Iron in the structure of Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli (pdb 2nya)

The binding sites of Iron atom in the structure of Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli (pdb code 2nya). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 2nya structure was solved by B.J.N.JEPSON, D.J.RICHARDSON, A.M.HEMMINGS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-2.5 Space group P1211 a (A) 69.449 b (A) 94.596 c (A) 131.211 alpha (°) 90.00 beta (°) 96.34 gamma (°) 90.00 Rfactor (%) 18.1 Rfree (%) 24.3 Iron Binding Sites: Iron binding site 1 out of 8 in 2nya Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 2nya. 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: Cys10, A: Cys13, A: Cys17, A: Asn44, A: Cys45, A: Lys47, A: Gly48, A: Pro185, A: Ile186, A: Sf42001, A: Hoh4250, conact list: Atom Atom Distance (A) Fe SG A:Cys10 4.93 Fe SG A:Cys13 4.80 Fe SG A:Cys17 4.91 Fe C A:Asn44 4.89 Fe O A:Cys45 4.89 Fe N A:Cys45 3.80 Fe CB A:Cys45 3.32 Fe SG A:Cys45 2.43 Fe C A:Cys45 4.78 Fe CA A:Cys45 4.11 Fe NZ A:Lys47 4.69 Fe N A:Gly48 4.39 Fe CA A:Gly48 4.81 Fe CD A:Pro185 4.77 Fe CG A:Pro185 4.76 Fe CD1 A:Ile186 4.45 Fe S1 A:Sf42001 3.84 Fe FE1 A:Sf42001 0.00 Fe FE3 A:Sf42001 2.66 Fe S4 A:Sf42001 2.32 Fe FE2 A:Sf42001 2.70 Fe S2 A:Sf42001 2.34 Fe FE4 A:Sf42001 2.72 Fe S3 A:Sf42001 2.30 Fe O A:Hoh4250 4.67 interactive model: Iron binding site 2 out of 8 in 2nya Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 2nya. 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: Cys10, A: Cys13, A: Thr15, A: Cys17, A: Cys45, A: Ile186, A: Sf42001, conact list: Atom Atom Distance (A) Fe CB A:Cys10 4.78 Fe SG A:Cys10 4.78 Fe SG A:Cys13 4.93 Fe CB A:Thr15 4.47 Fe CG2 A:Thr15 4.54 Fe N A:Cys17 4.15 Fe CB A:Cys17 3.13 Fe SG A:Cys17 2.32 Fe CA A:Cys17 4.23 Fe N A:Cys45 4.96 Fe CB A:Ile186 4.29 Fe CD1 A:Ile186 4.00 Fe CG1 A:Ile186 4.26 Fe S1 A:Sf42001 2.32 Fe FE1 A:Sf42001 2.70 Fe FE3 A:Sf42001 2.77 Fe S4 A:Sf42001 2.28 Fe FE2 A:Sf42001 0.00 Fe S2 A:Sf42001 3.99 Fe FE4 A:Sf42001 2.84 Fe S3 A:Sf42001 2.31 interactive model: Iron binding site 3 out of 8 in 2nya Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 2nya. 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: Cys10, A: Phe12, A: Cys13, A: Thr15, A: Cys17, A: Cys45, A: Pro185, A: Sf42001, A: Hoh4250, conact list: Atom Atom Distance (A) Fe SG A:Cys10 4.76 Fe C A:Phe12 4.83 Fe O A:Cys13 4.12 Fe N A:Cys13 3.80 Fe CB A:Cys13 3.44 Fe SG A:Cys13 2.45 Fe C A:Cys13 4.22 Fe CA A:Cys13 3.95 Fe N A:Thr15 4.76 Fe CB A:Thr15 3.98 Fe CG2 A:Thr15 4.88 Fe OG1 A:Thr15 4.03 Fe CA A:Thr15 4.96 Fe SG A:Cys17 4.78 Fe SG A:Cys45 4.76 Fe CD A:Pro185 4.78 Fe S1 A:Sf42001 2.32 Fe FE1 A:Sf42001 2.66 Fe FE3 A:Sf42001 0.00 Fe S4 A:Sf42001 2.30 Fe FE2 A:Sf42001 2.77 Fe S2 A:Sf42001 2.30 Fe FE4 A:Sf42001 2.71 Fe S3 A:Sf42001 3.87 Fe O A:Hoh4250 4.13 interactive model: Iron binding site 4 out of 8 in 2nya Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 2nya. 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: Cys10, A: Phe12, A: Cys13, A: Cys17, A: Cys45, A: Gly48, A: Sf42001, conact list: Atom Atom Distance (A) Fe CB A:Cys10 3.25 Fe SG A:Cys10 2.32 Fe CA A:Cys10 4.69 Fe N A:Phe12 4.62 Fe CB A:Phe12 4.22 Fe CD1 A:Phe12 4.90 Fe C A:Phe12 4.85 Fe CA A:Phe12 4.71 Fe N A:Cys13 4.41 Fe SG A:Cys13 4.99 Fe CB A:Cys17 4.71 Fe SG A:Cys17 4.83 Fe SG A:Cys45 4.59 Fe N A:Gly48 4.40 Fe CA A:Gly48 4.26 Fe S1 A:Sf42001 2.33 Fe FE1 A:Sf42001 2.72 Fe FE3 A:Sf42001 2.71 Fe S4 A:Sf42001 3.96 Fe FE2 A:Sf42001 2.84 Fe S2 A:Sf42001 2.26 Fe FE4 A:Sf42001 0.00 Fe S3 A:Sf42001 2.31 interactive model: Iron binding site 5 out of 8 in 2nya Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 2nya. 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: Cys13, F: Cys17, F: Cys45, F: Lys47, F: Gly48, F: Pro185, F: Ile186, F: Sf45001, F: Hoh7259, conact list: Atom Atom Distance (A) Fe SG F:Cys13 4.84 Fe SG F:Cys17 4.85 Fe N F:Cys45 4.05 Fe CB F:Cys45 3.15 Fe SG F:Cys45 2.48 Fe C F:Cys45 4.85 Fe CA F:Cys45 4.16 Fe CE F:Lys47 4.90 Fe NZ F:Lys47 4.64 Fe N F:Gly48 4.48 Fe CA F:Gly48 4.99 Fe CB F:Pro185 4.85 Fe CD F:Pro185 4.50 Fe CG F:Pro185 4.41 Fe CD1 F:Ile186 4.83 Fe S1 F:Sf45001 3.94 Fe FE1 F:Sf45001 0.00 Fe FE3 F:Sf45001 2.69 Fe S4 F:Sf45001 2.30 Fe FE2 F:Sf45001 2.73 Fe S2 F:Sf45001 2.32 Fe FE4 F:Sf45001 2.79 Fe S3 F:Sf45001 2.30 Fe O F:Hoh7259 4.44 interactive model: Iron binding site 6 out of 8 in 2nya Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 2nya. 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: Cys10, F: Thr15, F: Cys17, F: Ile186, F: Sf45001, conact list: Atom Atom Distance (A) Fe CB F:Cys10 4.83 Fe SG F:Cys10 4.76 Fe CB F:Thr15 4.66 Fe CG2 F:Thr15 4.84 Fe N F:Cys17 4.29 Fe CB F:Cys17 3.09 Fe SG F:Cys17 2.22 Fe CA F:Cys17 4.27 Fe CB F:Ile186 4.34 Fe CD1 F:Ile186 4.32 Fe CG1 F:Ile186 4.24 Fe S1 F:Sf45001 2.31 Fe FE1 F:Sf45001 2.73 Fe FE3 F:Sf45001 2.83 Fe S4 F:Sf45001 2.30 Fe FE2 F:Sf45001 0.00 Fe S2 F:Sf45001 3.96 Fe FE4 F:Sf45001 2.74 Fe S3 F:Sf45001 2.28 interactive model: Iron binding site 7 out of 8 in 2nya Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 2nya. 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: Cys10, F: Phe12, F: Cys13, F: Thr15, F: Cys17, F: Cys45, F: Pro185, F: Sf45001, F: Hoh7259, conact list: Atom Atom Distance (A) Fe SG F:Cys10 4.81 Fe CB F:Phe12 4.89 Fe C F:Phe12 4.81 Fe O F:Cys13 4.25 Fe N F:Cys13 3.69 Fe CB F:Cys13 3.51 Fe SG F:Cys13 2.51 Fe C F:Cys13 4.30 Fe CA F:Cys13 3.95 Fe N F:Thr15 4.82 Fe CB F:Thr15 4.06 Fe OG1 F:Thr15 3.96 Fe SG F:Cys17 4.66 Fe SG F:Cys45 4.90 Fe CD F:Pro185 4.58 Fe S1 F:Sf45001 2.34 Fe FE1 F:Sf45001 2.69 Fe FE3 F:Sf45001 0.00 Fe S4 F:Sf45001 2.34 Fe FE2 F:Sf45001 2.83 Fe S2 F:Sf45001 2.28 Fe FE4 F:Sf45001 2.62 Fe S3 F:Sf45001 3.86 Fe O F:Hoh7259 4.08 interactive model: Iron binding site 8 out of 8 in 2nya Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 2nya. 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: Cys10, F: Phe12, F: Cys13, F: Cys17, F: Cys45, F: Gly48, F: Sf45001, conact list: Atom Atom Distance (A) Fe CB F:Cys10 3.34 Fe SG F:Cys10 2.45 Fe CA F:Cys10 4.77 Fe N F:Phe12 4.67 Fe CB F:Phe12 4.15 Fe CD1 F:Phe12 4.92 Fe C F:Phe12 4.86 Fe CA F:Phe12 4.70 Fe N F:Cys13 4.30 Fe SG F:Cys13 4.95 Fe CB F:Cys17 4.65 Fe SG F:Cys17 4.67 Fe SG F:Cys45 4.67 Fe N F:Gly48 4.59 Fe CA F:Gly48 4.55 Fe S1 F:Sf45001 2.35 Fe FE1 F:Sf45001 2.79 Fe FE3 F:Sf45001 2.62 Fe S4 F:Sf45001 3.88 Fe FE2 F:Sf45001 2.74 Fe S2 F:Sf45001 2.28 Fe FE4 F:Sf45001 0.00 Fe S3 F:Sf45001 2.32 interactive model: