Iron in the structure of Crystal Structure of Human Myeloperoxidase With Covalent Thioxanthine Analog (pdb 4dl1)

The binding sites of Iron atom in the structure of Crystal Structure of Human Myeloperoxidase With Covalent Thioxanthine Analog (pdb code 4dl1). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 4dl1 structure was solved by F.VAJDOS, A.VARGHESE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 128.5-2.0 Space group P1211 a (A) 63.829 b (A) 242.636 c (A) 151.505 alpha (°) 90.00 beta (°) 91.19 gamma (°) 90.00 Rfactor (%) 19 Rfree (%) 24.6 Iron Binding Sites: Iron binding site 1 out of 8 in 4dl1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 4dl1. 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: Gln91, C: Arg333, C: His336, C: Leu417, C: Hem601, A: Hoh1701, conact list: Atom Atom Distance (A) Fe NE2 A:Gln91 4.85 Fe CG C:Arg333 4.89 Fe NE2 C:His336 2.21 Fe ND1 C:His336 4.30 Fe CD2 C:His336 3.20 Fe CE1 C:His336 3.18 Fe CG C:His336 4.34 Fe CD2 C:Leu417 4.73 Fe C2D C:Hem601 4.27 Fe NC C:Hem601 2.08 Fe CHB C:Hem601 3.42 Fe CHC C:Hem601 3.41 Fe C3D C:Hem601 4.27 Fe NA C:Hem601 2.04 Fe CHA C:Hem601 3.40 Fe C2A C:Hem601 4.30 Fe C1D C:Hem601 3.06 Fe C4A C:Hem601 3.06 Fe C4B C:Hem601 3.02 Fe C3A C:Hem601 4.28 Fe C4C C:Hem601 3.10 Fe C2B C:Hem601 4.23 Fe C1C C:Hem601 3.09 Fe C2C C:Hem601 4.31 Fe ND C:Hem601 2.10 Fe CHD C:Hem601 3.45 Fe C1B C:Hem601 3.02 Fe NB C:Hem601 2.03 Fe FE C:Hem601 0.00 Fe C3C C:Hem601 4.30 Fe C3B C:Hem601 4.24 Fe C4D C:Hem601 3.03 Fe C1A C:Hem601 3.06 Fe O A:Hoh1701 2.87 interactive model: Iron binding site 2 out of 8 in 4dl1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 4dl1. 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: His336, D: Leu417, B: Hem202, B: Hoh354, B: Hoh366, D: Hoh721, conact list: Atom Atom Distance (A) Fe NE2 D:His336 2.21 Fe ND1 D:His336 4.29 Fe CD2 D:His336 3.19 Fe CE1 D:His336 3.18 Fe CG D:His336 4.33 Fe CD2 D:Leu417 4.72 Fe C2D B:Hem202 4.23 Fe NC B:Hem202 2.08 Fe CHB B:Hem202 3.42 Fe CHC B:Hem202 3.47 Fe C3D B:Hem202 4.24 Fe NA B:Hem202 2.10 Fe CHA B:Hem202 3.45 Fe C2A B:Hem202 4.37 Fe C1D B:Hem202 3.01 Fe C4A B:Hem202 3.09 Fe C4B B:Hem202 3.07 Fe C3A B:Hem202 4.33 Fe C4C B:Hem202 3.06 Fe C2B B:Hem202 4.24 Fe C1C B:Hem202 3.14 Fe C2C B:Hem202 4.34 Fe ND B:Hem202 2.04 Fe CHD B:Hem202 3.37 Fe C1B B:Hem202 3.03 Fe NB B:Hem202 2.05 Fe FE B:Hem202 0.00 Fe C3C B:Hem202 4.30 Fe C3B B:Hem202 4.28 Fe C4D B:Hem202 3.03 Fe C1A B:Hem202 3.14 Fe O B:Hoh354 2.70 Fe O B:Hoh366 4.88 Fe O D:Hoh721 4.99 interactive model: Iron binding site 3 out of 8 in 4dl1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 4dl1. 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: Gln91, G: His336, G: Leu417, E: Hem1602, E: Hoh1703, conact list: Atom Atom Distance (A) Fe NE2 E:Gln91 4.83 Fe NE2 G:His336 2.22 Fe ND1 G:His336 4.33 Fe CD2 G:His336 3.15 Fe CE1 G:His336 3.24 Fe CG G:His336 4.32 Fe CD2 G:Leu417 4.69 Fe C2D E:Hem1602 4.21 Fe NC E:Hem1602 2.04 Fe CHB E:Hem1602 3.39 Fe CHC E:Hem1602 3.41 Fe C3D E:Hem1602 4.26 Fe NA E:Hem1602 2.11 Fe CHA E:Hem1602 3.49 Fe C2A E:Hem1602 4.37 Fe C1D E:Hem1602 2.98 Fe C4A E:Hem1602 3.09 Fe C4B E:Hem1602 2.99 Fe C3A E:Hem1602 4.34 Fe C4C E:Hem1602 3.02 Fe C2B E:Hem1602 4.19 Fe C1C E:Hem1602 3.08 Fe C2C E:Hem1602 4.28 Fe ND E:Hem1602 2.02 Fe CHD E:Hem1602 3.35 Fe C1B E:Hem1602 2.98 Fe NB E:Hem1602 1.95 Fe FE E:Hem1602 0.00 Fe C3C E:Hem1602 4.24 Fe C3B E:Hem1602 4.19 Fe C4D E:Hem1602 3.07 Fe C1A E:Hem1602 3.15 Fe O E:Hoh1703 2.87 interactive model: Iron binding site 4 out of 8 in 4dl1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 4dl1. 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: Gln91, H: His336, H: Leu417, F: Hem202, F: Hoh307, conact list: Atom Atom Distance (A) Fe NE2 F:Gln91 4.92 Fe NE2 H:His336 2.21 Fe ND1 H:His336 4.31 Fe CD2 H:His336 3.18 Fe CE1 H:His336 3.20 Fe CG H:His336 4.34 Fe CD2 H:Leu417 4.94 Fe C2D F:Hem202 4.28 Fe NC F:Hem202 2.15 Fe CHB F:Hem202 3.35 Fe CHC F:Hem202 3.46 Fe C3D F:Hem202 4.28 Fe NA F:Hem202 2.07 Fe CHA F:Hem202 3.45 Fe C2A F:Hem202 4.34 Fe C1D F:Hem202 3.06 Fe C4A F:Hem202 3.06 Fe C4B F:Hem202 3.02 Fe C3A F:Hem202 4.29 Fe C4C F:Hem202 3.14 Fe C2B F:Hem202 4.17 Fe C1C F:Hem202 3.16 Fe C2C F:Hem202 4.38 Fe ND F:Hem202 2.10 Fe CHD F:Hem202 3.43 Fe C1B F:Hem202 2.96 Fe NB F:Hem202 2.00 Fe FE F:Hem202 0.00 Fe C3C F:Hem202 4.37 Fe C3B F:Hem202 4.20 Fe C4D F:Hem202 3.06 Fe C1A F:Hem202 3.11 Fe O F:Hoh307 2.88 interactive model: Iron binding site 5 out of 8 in 4dl1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 4dl1. 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: K: His336, K: Leu417, I: Hem1602, I: Hoh1770, conact list: Atom Atom Distance (A) Fe NE2 K:His336 2.20 Fe ND1 K:His336 4.30 Fe CD2 K:His336 3.18 Fe CE1 K:His336 3.19 Fe CG K:His336 4.33 Fe CD2 K:Leu417 4.80 Fe C2D I:Hem1602 4.29 Fe NC I:Hem1602 2.08 Fe CHB I:Hem1602 3.42 Fe CHC I:Hem1602 3.43 Fe C3D I:Hem1602 4.31 Fe NA I:Hem1602 2.15 Fe CHA I:Hem1602 3.48 Fe C2A I:Hem1602 4.39 Fe C1D I:Hem1602 3.07 Fe C4A I:Hem1602 3.14 Fe C4B I:Hem1602 3.06 Fe C3A I:Hem1602 4.38 Fe C4C I:Hem1602 3.08 Fe C2B I:Hem1602 4.24 Fe C1C I:Hem1602 3.08 Fe C2C I:Hem1602 4.31 Fe ND I:Hem1602 2.11 Fe CHD I:Hem1602 3.42 Fe C1B I:Hem1602 3.01 Fe NB I:Hem1602 2.01 Fe FE I:Hem1602 0.00 Fe C3C I:Hem1602 4.31 Fe C3B I:Hem1602 4.27 Fe C4D I:Hem1602 3.10 Fe C1A I:Hem1602 3.15 Fe O I:Hoh1770 2.66 interactive model: Iron binding site 6 out of 8 in 4dl1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 4dl1. 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: J: Gln91, L: His336, L: Leu417, J: Hem202, J: Hoh302, J: Hoh349, L: Hoh794, conact list: Atom Atom Distance (A) Fe NE2 J:Gln91 4.89 Fe CG J:Gln91 4.94 Fe NE2 L:His336 2.18 Fe ND1 L:His336 4.24 Fe CD2 L:His336 3.24 Fe CE1 L:His336 3.08 Fe CG L:His336 4.34 Fe CD2 L:Leu417 4.72 Fe C2D J:Hem202 4.33 Fe NC J:Hem202 2.10 Fe CHB J:Hem202 3.46 Fe CHC J:Hem202 3.44 Fe C3D J:Hem202 4.32 Fe NA J:Hem202 2.12 Fe CHA J:Hem202 3.45 Fe C2A J:Hem202 4.35 Fe C1D J:Hem202 3.12 Fe C4A J:Hem202 3.13 Fe C4B J:Hem202 3.05 Fe C3A J:Hem202 4.35 Fe C4C J:Hem202 3.10 Fe C2B J:Hem202 4.25 Fe C1C J:Hem202 3.10 Fe C2C J:Hem202 4.31 Fe ND J:Hem202 2.16 Fe CHD J:Hem202 3.46 Fe C1B J:Hem202 3.04 Fe NB J:Hem202 2.03 Fe FE J:Hem202 0.00 Fe C3C J:Hem202 4.31 Fe C3B J:Hem202 4.25 Fe C4D J:Hem202 3.10 Fe C1A J:Hem202 3.11 Fe O J:Hoh302 2.87 Fe O J:Hoh349 4.89 Fe O L:Hoh794 4.97 interactive model: Iron binding site 7 out of 8 in 4dl1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 4dl1. 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: M: Gln91, O: His336, O: Leu417, M: Hem1602, M: Hoh1713, conact list: Atom Atom Distance (A) Fe NE2 M:Gln91 4.75 Fe NE2 O:His336 2.20 Fe ND1 O:His336 4.30 Fe CD2 O:His336 3.19 Fe CE1 O:His336 3.18 Fe CG O:His336 4.33 Fe CD2 O:Leu417 4.74 Fe C2D M:Hem1602 4.28 Fe NC M:Hem1602 2.13 Fe CHB M:Hem1602 3.44 Fe CHC M:Hem1602 3.45 Fe C3D M:Hem1602 4.26 Fe NA M:Hem1602 2.06 Fe CHA M:Hem1602 3.38 Fe C2A M:Hem1602 4.29 Fe C1D M:Hem1602 3.07 Fe C4A M:Hem1602 3.11 Fe C4B M:Hem1602 3.02 Fe C3A M:Hem1602 4.32 Fe C4C M:Hem1602 3.14 Fe C2B M:Hem1602 4.21 Fe C1C M:Hem1602 3.14 Fe C2C M:Hem1602 4.36 Fe ND M:Hem1602 2.08 Fe CHD M:Hem1602 3.47 Fe C1B M:Hem1602 3.01 Fe NB M:Hem1602 2.01 Fe FE M:Hem1602 0.00 Fe C3C M:Hem1602 4.35 Fe C3B M:Hem1602 4.22 Fe C4D M:Hem1602 3.03 Fe C1A M:Hem1602 3.05 Fe O M:Hoh1713 2.88 interactive model: Iron binding site 8 out of 8 in 4dl1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 4dl1. 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: N: Gln91, P: His336, N: Hem202, N: Hoh307, conact list: Atom Atom Distance (A) Fe NE2 N:Gln91 4.78 Fe NE2 P:His336 2.20 Fe ND1 P:His336 4.30 Fe CD2 P:His336 3.16 Fe CE1 P:His336 3.19 Fe CG P:His336 4.32 Fe C2D N:Hem202 4.29 Fe NC N:Hem202 2.08 Fe CHB N:Hem202 3.48 Fe CHC N:Hem202 3.42 Fe C3D N:Hem202 4.26 Fe NA N:Hem202 2.06 Fe CHA N:Hem202 3.39 Fe C2A N:Hem202 4.29 Fe C1D N:Hem202 3.08 Fe C4A N:Hem202 3.10 Fe C4B N:Hem202 3.05 Fe C3A N:Hem202 4.31 Fe C4C N:Hem202 3.10 Fe C2B N:Hem202 4.30 Fe C1C N:Hem202 3.09 Fe C2C N:Hem202 4.30 Fe ND N:Hem202 2.09 Fe CHD N:Hem202 3.46 Fe C1B N:Hem202 3.10 Fe NB N:Hem202 2.09 Fe FE N:Hem202 0.00 Fe C3C N:Hem202 4.30 Fe C3B N:Hem202 4.28 Fe C4D N:Hem202 3.03 Fe C1A N:Hem202 3.06 Fe O N:Hoh307 2.88 interactive model: