM3002 4.3 10.6 1.0 C2D C:HEM3002 4.3 12.1 1.0 C2B C:HEM3002 4.3 11.7 1.0 O C:HOH2049 4.3 15.7 1.0 CZ C:PHE156 4.4 12.3 1.0 NH2 C:ARG349 4.4 11.6 1.0 NE2 C:HIS71 4.4 12.5 1.0 CD2 C:HIS71 4.5 11.9 1.0 CZ C:ARG349 4.7 11.0 1.0 CE1 C:PHE156 4.8 13.3 1.0 CD C:PRO70 4.9 8.9 1.0

Iron binding site 4 out of 4 in the Structure of A Liganded Bacterial Catalase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of A Liganded Bacterial Catalase within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe3003 b:12.3 occ:1.00 FE D:HEM3003 0.0 12.3 1.0 N D:NO1520 1.5 20.0 1.0 OH D:TYR353 2.0 13.1 1.0 NB D:HEM3003 2.0 13.4 1.0 NC D:HEM3003 2.0 10.7 1.0 NA D:HEM3003 2.0 10.0 1.0 ND D:HEM3003 2.0 11.8 1.0 O D:NO1520 2.5 20.0 1.0 CZ D:TYR353 3.0 11.2 1.0 C4C D:HEM3003 3.0 13.8 1.0 C1D D:HEM3003 3.0 10.7 1.0 C4B D:HEM3003 3.0 13.4 1.0 C4A D:HEM3003 3.0 10.2 1.0 C1C D:HEM3003 3.1 13.2 1.0 C1B D:HEM3003 3.1 10.7 1.0 C1A D:HEM3003 3.1 10.8 1.0 C4D D:HEM3003 3.1 9.7 1.0 CHD D:HEM3003 3.4 13.0 1.0 CHC D:HEM3003 3.4 11.8 1.0 CHB D:HEM3003 3.4 12.8 1.0 CHA D:HEM3003 3.4 10.2 1.0 CE2 D:TYR353 3.8 11.2 1.0 CE1 D:TYR353 3.9 9.2 1.0 NE D:ARG349 4.1 10.4 1.0 C3C D:HEM3003 4.2 10.7 1.0 C2C D:HEM3003 4.3 11.0 1.0 C3A D:HEM3003 4.3 9.3 1.0 C3B D:HEM3003 4.3 11.4 1.0 C2B D:HEM3003 4.3 11.9 1.0 C2A D:HEM3003 4.3 7.2 1.0 C2D D:HEM3003 4.3 11.6 1.0 C3D D:HEM3003 4.3 10.8 1.0 NH2 D:ARG349 4.3 10.4 1.0 O D:HOH2025 4.4 15.7 1.0 CZ D:PHE156 4.4 12.7 1.0 NE2 D:HIS71 4.5 13.4 1.0 CD2 D:HIS71 4.5 11.2 1.0 CZ D:ARG349 4.6 11.1 1.0 CE1 D:PHE156 4.8 15.4 1.0 CD D:PRO70 4.9 12.6 1.0 CD D:ARG349 5.0 12.3 1.0

M.Candelaresi, A.Gumiero, K.Adamczyk, K.Robb, C.Bellota-Anton, V.Sangal, J.Munnoch, G.M.Greetham, M.Towrie, P.A.Hoskisson, A.W.Parker, N.P.Tucker, M.A.Walsh, N.T.Hunt. A Structural and Dynamic Investigation of the Inhibition of Catalase By Nitric Oxide. Org.Biomol.Chem. V. 11 7778 2013.
ISSN: ISSN 1477-0520
PubMed: 24121528
DOI: 10.1039/C3OB41977K