Zinc in the structure of Catalytic Antibody D2.3 Complex (pdb 1yei)

The binding sites of Zinc atom in the structure of Catalytic Antibody D2.3 Complex (pdb code 1yei). This binding sites where shown with 5.0 Angstroms radius around Zinc atom. The 1yei structure was solved by B.GIGANT, M.KNOSSOW, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 7.0-1.9 Space group P3121 a (A) 78.345 b (A) 78.345 c (A) 159.278 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 20.4 Rfree (%) 24.1 Zinc Binding Sites: Zinc binding site 1 out of 7 in 1yei Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 1yei. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: L: Ile150, L: Asp151, L: Arg188, L: His189, L: Asn190, L: Zn604, L: Zn605, L: Zn606, L: Hoh650, L: Hoh658, L: Hoh683, L: Hoh684, L: Hoh685, L: Hoh686, conact list: Atom Atom Distance (A) Zn O L:Ile150 4.92 Zn CG2 L:Ile150 4.42 Zn CB L:Asp151 3.40 Zn OD2 L:Asp151 1.96 Zn OD1 L:Asp151 4.09 Zn CG L:Asp151 2.98 Zn CA L:Asp151 4.82 Zn O L:Arg188 4.24 Zn C L:Arg188 4.75 Zn NE2 L:His189 4.55 Zn N L:His189 4.54 Zn CB L:His189 3.45 Zn ND1 L:His189 2.54 Zn CD2 L:His189 4.48 Zn C L:His189 4.71 Zn CE1 L:His189 3.53 Zn CG L:His189 3.33 Zn CA L:His189 3.65 Zn N L:Asn190 4.64 Zn ZN L:Zn604 4.92 Zn ZN L:Zn605 3.30 Zn ZN L:Zn606 3.40 Zn O L:Hoh650 3.89 Zn O L:Hoh658 3.98 Zn O L:Hoh683 4.34 Zn O L:Hoh684 1.78 Zn O L:Hoh685 3.87 Zn O L:Hoh686 1.85 interactive model: Zinc binding site 2 out of 7 in 1yei Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 1yei. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: L: His93, L: Zn602, L: Hoh619, L: Hoh639, L: Hoh654, L: Hoh666, L: Hoh669, L: Hoh682, conact list: Atom Atom Distance (A) Zn ND1 L:His93 4.90 Zn ZN L:Zn602 3.35 Zn O L:Hoh619 2.07 Zn O L:Hoh639 4.41 Zn O L:Hoh654 4.34 Zn O L:Hoh666 1.70 Zn O L:Hoh669 3.58 Zn O L:Hoh682 4.28 interactive model: Zinc binding site 3 out of 7 in 1yei Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 1yei. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: L: His49, L: Leu50, L: Lys53, H: Asp100C, H: Tyr100D, L: Hoh629, H: Hoh292, conact list: Atom Atom Distance (A) Zn NE2 L:His49 2.34 Zn ND1 L:His49 4.34 Zn CD2 L:His49 3.22 Zn CE1 L:His49 3.29 Zn CG L:His49 4.35 Zn CD1 L:Leu50 4.96 Zn CB L:Lys53 4.37 Zn CG L:Lys53 4.63 Zn CB H:Asp100C 4.32 Zn OD2 H:Asp100C 2.96 Zn OD1 H:Asp100C 2.09 Zn CG H:Asp100C 2.86 Zn CA H:Asp100C 4.83 Zn O H:Tyr100D 4.54 Zn N H:Tyr100D 4.33 Zn CD1 H:Tyr100D 4.98 Zn O L:Hoh629 1.81 Zn O H:Hoh292 1.68 interactive model: Zinc binding site 4 out of 7 in 1yei Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 1yei. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: L: Thr92, L: His93, L: Phe94, L: Zn607, L: Hoh619, L: Hoh625, L: Hoh639, L: Hoh666, L: Hoh682, conact list: Atom Atom Distance (A) Zn O L:Thr92 4.73 Zn NE2 L:His93 4.45 Zn N L:His93 4.95 Zn CB L:His93 3.50 Zn ND1 L:His93 2.43 Zn CD2 L:His93 4.43 Zn C L:His93 4.95 Zn CE1 L:His93 3.40 Zn CG L:His93 3.29 Zn CA L:His93 3.96 Zn N L:Phe94 4.92 Zn ZN L:Zn607 3.35 Zn O L:Hoh619 1.77 Zn O L:Hoh625 4.63 Zn O L:Hoh639 3.53 Zn O L:Hoh666 3.58 Zn O L:Hoh682 1.69 interactive model: Zinc binding site 5 out of 7 in 1yei Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Zinc in the PDB 1yei. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: L: Zn603, L: Zn605, L: Zn606, L: Hoh608, L: Hoh658, L: Hoh680, L: Hoh683, L: Hoh684, L: Hoh685, L: Hoh686, conact list: Atom Atom Distance (A) Zn ZN L:Zn603 4.92 Zn ZN L:Zn605 3.43 Zn ZN L:Zn606 3.24 Zn O L:Hoh608 1.88 Zn O L:Hoh658 3.85 Zn O L:Hoh680 4.65 Zn O L:Hoh683 1.67 Zn O L:Hoh684 4.32 Zn O L:Hoh685 2.01 Zn O L:Hoh686 4.06 interactive model: Zinc binding site 6 out of 7 in 1yei Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Zinc in the PDB 1yei. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: L: Asp151, L: Ser153, L: Zn603, L: Zn604, L: Zn606, L: Hoh608, L: Hoh650, L: Hoh683, L: Hoh684, L: Hoh685, L: Hoh686, conact list: Atom Atom Distance (A) Zn CB L:Asp151 4.38 Zn OD2 L:Asp151 4.67 Zn OG L:Ser153 4.80 Zn ZN L:Zn603 3.30 Zn ZN L:Zn604 3.43 Zn ZN L:Zn606 4.50 Zn O L:Hoh608 3.86 Zn O L:Hoh650 3.45 Zn O L:Hoh683 4.11 Zn O L:Hoh684 1.70 Zn O L:Hoh685 1.63 Zn O L:Hoh686 3.95 interactive model: Zinc binding site 7 out of 7 in 1yei Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Zinc in the PDB 1yei. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: L: Asp151, L: Arg188, L: Asn190, L: Zn603, L: Zn604, L: Zn605, L: Hoh608, L: Hoh658, L: Hoh680, L: Hoh683, L: Hoh684, L: Hoh685, L: Hoh686, conact list: Atom Atom Distance (A) Zn OD2 L:Asp151 3.97 Zn CG L:Asp151 4.67 Zn O L:Arg188 4.05 Zn OD1 L:Asn190 3.97 Zn ZN L:Zn603 3.40 Zn ZN L:Zn604 3.24 Zn ZN L:Zn605 4.50 Zn O L:Hoh608 4.64 Zn O L:Hoh658 2.24 Zn O L:Hoh680 4.93 Zn O L:Hoh683 1.73 Zn O L:Hoh684 4.13 Zn O L:Hoh685 3.84 Zn O L:Hoh686 1.65 interactive model: