Zinc in the structure of Crystal Structure Of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits. (pdb 1yhu)

The binding sites of Zinc atom in the structure of Crystal Structure Of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits. (pdb code 1yhu). This binding sites where shown with 5.0 Angstroms radius around Zinc atom. The 1yhu structure was solved by J.F.FLORES, C.R.FISHER, S.L.CARNEY, B.N.GREEN, J.K.FREYTAG, S.W.SCHAEFFER, W.E.ROYER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-3.1 Space group P41212 a (A) 195.840 b (A) 195.840 c (A) 308.820 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 24.3 Rfree (%) 27.1 Zinc Binding Sites: Zinc binding site 1 out of 12 in 1yhu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 1yhu. 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: B: His31, B: Ser35, B: Ile56, B: His57, J: Glu118, J: Ser123, conact list: Atom Atom Distance (A) Zn NE2 B:His31 2.12 Zn ND1 B:His31 4.06 Zn CD2 B:His31 3.30 Zn CE1 B:His31 2.85 Zn CG B:His31 4.30 Zn OG B:Ser35 4.70 Zn CD1 B:Ile56 4.32 Zn CG1 B:Ile56 4.78 Zn NE2 B:His57 2.02 Zn ND1 B:His57 3.96 Zn CD2 B:His57 3.21 Zn CE1 B:His57 2.74 Zn CG B:His57 4.21 Zn OE1 J:Glu118 2.49 Zn OE2 J:Glu118 2.22 Zn CD J:Glu118 2.70 Zn CG J:Glu118 4.23 Zn CB J:Ser123 4.61 interactive model: Zinc binding site 2 out of 12 in 1yhu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 1yhu. 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: B: His36, B: His40, B: His111, B: Met115, conact list: Atom Atom Distance (A) Zn NE2 B:His36 2.26 Zn ND1 B:His36 3.97 Zn CD2 B:His36 3.54 Zn CE1 B:His36 2.70 Zn CG B:His36 4.40 Zn NE2 B:His40 2.18 Zn ND1 B:His40 4.08 Zn CD2 B:His40 3.39 Zn CE1 B:His40 2.84 Zn CG B:His40 4.37 Zn NE2 B:His111 2.24 Zn ND1 B:His111 4.21 Zn CD2 B:His111 3.39 Zn CE1 B:His111 2.99 Zn CG B:His111 4.43 Zn CE B:Met115 4.39 Zn CG B:Met115 4.49 Zn SD B:Met115 4.84 interactive model: Zinc binding site 3 out of 12 in 1yhu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 1yhu. 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: B: Glu118, B: Ser123, F: His31, F: Ser35, F: Ile56, F: His57, conact list: Atom Atom Distance (A) Zn OE1 B:Glu118 2.43 Zn OE2 B:Glu118 2.28 Zn CD B:Glu118 2.71 Zn CG B:Glu118 4.24 Zn CB B:Ser123 4.67 Zn NE2 F:His31 2.17 Zn ND1 F:His31 4.10 Zn CD2 F:His31 3.34 Zn CE1 F:His31 2.89 Zn CG F:His31 4.34 Zn OG F:Ser35 4.67 Zn CD1 F:Ile56 4.30 Zn CG1 F:Ile56 4.74 Zn NE2 F:His57 2.00 Zn ND1 F:His57 3.92 Zn CD2 F:His57 3.21 Zn CE1 F:His57 2.69 Zn CG F:His57 4.19 interactive model: Zinc binding site 4 out of 12 in 1yhu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 1yhu. 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: F: His36, F: His40, F: His111, F: Met115, conact list: Atom Atom Distance (A) Zn NE2 F:His36 2.22 Zn ND1 F:His36 3.96 Zn CD2 F:His36 3.50 Zn CE1 F:His36 2.69 Zn CG F:His36 4.37 Zn NE2 F:His40 2.21 Zn ND1 F:His40 4.13 Zn CD2 F:His40 3.41 Zn CE1 F:His40 2.90 Zn CG F:His40 4.41 Zn NE2 F:His111 2.16 Zn ND1 F:His111 4.13 Zn CD2 F:His111 3.32 Zn CE1 F:His111 2.92 Zn CG F:His111 4.35 Zn CE F:Met115 4.36 Zn CG F:Met115 4.42 Zn SD F:Met115 4.76 interactive model: Zinc binding site 5 out of 12 in 1yhu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Zinc in the PDB 1yhu. 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: F: Glu118, F: Ser123, J: His31, J: Ser35, J: Ile56, J: His57, conact list: Atom Atom Distance (A) Zn OE1 F:Glu118 2.48 Zn OE2 F:Glu118 2.12 Zn CD F:Glu118 2.63 Zn CG F:Glu118 4.14 Zn CB F:Ser123 4.34 Zn NE2 J:His31 2.12 Zn ND1 J:His31 4.08 Zn CD2 J:His31 3.27 Zn CE1 J:His31 2.87 Zn CG J:His31 4.29 Zn OG J:Ser35 4.79 Zn CD1 J:Ile56 4.35 Zn CG1 J:Ile56 4.79 Zn NE2 J:His57 1.94 Zn ND1 J:His57 3.88 Zn CD2 J:His57 3.13 Zn CE1 J:His57 2.68 Zn CG J:His57 4.12 interactive model: Zinc binding site 6 out of 12 in 1yhu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Zinc in the PDB 1yhu. 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: J: His36, J: His40, J: His111, J: Met115, conact list: Atom Atom Distance (A) Zn NE2 J:His36 2.26 Zn ND1 J:His36 3.98 Zn CD2 J:His36 3.55 Zn CE1 J:His36 2.70 Zn CG J:His36 4.41 Zn NE2 J:His40 2.28 Zn ND1 J:His40 4.17 Zn CD2 J:His40 3.49 Zn CE1 J:His40 2.93 Zn CG J:His40 4.47 Zn NE2 J:His111 2.26 Zn ND1 J:His111 4.21 Zn CD2 J:His111 3.43 Zn CE1 J:His111 2.99 Zn CG J:His111 4.45 Zn CE J:Met115 4.35 Zn CG J:Met115 4.46 Zn SD J:Met115 4.82 interactive model: Zinc binding site 7 out of 12 in 1yhu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Zinc in the PDB 1yhu. 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: N: His31, N: Ser35, N: Ile56, N: His57, V: Glu118, V: Ser123, conact list: Atom Atom Distance (A) Zn NE2 N:His31 2.26 Zn ND1 N:His31 4.16 Zn CD2 N:His31 3.45 Zn CE1 N:His31 2.93 Zn CG N:His31 4.43 Zn OG N:Ser35 4.63 Zn CD1 N:Ile56 4.34 Zn CG1 N:Ile56 4.81 Zn NE2 N:His57 2.09 Zn ND1 N:His57 3.99 Zn CD2 N:His57 3.32 Zn CE1 N:His57 2.75 Zn CG N:His57 4.28 Zn OE1 V:Glu118 2.45 Zn OE2 V:Glu118 2.30 Zn CD V:Glu118 2.70 Zn CG V:Glu118 4.21 Zn CB V:Ser123 4.57 interactive model: Zinc binding site 8 out of 12 in 1yhu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Zinc in the PDB 1yhu. 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: N: His36, N: His40, N: His111, N: Met115, conact list: Atom Atom Distance (A) Zn NE2 N:His36 2.36 Zn ND1 N:His36 4.05 Zn CD2 N:His36 3.66 Zn CE1 N:His36 2.76 Zn CG N:His36 4.50 Zn NE2 N:His40 2.30 Zn ND1 N:His40 4.18 Zn CD2 N:His40 3.53 Zn CE1 N:His40 2.92 Zn CG N:His40 4.50 Zn NE2 N:His111 2.26 Zn ND1 N:His111 4.19 Zn CD2 N:His111 3.46 Zn CE1 N:His111 2.95 Zn CG N:His111 4.46 Zn CE N:Met115 4.32 Zn CG N:Met115 4.50 Zn SD N:Met115 4.78 interactive model: Zinc binding site 9 out of 12 in 1yhu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Zinc in the PDB 1yhu. 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: N: Glu118, N: Ser123, R: His31, R: Ser35, R: Ile56, R: His57, conact list: Atom Atom Distance (A) Zn OE1 N:Glu118 2.52 Zn OE2 N:Glu118 2.28 Zn CD N:Glu118 2.75 Zn CG N:Glu118 4.27 Zn CB N:Ser123 4.58 Zn NE2 R:His31 2.12 Zn ND1 R:His31 4.04 Zn CD2 R:His31 3.30 Zn CE1 R:His31 2.83 Zn CG R:His31 4.29 Zn OG R:Ser35 4.58 Zn CD1 R:Ile56 4.29 Zn CG1 R:Ile56 4.77 Zn NE2 R:His57 2.07 Zn ND1 R:His57 4.00 Zn CD2 R:His57 3.26 Zn CE1 R:His57 2.79 Zn CG R:His57 4.25 interactive model: Zinc binding site 10 out of 12 in 1yhu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Zinc in the PDB 1yhu. 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: R: His36, R: His40, R: His111, R: Met115, conact list: Atom Atom Distance (A) Zn NE2 R:His36 2.20 Zn ND1 R:His36 3.91 Zn CD2 R:His36 3.49 Zn CE1 R:His36 2.63 Zn CG R:His36 4.34 Zn NE2 R:His40 2.27 Zn ND1 R:His40 4.19 Zn CD2 R:His40 3.47 Zn CE1 R:His40 2.95 Zn CG R:His40 4.46 Zn NE2 R:His111 2.24 Zn ND1 R:His111 4.19 Zn CD2 R:His111 3.42 Zn CE1 R:His111 2.96 Zn CG R:His111 4.44 Zn CE R:Met115 4.30 Zn CG R:Met115 4.41 Zn SD R:Met115 4.76 interactive model: Zinc binding site 11 out of 12 in 1yhu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Zinc in the PDB 1yhu. 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: R: Glu118, R: Ser123, V: His31, V: Ser35, V: Ile56, V: His57, conact list: Atom Atom Distance (A) Zn OE1 R:Glu118 2.47 Zn OE2 R:Glu118 2.17 Zn CD R:Glu118 2.64 Zn CG R:Glu118 4.17 Zn CB R:Ser123 4.49 Zn NE2 V:His31 2.15 Zn ND1 V:His31 4.05 Zn CD2 V:His31 3.35 Zn CE1 V:His31 2.82 Zn CG V:His31 4.33 Zn OG V:Ser35 4.62 Zn CD1 V:Ile56 4.36 Zn CG1 V:Ile56 4.81 Zn NE2 V:His57 2.09 Zn ND1 V:His57 4.02 Zn CD2 V:His57 3.28 Zn CE1 V:His57 2.80 Zn CG V:His57 4.28 interactive model: Zinc binding site 12 out of 12 in 1yhu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Zinc in the PDB 1yhu. 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: V: His36, V: His40, V: His111, V: Met115, conact list: Atom Atom Distance (A) Zn NE2 V:His36 2.23 Zn ND1 V:His36 3.93 Zn CD2 V:His36 3.53 Zn CE1 V:His36 2.65 Zn CG V:His36 4.37 Zn NE2 V:His40 2.29 Zn ND1 V:His40 4.20 Zn CD2 V:His40 3.49 Zn CE1 V:His40 2.97 Zn CG V:His40 4.48 Zn NE2 V:His111 2.22 Zn ND1 V:His111 4.17 Zn CD2 V:His111 3.40 Zn CE1 V:His111 2.94 Zn CG V:His111 4.42 Zn CE V:Met115 4.29 Zn CG V:Met115 4.39 Zn SD V:Met115 4.74 interactive model: