Iron in the structure of Crystal Structure of Vibrio Salmonicida Catalase (pdb 2isa)

The binding sites of Iron atom in the structure of Crystal Structure of Vibrio Salmonicida Catalase (pdb code 2isa). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 2isa structure was solved by E.K.RIISE, M.S.LORENTZEN, R.HELLAND, A.O.SMALAS, H.K.S.LEIROS, N.P.WILLASSEN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.0 Space group P1211 a (A) 98.150 b (A) 217.760 c (A) 99.280 alpha (°) 90.00 beta (°) 110.48 gamma (°) 90.00 Rfactor (%) 14.8 Rfree (%) 20 Iron Binding Sites: Iron binding site 1 out of 8 in 2isa Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 2isa. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: His54, A: Phe140, A: Arg333, A: Tyr337, A: Hem486, A: Hoh5671, conact list: Atom Atom Distance (A) Fe NE2 A:His54 4.71 Fe CD2 A:His54 4.72 Fe CZ A:Phe140 4.46 Fe CE1 A:Phe140 4.92 Fe CZ A:Arg333 4.57 Fe NE A:Arg333 4.12 Fe NH2 A:Arg333 4.19 Fe CE2 A:Tyr337 3.77 Fe CZ A:Tyr337 3.05 Fe CE1 A:Tyr337 3.92 Fe OH A:Tyr337 1.96 Fe C2D A:Hem486 4.29 Fe NC A:Hem486 2.04 Fe CHB A:Hem486 3.51 Fe CHC A:Hem486 3.42 Fe C3D A:Hem486 4.30 Fe NA A:Hem486 2.06 Fe CHA A:Hem486 3.39 Fe C2A A:Hem486 4.26 Fe C1D A:Hem486 3.07 Fe C4A A:Hem486 3.10 Fe C4B A:Hem486 3.09 Fe C3A A:Hem486 4.30 Fe C4C A:Hem486 3.03 Fe C2B A:Hem486 4.34 Fe C1C A:Hem486 3.06 Fe C2C A:Hem486 4.27 Fe ND A:Hem486 2.08 Fe CHD A:Hem486 3.40 Fe C1B A:Hem486 3.15 Fe NB A:Hem486 2.14 Fe FE A:Hem486 0.00 Fe C3C A:Hem486 4.26 Fe C3B A:Hem486 4.31 Fe C4D A:Hem486 3.07 Fe C1A A:Hem486 3.03 Fe O A:Hoh5671 3.83 interactive model: Iron binding site 2 out of 8 in 2isa Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 2isa. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: His54, B: Phe140, B: Arg333, B: Tyr337, B: Hem486, B: Hoh6594, conact list: Atom Atom Distance (A) Fe NE2 B:His54 4.55 Fe CD2 B:His54 4.65 Fe CZ B:Phe140 4.38 Fe CE1 B:Phe140 4.83 Fe CZ B:Arg333 4.61 Fe NE B:Arg333 4.23 Fe NH2 B:Arg333 4.13 Fe CE2 B:Tyr337 3.69 Fe CD2 B:Tyr337 4.98 Fe CZ B:Tyr337 2.94 Fe CE1 B:Tyr337 3.84 Fe OH B:Tyr337 1.81 Fe C2D B:Hem486 4.30 Fe NC B:Hem486 2.09 Fe CHB B:Hem486 3.45 Fe CHC B:Hem486 3.48 Fe C3D B:Hem486 4.29 Fe NA B:Hem486 2.09 Fe CHA B:Hem486 3.41 Fe C2A B:Hem486 4.30 Fe C1D B:Hem486 3.07 Fe C4A B:Hem486 3.10 Fe C4B B:Hem486 3.08 Fe C3A B:Hem486 4.32 Fe C4C B:Hem486 3.07 Fe C2B B:Hem486 4.28 Fe C1C B:Hem486 3.11 Fe C2C B:Hem486 4.31 Fe ND B:Hem486 2.07 Fe CHD B:Hem486 3.42 Fe C1B B:Hem486 3.07 Fe NB B:Hem486 2.06 Fe FE B:Hem486 0.00 Fe C3C B:Hem486 4.29 Fe C3B B:Hem486 4.28 Fe C4D B:Hem486 3.06 Fe C1A B:Hem486 3.07 Fe O B:Hoh6594 4.10 interactive model: Iron binding site 3 out of 8 in 2isa Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 2isa. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: His54, C: Phe140, C: Arg333, C: Tyr337, C: Hem485, C: Hoh5626, conact list: Atom Atom Distance (A) Fe NE2 C:His54 4.61 Fe CD2 C:His54 4.67 Fe CZ C:Phe140 4.35 Fe CE1 C:Phe140 4.79 Fe CZ C:Arg333 4.60 Fe NE C:Arg333 4.20 Fe NH2 C:Arg333 4.16 Fe CE2 C:Tyr337 3.77 Fe CZ C:Tyr337 3.00 Fe CE1 C:Tyr337 3.88 Fe OH C:Tyr337 1.85 Fe C2D C:Hem485 4.36 Fe NC C:Hem485 2.04 Fe CHB C:Hem485 3.50 Fe CHC C:Hem485 3.44 Fe C3D C:Hem485 4.34 Fe NA C:Hem485 2.05 Fe CHA C:Hem485 3.40 Fe C2A C:Hem485 4.27 Fe C1D C:Hem485 3.13 Fe C4A C:Hem485 3.10 Fe C4B C:Hem485 3.09 Fe C3A C:Hem485 4.30 Fe C4C C:Hem485 3.06 Fe C2B C:Hem485 4.31 Fe C1C C:Hem485 3.07 Fe C2C C:Hem485 4.28 Fe ND C:Hem485 2.12 Fe CHD C:Hem485 3.45 Fe C1B C:Hem485 3.12 Fe NB C:Hem485 2.10 Fe FE C:Hem485 0.00 Fe C3C C:Hem485 4.27 Fe C3B C:Hem485 4.30 Fe C4D C:Hem485 3.10 Fe C1A C:Hem485 3.04 Fe O C:Hoh5626 4.09 interactive model: Iron binding site 4 out of 8 in 2isa Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 2isa. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: His54, D: Phe140, D: Arg333, D: Tyr337, D: Hem485, D: Hoh5669, conact list: Atom Atom Distance (A) Fe NE2 D:His54 4.65 Fe CD2 D:His54 4.68 Fe CZ D:Phe140 4.33 Fe CE1 D:Phe140 4.78 Fe CZ D:Arg333 4.61 Fe NE D:Arg333 4.12 Fe NH2 D:Arg333 4.24 Fe CE2 D:Tyr337 3.78 Fe CZ D:Tyr337 3.01 Fe CE1 D:Tyr337 3.88 Fe OH D:Tyr337 1.91 Fe C2D D:Hem485 4.35 Fe NC D:Hem485 2.09 Fe CHB D:Hem485 3.41 Fe CHC D:Hem485 3.46 Fe C3D D:Hem485 4.36 Fe NA D:Hem485 2.10 Fe CHA D:Hem485 3.47 Fe C2A D:Hem485 4.32 Fe C1D D:Hem485 3.10 Fe C4A D:Hem485 3.09 Fe C4B D:Hem485 3.08 Fe C3A D:Hem485 4.31 Fe C4C D:Hem485 3.08 Fe C2B D:Hem485 4.24 Fe C1C D:Hem485 3.10 Fe C2C D:Hem485 4.30 Fe ND D:Hem485 2.11 Fe CHD D:Hem485 3.43 Fe C1B D:Hem485 3.04 Fe NB D:Hem485 2.07 Fe FE D:Hem485 0.00 Fe C3C D:Hem485 4.29 Fe C3B D:Hem485 4.26 Fe C4D D:Hem485 3.12 Fe C1A D:Hem485 3.12 Fe O D:Hoh5669 4.24 interactive model: Iron binding site 5 out of 8 in 2isa Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 2isa. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: E: His54, E: Phe140, E: Arg333, E: Tyr337, E: Hem486, E: Hoh5718, E: Hoh5919, conact list: Atom Atom Distance (A) Fe NE2 E:His54 4.72 Fe CD2 E:His54 4.71 Fe CZ E:Phe140 4.38 Fe CE1 E:Phe140 4.79 Fe CZ E:Arg333 4.53 Fe NE E:Arg333 4.11 Fe NH2 E:Arg333 4.13 Fe CE2 E:Tyr337 3.62 Fe CD2 E:Tyr337 4.92 Fe CZ E:Tyr337 2.93 Fe CE1 E:Tyr337 3.88 Fe OH E:Tyr337 1.84 Fe C2D E:Hem486 4.31 Fe NC E:Hem486 2.09 Fe CHB E:Hem486 3.47 Fe CHC E:Hem486 3.47 Fe C3D E:Hem486 4.28 Fe NA E:Hem486 2.06 Fe CHA E:Hem486 3.39 Fe C2A E:Hem486 4.26 Fe C1D E:Hem486 3.08 Fe C4A E:Hem486 3.09 Fe C4B E:Hem486 3.11 Fe C3A E:Hem486 4.30 Fe C4C E:Hem486 3.07 Fe C2B E:Hem486 4.31 Fe C1C E:Hem486 3.11 Fe C2C E:Hem486 4.31 Fe ND E:Hem486 2.07 Fe CHD E:Hem486 3.43 Fe C1B E:Hem486 3.11 Fe NB E:Hem486 2.11 Fe FE E:Hem486 0.00 Fe C3C E:Hem486 4.29 Fe C3B E:Hem486 4.31 Fe C4D E:Hem486 3.05 Fe C1A E:Hem486 3.04 Fe O E:Hoh5718 4.45 Fe O E:Hoh5919 3.15 interactive model: Iron binding site 6 out of 8 in 2isa Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 2isa. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: F: His54, F: Phe140, F: Arg333, F: Tyr337, F: Hem486, F: Hoh8597, conact list: Atom Atom Distance (A) Fe NE2 F:His54 4.66 Fe CD2 F:His54 4.73 Fe CZ F:Phe140 4.40 Fe CE1 F:Phe140 4.82 Fe CZ F:Arg333 4.67 Fe NE F:Arg333 4.22 Fe NH2 F:Arg333 4.28 Fe CE2 F:Tyr337 3.75 Fe CZ F:Tyr337 2.98 Fe CE1 F:Tyr337 3.84 Fe OH F:Tyr337 1.85 Fe C2D F:Hem486 4.25 Fe NC F:Hem486 2.11 Fe CHB F:Hem486 3.42 Fe CHC F:Hem486 3.58 Fe C3D F:Hem486 4.26 Fe NA F:Hem486 2.06 Fe CHA F:Hem486 3.42 Fe C2A F:Hem486 4.29 Fe C1D F:Hem486 3.01 Fe C4A F:Hem486 3.06 Fe C4B F:Hem486 3.17 Fe C3A F:Hem486 4.29 Fe C4C F:Hem486 3.05 Fe C2B F:Hem486 4.31 Fe C1C F:Hem486 3.18 Fe C2C F:Hem486 4.36 Fe ND F:Hem486 2.03 Fe CHD F:Hem486 3.35 Fe C1B F:Hem486 3.08 Fe NB F:Hem486 2.12 Fe FE F:Hem486 0.00 Fe C3C F:Hem486 4.30 Fe C3B F:Hem486 4.35 Fe C4D F:Hem486 3.04 Fe C1A F:Hem486 3.07 Fe O F:Hoh8597 3.96 interactive model: Iron binding site 7 out of 8 in 2isa Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 2isa. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: G: His54, G: Phe140, G: Arg333, G: Tyr337, G: Hem485, G: Hoh5654, conact list: Atom Atom Distance (A) Fe NE2 G:His54 4.60 Fe CD2 G:His54 4.63 Fe CZ G:Phe140 4.34 Fe CE1 G:Phe140 4.80 Fe CZ G:Arg333 4.62 Fe NE G:Arg333 4.15 Fe NH2 G:Arg333 4.22 Fe CE2 G:Tyr337 3.69 Fe CD2 G:Tyr337 4.97 Fe CZ G:Tyr337 2.95 Fe CE1 G:Tyr337 3.83 Fe OH G:Tyr337 1.90 Fe C2D G:Hem485 4.29 Fe NC G:Hem485 2.09 Fe CHB G:Hem485 3.44 Fe CHC G:Hem485 3.52 Fe C3D G:Hem485 4.31 Fe NA G:Hem485 2.04 Fe CHA G:Hem485 3.43 Fe C2A G:Hem485 4.27 Fe C1D G:Hem485 3.05 Fe C4A G:Hem485 3.07 Fe C4B G:Hem485 3.15 Fe C3A G:Hem485 4.28 Fe C4C G:Hem485 3.05 Fe C2B G:Hem485 4.34 Fe C1C G:Hem485 3.15 Fe C2C G:Hem485 4.34 Fe ND G:Hem485 2.06 Fe CHD G:Hem485 3.38 Fe C1B G:Hem485 3.12 Fe NB G:Hem485 2.14 Fe FE G:Hem485 0.00 Fe C3C G:Hem485 4.29 Fe C3B G:Hem485 4.35 Fe C4D G:Hem485 3.08 Fe C1A G:Hem485 3.05 Fe O G:Hoh5654 4.21 interactive model: Iron binding site 8 out of 8 in 2isa Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 2isa. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: H: His54, H: Phe140, H: Arg333, H: Tyr337, H: Hem485, H: Hoh7765, H: Hoh7891, conact list: Atom Atom Distance (A) Fe NE2 H:His54 4.56 Fe CD2 H:His54 4.63 Fe CZ H:Phe140 4.37 Fe CE1 H:Phe140 4.82 Fe CZ H:Arg333 4.50 Fe NE H:Arg333 4.05 Fe NH2 H:Arg333 4.13 Fe CE2 H:Tyr337 3.73 Fe CD2 H:Tyr337 5.00 Fe CZ H:Tyr337 2.96 Fe CE1 H:Tyr337 3.82 Fe OH H:Tyr337 1.86 Fe C2D H:Hem485 4.35 Fe NC H:Hem485 2.07 Fe CHB H:Hem485 3.40 Fe CHC H:Hem485 3.43 Fe C3D H:Hem485 4.34 Fe NA H:Hem485 2.08 Fe CHA H:Hem485 3.48 Fe C2A H:Hem485 4.32 Fe C1D H:Hem485 3.10 Fe C4A H:Hem485 3.07 Fe C4B H:Hem485 3.05 Fe C3A H:Hem485 4.30 Fe C4C H:Hem485 3.08 Fe C2B H:Hem485 4.25 Fe C1C H:Hem485 3.07 Fe C2C H:Hem485 4.28 Fe ND H:Hem485 2.10 Fe CHD H:Hem485 3.45 Fe C1B H:Hem485 3.04 Fe NB H:Hem485 2.05 Fe FE H:Hem485 0.00 Fe C3C H:Hem485 4.29 Fe C3B H:Hem485 4.26 Fe C4D H:Hem485 3.11 Fe C1A H:Hem485 3.11 Fe O H:Hoh7765 4.60 Fe O H:Hoh7891 3.21 interactive model: