Zinc in the structure of Structure of IGG2A Fab Fragment (D2.3) Complexed With Reaction Product (pdb 1yeg)

The binding sites of Zinc atom in the structure of Structure of IGG2A Fab Fragment (D2.3) Complexed With Reaction Product (pdb code 1yeg). This binding sites where shown with 5.0 Angstroms radius around Zinc atom. The 1yeg structure was solved by B.GIGANT, M.KNOSSOW, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 7.0-2.0 Space group P3121 a (A) 78.550 b (A) 78.550 c (A) 159.500 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 19.9 Rfree (%) 24 Zinc Binding Sites: Zinc binding site 1 out of 7 in 1yeg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 1yeg. 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: Zn219, L: Zn220, L: Zn221, L: Hoh578, L: Hoh584, L: Hoh598, L: Hoh599, L: Hoh600, L: Hoh608, L: Hoh632, conact list: Atom Atom Distance (A) Zn OD2 L:Asp151 3.90 Zn CG L:Asp151 4.69 Zn O L:Arg188 3.98 Zn OD1 L:Asn190 4.06 Zn ZN L:Zn219 3.41 Zn ZN L:Zn220 4.48 Zn ZN L:Zn221 3.28 Zn O L:Hoh578 3.22 Zn O L:Hoh584 4.24 Zn O L:Hoh598 1.76 Zn O L:Hoh599 1.61 Zn O L:Hoh600 3.70 Zn O L:Hoh608 4.36 Zn O L:Hoh632 4.87 interactive model: Zinc binding site 2 out of 7 in 1yeg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 1yeg. 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: Zn218, L: Hoh586, L: Hoh607, L: Hoh614, L: Hoh630, L: Hoh638, conact list: Atom Atom Distance (A) Zn ND1 L:His93 4.86 Zn ZN L:Zn218 3.33 Zn O L:Hoh586 4.08 Zn O L:Hoh607 1.85 Zn O L:Hoh614 1.73 Zn O L:Hoh630 4.31 Zn O L:Hoh638 1.72 interactive model: Zinc binding site 3 out of 7 in 1yeg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 1yeg. 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: Lys53, H: Asp100C, H: Tyr100D, H: Hoh582, H: Hoh587, H: Hoh618, conact list: Atom Atom Distance (A) Zn NE2 L:His49 2.29 Zn ND1 L:His49 4.29 Zn CD2 L:His49 3.30 Zn CE1 L:His49 3.16 Zn CG L:His49 4.39 Zn CB L:Lys53 4.34 Zn CG L:Lys53 4.52 Zn CB H:Asp100C 4.32 Zn OD2 H:Asp100C 2.95 Zn OD1 H:Asp100C 2.09 Zn CG H:Asp100C 2.86 Zn CA H:Asp100C 4.85 Zn O H:Tyr100D 4.47 Zn N H:Tyr100D 4.30 Zn O H:Hoh582 1.73 Zn O H:Hoh587 1.58 Zn O H:Hoh618 3.36 interactive model: Zinc binding site 4 out of 7 in 1yeg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 1yeg. 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: Zn216, L: Hoh563, L: Hoh586, L: Hoh607, L: Hoh614, L: Hoh630, L: Hoh638, conact list: Atom Atom Distance (A) Zn O L:Thr92 4.71 Zn NE2 L:His93 4.37 Zn N L:His93 4.96 Zn CB L:His93 3.55 Zn ND1 L:His93 2.43 Zn CD2 L:His93 4.38 Zn C L:His93 4.94 Zn CE1 L:His93 3.33 Zn CG L:His93 3.30 Zn CA L:His93 3.95 Zn N L:Phe94 4.84 Zn ZN L:Zn216 3.33 Zn O L:Hoh563 4.91 Zn O L:Hoh586 1.63 Zn O L:Hoh607 1.74 Zn O L:Hoh614 3.51 Zn O L:Hoh630 3.49 Zn O L:Hoh638 4.05 interactive model: Zinc binding site 5 out of 7 in 1yeg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Zinc in the PDB 1yeg. 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: Zn215, L: Zn220, L: Zn221, L: Hoh558, L: Hoh578, L: Hoh584, L: Hoh598, L: Hoh599, L: Hoh600, L: Hoh608, L: Hoh610, conact list: Atom Atom Distance (A) Zn O L:Ile150 4.92 Zn CG2 L:Ile150 4.37 Zn CB L:Asp151 3.44 Zn OD2 L:Asp151 1.95 Zn OD1 L:Asp151 4.10 Zn CG L:Asp151 3.00 Zn CA L:Asp151 4.85 Zn O L:Arg188 4.10 Zn C L:Arg188 4.66 Zn NE2 L:His189 4.50 Zn N L:His189 4.53 Zn CB L:His189 3.34 Zn ND1 L:His189 2.42 Zn CD2 L:His189 4.41 Zn C L:His189 4.77 Zn CE1 L:His189 3.46 Zn CG L:His189 3.22 Zn CA L:His189 3.66 Zn N L:Asn190 4.73 Zn ZN L:Zn215 3.41 Zn ZN L:Zn220 3.33 Zn ZN L:Zn221 4.94 Zn O L:Hoh558 4.02 Zn O L:Hoh578 3.65 Zn O L:Hoh584 1.76 Zn O L:Hoh598 2.07 Zn O L:Hoh599 4.12 Zn O L:Hoh600 3.83 Zn O L:Hoh608 3.64 Zn O L:Hoh610 4.68 interactive model: Zinc binding site 6 out of 7 in 1yeg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Zinc in the PDB 1yeg. 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: His189, L: Zn215, L: Zn219, L: Zn221, L: Hoh558, L: Hoh571, L: Hoh578, L: Hoh584, L: Hoh594, L: Hoh598, L: Hoh599, L: Hoh600, L: Hoh601, L: Hoh608, L: Hoh610, conact list: Atom Atom Distance (A) Zn O L:Asp151 4.99 Zn CB L:Asp151 4.39 Zn OD2 L:Asp151 4.62 Zn OG L:Ser153 4.67 Zn ND1 L:His189 4.98 Zn ZN L:Zn215 4.48 Zn ZN L:Zn219 3.33 Zn ZN L:Zn221 3.36 Zn O L:Hoh558 3.52 Zn O L:Hoh571 3.67 Zn O L:Hoh578 4.92 Zn O L:Hoh584 1.85 Zn O L:Hoh594 4.44 Zn O L:Hoh598 4.31 Zn O L:Hoh599 4.06 Zn O L:Hoh600 1.74 Zn O L:Hoh601 3.26 Zn O L:Hoh608 1.87 Zn O L:Hoh610 1.64 interactive model: Zinc binding site 7 out of 7 in 1yeg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Zinc in the PDB 1yeg. 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: Zn215, L: Zn219, L: Zn220, L: Hoh571, L: Hoh584, L: Hoh594, L: Hoh598, L: Hoh599, L: Hoh600, L: Hoh601, L: Hoh608, L: Hoh610, L: Hoh632, conact list: Atom Atom Distance (A) Zn ZN L:Zn215 3.28 Zn ZN L:Zn219 4.94 Zn ZN L:Zn220 3.36 Zn O L:Hoh571 3.73 Zn O L:Hoh584 4.48 Zn O L:Hoh594 4.66 Zn O L:Hoh598 4.45 Zn O L:Hoh599 1.98 Zn O L:Hoh600 1.93 Zn O L:Hoh601 2.54 Zn O L:Hoh608 3.63 Zn O L:Hoh610 4.36 Zn O L:Hoh632 2.40 interactive model: