Cobalt in the structure of Crystal Structure of Tnf-TNFR2 Complex (pdb 3alq)

The binding sites of Cobalt atom in the structure of Crystal Structure of Tnf-TNFR2 Complex (pdb code 3alq). This binding sites where shown with 5.0 Angstroms radius around Cobalt atom. The 3alq structure was solved by Y.MUKAI, T.NAKAMURA, Y.YAMAGATA, Y.TSUTSUMI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-3.0 Space group P212121 a (A) 74.470 b (A) 117.356 c (A) 246.835 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.3 Rfree (%) 28.1 Cobalt Binding Sites: Cobalt binding site 1 out of 6 in 3alq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cobalt in the PDB 3alq. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: R: His40, R: Asp54, R: Ser55, R: Glu57, R: Glu70, conact list: Atom Atom Distance (A) Co NE2 R:His40 2.31 Co ND1 R:His40 4.32 Co CD2 R:His40 3.37 Co CE1 R:His40 3.16 Co CG R:His40 4.45 Co CB R:Asp54 4.26 Co OD2 R:Asp54 4.24 Co OD1 R:Asp54 2.14 Co CG R:Asp54 3.39 Co O R:Ser55 3.91 Co OE1 R:Glu57 3.44 Co OE2 R:Glu57 3.05 Co CD R:Glu57 3.61 Co OE1 R:Glu70 4.14 interactive model: Cobalt binding site 2 out of 6 in 3alq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cobalt in the PDB 3alq. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: S: His40, S: Asp54, S: Ser55, S: Glu57, S: Glu70, conact list: Atom Atom Distance (A) Co NE2 S:His40 2.17 Co ND1 S:His40 4.22 Co CD2 S:His40 3.25 Co CE1 S:His40 3.05 Co CG S:His40 4.34 Co O S:Asp54 4.93 Co CB S:Asp54 3.82 Co OD2 S:Asp54 4.39 Co C S:Asp54 4.98 Co OD1 S:Asp54 2.25 Co CG S:Asp54 3.33 Co O S:Ser55 4.14 Co OE1 S:Glu57 3.35 Co OE2 S:Glu57 3.60 Co CD S:Glu57 3.75 Co OE1 S:Glu70 4.23 Co OE2 S:Glu70 4.73 Co CD S:Glu70 4.89 interactive model: Cobalt binding site 3 out of 6 in 3alq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cobalt in the PDB 3alq. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: T: His40, T: Asp54, T: Ser55, T: Glu57, T: Glu70, conact list: Atom Atom Distance (A) Co NE2 T:His40 2.37 Co ND1 T:His40 4.25 Co CD2 T:His40 3.58 Co CE1 T:His40 3.01 Co CG T:His40 4.55 Co CB T:Asp54 3.93 Co OD2 T:Asp54 4.47 Co OD1 T:Asp54 2.28 Co CG T:Asp54 3.41 Co O T:Ser55 4.43 Co OE1 T:Glu57 2.94 Co OE2 T:Glu57 2.75 Co CD T:Glu57 3.22 Co CG T:Glu57 4.75 Co OE1 T:Glu70 3.86 Co OE2 T:Glu70 4.67 Co CD T:Glu70 4.66 interactive model: Cobalt binding site 4 out of 6 in 3alq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cobalt in the PDB 3alq. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: U: His40, U: Asp54, U: Ser55, U: Glu70, conact list: Atom Atom Distance (A) Co NE2 U:His40 2.19 Co ND1 U:His40 4.22 Co CD2 U:His40 3.28 Co CE1 U:His40 3.04 Co CG U:His40 4.36 Co O U:Asp54 4.93 Co CB U:Asp54 3.75 Co OD2 U:Asp54 4.55 Co C U:Asp54 4.97 Co OD1 U:Asp54 2.47 Co CG U:Asp54 3.44 Co CA U:Asp54 4.98 Co O U:Ser55 4.16 Co OE1 U:Glu70 4.17 Co OE2 U:Glu70 4.81 Co CD U:Glu70 4.93 interactive model: Cobalt binding site 5 out of 6 in 3alq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cobalt in the PDB 3alq. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: V: His40, V: Asp54, V: Ser55, V: Glu57, V: Glu70, conact list: Atom Atom Distance (A) Co NE2 V:His40 2.31 Co ND1 V:His40 4.35 Co CD2 V:His40 3.36 Co CE1 V:His40 3.19 Co CG V:His40 4.46 Co O V:Asp54 4.80 Co CB V:Asp54 3.82 Co OD2 V:Asp54 4.85 Co C V:Asp54 4.88 Co OD1 V:Asp54 2.77 Co CG V:Asp54 3.68 Co CA V:Asp54 4.96 Co O V:Ser55 4.11 Co OE1 V:Glu57 3.71 Co OE2 V:Glu57 4.04 Co CD V:Glu57 4.30 Co OE1 V:Glu70 4.23 interactive model: Cobalt binding site 6 out of 6 in 3alq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cobalt in the PDB 3alq. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: W: His40, W: Asp54, W: Ser55, W: Glu57, W: Glu70, conact list: Atom Atom Distance (A) Co NE2 W:His40 2.44 Co ND1 W:His40 4.51 Co CD2 W:His40 3.37 Co CE1 W:His40 3.40 Co CG W:His40 4.53 Co CB W:Asp54 4.13 Co OD2 W:Asp54 4.41 Co OD1 W:Asp54 2.36 Co CG W:Asp54 3.47 Co O W:Ser55 4.05 Co OE1 W:Glu57 4.09 Co OE2 W:Glu57 3.19 Co CD W:Glu57 3.86 Co CG W:Glu57 5.00 Co OE1 W:Glu70 4.30 interactive model: