Iron in the structure of A New Catalytic Mechanism Of Periplasmic Nitrate Reductase From Desulfovibrio Desulfuricans Atcc 27774 From Crystallographic And Epr Data and Based on Detailed Analysis of the Sixth Ligand (pdb 2v45)

The binding sites of Iron atom in the structure of A New Catalytic Mechanism Of Periplasmic Nitrate Reductase From Desulfovibrio Desulfuricans Atcc 27774 From Crystallographic And Epr Data and Based on Detailed Analysis of the Sixth Ligand (pdb code 2v45). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 2v45 structure was solved by S.NAJMUDIN, P.J.GONZALEZ, J.TRINCAO, C.COELHO, A.MUKHOPADHYAY, C.C.ROMAO, I.MOURA, J.J.MOURA, C.D.BRONDINO, M.J.ROMAO, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 91.7-2.4 Space group P3121 a (A) 105.902 b (A) 105.902 c (A) 130.241 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 16.5 Rfree (%) 24 Iron Binding Sites: Iron binding site 1 out of 4 in 2v45 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 2v45. 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: Cys13, A: Cys16, A: Cys20, A: Leu46, A: Cys47, A: Gly50, A: Pro182, A: Val183, A: Sf4800, A: Hoh2035, conact list: Atom Atom Distance (A) Fe SG A:Cys13 4.80 Fe SG A:Cys16 4.48 Fe SG A:Cys20 4.90 Fe C A:Leu46 4.78 Fe O A:Cys47 4.91 Fe N A:Cys47 3.62 Fe CB A:Cys47 3.20 Fe SG A:Cys47 2.40 Fe C A:Cys47 4.65 Fe CA A:Cys47 3.93 Fe N A:Gly50 4.62 Fe CB A:Pro182 4.95 Fe CD A:Pro182 4.30 Fe CG A:Pro182 4.54 Fe CG2 A:Val183 4.27 Fe S1 A:Sf4800 3.93 Fe FE1 A:Sf4800 0.00 Fe FE3 A:Sf4800 2.69 Fe S4 A:Sf4800 2.31 Fe FE2 A:Sf4800 2.78 Fe S2 A:Sf4800 2.24 Fe FE4 A:Sf4800 2.80 Fe S3 A:Sf4800 2.38 Fe O A:Hoh2035 4.75 interactive model: Iron binding site 2 out of 4 in 2v45 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 2v45. 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: Cys13, A: Tyr15, A: Cys16, A: Thr18, A: Gly19, A: Cys20, A: Cys47, A: Pro182, A: Sf4800, A: Hoh2035, conact list: Atom Atom Distance (A) Fe SG A:Cys13 4.66 Fe CB A:Tyr15 4.71 Fe C A:Tyr15 4.58 Fe O A:Cys16 4.42 Fe N A:Cys16 3.45 Fe CB A:Cys16 3.32 Fe SG A:Cys16 2.04 Fe C A:Cys16 4.35 Fe CA A:Cys16 3.75 Fe N A:Thr18 4.77 Fe CB A:Thr18 3.95 Fe CG2 A:Thr18 4.85 Fe OG1 A:Thr18 4.12 Fe CA A:Thr18 4.89 Fe N A:Gly19 4.91 Fe SG A:Cys20 4.87 Fe SG A:Cys47 4.78 Fe CD A:Pro182 4.55 Fe S1 A:Sf4800 2.28 Fe FE1 A:Sf4800 2.78 Fe FE3 A:Sf4800 2.82 Fe S4 A:Sf4800 2.35 Fe FE2 A:Sf4800 0.00 Fe S2 A:Sf4800 3.88 Fe FE4 A:Sf4800 2.64 Fe S3 A:Sf4800 2.27 Fe O A:Hoh2035 4.30 interactive model: Iron binding site 3 out of 4 in 2v45 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 2v45. 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: Cys13, A: Cys16, A: Thr18, A: Cys20, A: Leu46, A: Cys47, A: Val183, A: Sf4800, conact list: Atom Atom Distance (A) Fe CB A:Cys13 4.82 Fe SG A:Cys13 4.73 Fe SG A:Cys16 4.52 Fe CB A:Thr18 4.29 Fe CG2 A:Thr18 4.29 Fe N A:Cys20 4.17 Fe CB A:Cys20 3.17 Fe SG A:Cys20 2.32 Fe CA A:Cys20 4.28 Fe CD2 A:Leu46 4.78 Fe CA A:Leu46 4.88 Fe N A:Cys47 4.65 Fe CB A:Val183 4.15 Fe CG2 A:Val183 3.79 Fe CG1 A:Val183 4.94 Fe S1 A:Sf4800 2.36 Fe FE1 A:Sf4800 2.69 Fe FE3 A:Sf4800 0.00 Fe S4 A:Sf4800 2.29 Fe FE2 A:Sf4800 2.82 Fe S2 A:Sf4800 2.26 Fe FE4 A:Sf4800 2.75 Fe S3 A:Sf4800 3.92 interactive model: Iron binding site 4 out of 4 in 2v45 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 2v45. 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: Cys13, A: Tyr15, A: Cys16, A: Cys20, A: Cys47, A: Gly50, A: Sf4800, conact list: Atom Atom Distance (A) Fe CB A:Cys13 3.13 Fe SG A:Cys13 2.25 Fe CA A:Cys13 4.58 Fe N A:Tyr15 4.77 Fe CB A:Tyr15 4.26 Fe CD1 A:Tyr15 4.60 Fe C A:Tyr15 4.78 Fe CG A:Tyr15 4.97 Fe CA A:Tyr15 4.77 Fe N A:Cys16 4.25 Fe SG A:Cys16 4.60 Fe CB A:Cys20 4.52 Fe SG A:Cys20 4.63 Fe SG A:Cys47 4.76 Fe N A:Gly50 4.66 Fe CA A:Gly50 4.43 Fe S1 A:Sf4800 2.26 Fe FE1 A:Sf4800 2.80 Fe FE3 A:Sf4800 2.75 Fe S4 A:Sf4800 3.89 Fe FE2 A:Sf4800 2.64 Fe S2 A:Sf4800 2.33 Fe FE4 A:Sf4800 0.00 Fe S3 A:Sf4800 2.25 interactive model: