Iron in PDB 2j2m: Crystal Structure Analysis of Catalase From Exiguobacterium Oxidotolerans

All present enzymatic activity of Crystal Structure Analysis of Catalase From Exiguobacterium Oxidotolerans:
1.11.1.6;

The structure of Crystal Structure Analysis of Catalase From Exiguobacterium Oxidotolerans, PDB code: 2j2m was solved by I.Hara, N.Ichise, K.Kojima, H.Kondo, S.Ohgiya, H.Matsuyama, I.Yumoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.4
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	94.267, 131.935, 110.642, 90.00, 107.61, 90.00
R / Rfree (%)	19.9 / 23

The binding sites of Iron atom in the Crystal Structure Analysis of Catalase From Exiguobacterium Oxidotolerans (pdb code 2j2m). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure Analysis of Catalase From Exiguobacterium Oxidotolerans, PDB code: 2j2m:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure Analysis of Catalase From Exiguobacterium Oxidotolerans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure Analysis of Catalase From Exiguobacterium Oxidotolerans within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:6.7 occ:1.00 FE A:HEM501 0.0 6.7 1.0 OH A:TYR339 1.9 5.4 1.0 NA A:HEM501 2.1 6.4 1.0 NC A:HEM501 2.1 6.4 1.0 ND A:HEM501 2.1 5.7 1.0 NB A:HEM501 2.1 5.8 1.0 CZ A:TYR339 2.9 7.1 1.0 C4C A:HEM501 3.0 5.7 1.0 C1A A:HEM501 3.1 6.1 1.0 C4A A:HEM501 3.1 5.1 1.0 C4B A:HEM501 3.1 6.9 1.0 C1D A:HEM501 3.1 4.9 1.0 C4D A:HEM501 3.1 5.1 1.0 C1C A:HEM501 3.1 5.1 1.0 C1B A:HEM501 3.1 5.9 1.0 CHD A:HEM501 3.4 4.9 1.0 CHA A:HEM501 3.4 4.0 1.0 CHC A:HEM501 3.5 6.3 1.0 CHB A:HEM501 3.5 6.3 1.0 CE1 A:TYR339 3.6 6.2 1.0 CE2 A:TYR339 3.7 4.8 1.0 NE A:ARG335 3.9 8.9 1.0 C2A A:HEM501 4.3 5.6 1.0 C3C A:HEM501 4.3 6.6 1.0 C3B A:HEM501 4.3 7.8 1.0 C3A A:HEM501 4.3 4.9 1.0 C2B A:HEM501 4.3 7.9 1.0 C2C A:HEM501 4.3 6.5 1.0 C3D A:HEM501 4.3 4.3 1.0 C2D A:HEM501 4.3 4.2 1.0 NH2 A:ARG335 4.3 3.1 1.0 CZ A:PHE142 4.6 6.1 1.0 CZ A:ARG335 4.6 7.0 1.0 CG2 A:VAL55 4.7 3.3 1.0 CD2 A:HIS56 4.8 3.6 1.0 NE2 A:HIS56 4.8 5.7 1.0 CD A:ARG335 4.8 9.5 1.0 CD1 A:TYR339 4.9 3.9 1.0 CD2 A:TYR339 4.9 4.3 1.0 CG A:ARG335 5.0 6.8 1.0

Iron binding site 2 out of 4 in the Crystal Structure Analysis of Catalase From Exiguobacterium Oxidotolerans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure Analysis of Catalase From Exiguobacterium Oxidotolerans within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:7.2 occ:1.00 FE B:HEM501 0.0 7.2 1.0 OH B:TYR339 1.9 4.3 1.0 NC B:HEM501 2.1 6.8 1.0 NA B:HEM501 2.1 5.2 1.0 NB B:HEM501 2.1 6.7 1.0 ND B:HEM501 2.1 5.5 1.0 CZ B:TYR339 2.9 6.2 1.0 C4B B:HEM501 3.0 8.3 1.0 C1A B:HEM501 3.1 5.3 1.0 C4C B:HEM501 3.1 5.2 1.0 C1C B:HEM501 3.1 6.1 1.0 C4A B:HEM501 3.1 3.4 1.0 C1B B:HEM501 3.1 5.0 1.0 C1D B:HEM501 3.1 4.4 1.0 C4D B:HEM501 3.1 4.4 1.0 CHC B:HEM501 3.4 5.8 1.0 CHD B:HEM501 3.4 3.9 1.0 CHA B:HEM501 3.4 3.7 1.0 CHB B:HEM501 3.5 4.8 1.0 CE1 B:TYR339 3.6 5.7 1.0 CE2 B:TYR339 3.8 4.2 1.0 NE B:ARG335 4.0 9.6 1.0 NH2 B:ARG335 4.1 4.2 1.0 C3B B:HEM501 4.2 8.3 1.0 C2A B:HEM501 4.3 4.5 1.0 C3C B:HEM501 4.3 6.3 1.0 C3A B:HEM501 4.3 3.5 1.0 C2C B:HEM501 4.3 6.0 1.0 C2B B:HEM501 4.3 7.8 1.0 C2D B:HEM501 4.4 3.5 1.0 C3D B:HEM501 4.4 3.9 1.0 O B:HOH2029 4.5 21.3 1.0 CZ B:PHE142 4.5 6.2 1.0 CZ B:ARG335 4.5 8.6 1.0 CG2 B:VAL55 4.6 2.6 1.0 CD2 B:HIS56 4.8 3.4 1.0 NE2 B:HIS56 4.9 3.4 1.0 CD1 B:TYR339 4.9 3.8 1.0 CD2 B:TYR339 5.0 3.8 1.0

Iron binding site 3 out of 4 in the Crystal Structure Analysis of Catalase From Exiguobacterium Oxidotolerans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure Analysis of Catalase From Exiguobacterium Oxidotolerans within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:9.0 occ:1.00 FE C:HEM501 0.0 9.0 1.0 OH C:TYR339 1.9 13.3 1.0 NA C:HEM501 2.0 7.0 1.0 NC C:HEM501 2.1 9.0 1.0 NB C:HEM501 2.1 9.1 1.0 ND C:HEM501 2.1 9.1 1.0 CZ C:TYR339 2.9 13.3 1.0 C4A C:HEM501 3.0 8.3 1.0 C4C C:HEM501 3.0 9.8 1.0 C1A C:HEM501 3.1 7.1 1.0 C1B C:HEM501 3.1 9.4 1.0 C1D C:HEM501 3.1 8.7 1.0 C1C C:HEM501 3.1 10.6 1.0 C4D C:HEM501 3.1 8.6 1.0 C4B C:HEM501 3.1 10.9 1.0 CHB C:HEM501 3.4 9.3 1.0 CHD C:HEM501 3.4 7.9 1.0 CHA C:HEM501 3.5 7.3 1.0 CHC C:HEM501 3.5 10.7 1.0 CE1 C:TYR339 3.6 13.6 1.0 CE2 C:TYR339 3.8 11.3 1.0 NE C:ARG335 4.1 10.6 1.0 NH2 C:ARG335 4.2 10.0 1.0 C3A C:HEM501 4.2 8.2 1.0 C3C C:HEM501 4.3 10.4 1.0 C2A C:HEM501 4.3 7.5 1.0 C2C C:HEM501 4.3 11.2 1.0 C2B C:HEM501 4.3 10.5 1.0 C3B C:HEM501 4.3 11.5 1.0 C2D C:HEM501 4.4 9.8 1.0 C3D C:HEM501 4.4 8.7 1.0 CZ C:PHE142 4.4 9.0 1.0 NE2 C:HIS56 4.6 10.7 1.0 CG2 C:VAL55 4.6 11.8 1.0 CZ C:ARG335 4.6 12.2 1.0 CD2 C:HIS56 4.7 11.8 1.0 CD1 C:TYR339 4.9 12.2 1.0 CE1 C:PHE142 4.9 7.9 1.0 CD2 C:TYR339 5.0 12.7 1.0

Iron binding site 4 out of 4 in the Crystal Structure Analysis of Catalase From Exiguobacterium Oxidotolerans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure Analysis of Catalase From Exiguobacterium Oxidotolerans within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:10.5 occ:1.00 FE D:HEM501 0.0 10.5 1.0 OH D:TYR339 1.8 13.0 1.0 NC D:HEM501 2.1 10.7 1.0 NA D:HEM501 2.1 10.5 1.0 NB D:HEM501 2.1 11.7 1.0 ND D:HEM501 2.2 10.2 1.0 CZ D:TYR339 2.8 13.4 1.0 C4A D:HEM501 3.0 10.0 1.0 C4C D:HEM501 3.0 10.7 1.0 C4B D:HEM501 3.1 13.3 1.0 C1B D:HEM501 3.1 9.9 1.0 C1C D:HEM501 3.1 11.5 1.0 C1D D:HEM501 3.1 9.2 1.0 C1A D:HEM501 3.1 9.9 1.0 C4D D:HEM501 3.2 10.1 1.0 CHB D:HEM501 3.4 9.3 1.0 CHD D:HEM501 3.4 8.1 1.0 CHC D:HEM501 3.4 12.0 1.0 CHA D:HEM501 3.5 9.3 1.0 CE1 D:TYR339 3.6 12.4 1.0 CE2 D:TYR339 3.7 12.7 1.0 NE D:ARG335 4.0 9.8 1.0 NH2 D:ARG335 4.2 10.5 1.0 C3A D:HEM501 4.3 8.8 1.0 C3C D:HEM501 4.3 11.5 1.0 C3B D:HEM501 4.3 12.1 1.0 C2C D:HEM501 4.3 12.6 1.0 C2B D:HEM501 4.3 11.3 1.0 C2A D:HEM501 4.3 8.8 1.0 C2D D:HEM501 4.4 9.4 1.0 C3D D:HEM501 4.4 9.0 1.0 CZ D:ARG335 4.5 11.5 1.0 CZ D:PHE142 4.6 13.3 1.0 NE2 D:HIS56 4.7 14.8 1.0 CD2 D:HIS56 4.7 13.6 1.0 CG2 D:VAL55 4.8 11.6 1.0 CD1 D:TYR339 4.9 10.9 1.0 CD2 D:TYR339 4.9 11.8 1.0

I.Hara, N.Ichise, K.Kojima, H.Kondo, S.Ohgiya, H.Matsuyama, I.Yumoto. Relationship Between the Size of the Bottleneck 15 A From Iron in the Main Channel and the Reactivity of Catalase Corresponding to the Molecular Size of Substrates. Biochemistry V. 46 11 2007.
ISSN: ISSN 0006-2960
PubMed: 17198371
DOI: 10.1021/BI061519W