Calcium in the structure of Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain. (pdb 2ox8)

The binding sites of Calcium atom in the structure of Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain. (pdb code 2ox8). This binding sites where shown with 5.0 Angstroms radius around Calcium atom. The 2ox8 structure was solved by W.I.WEIS, H.FEINBERG, K.DRICKAMER, M.E.TAYLOR, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.9-2.5 Space group P32 a (A) 80.422 b (A) 80.422 c (A) 67.159 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 23.3 Rfree (%) 30.8 Calcium Binding Sites: Calcium binding site 1 out of 6 in 2ox8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Calcium in the PDB 2ox8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Asp670, C: Glu674, C: Trp677, C: Asn697, C: Glu706, C: Asp707, C: Asp719, conact list: Atom Atom Distance (A) Ca CB C:Asp670 4.83 Ca OD2 C:Asp670 3.02 Ca OD1 C:Asp670 3.08 Ca CG C:Asp670 3.39 Ca OE1 C:Glu674 4.05 Ca OE2 C:Glu674 2.24 Ca CD C:Glu674 3.44 Ca CG C:Glu674 4.58 Ca CZ2 C:Trp677 4.13 Ca CE2 C:Trp677 4.96 Ca CH2 C:Trp677 4.58 Ca CB C:Asn697 3.66 Ca ND2 C:Asn697 4.31 Ca OD1 C:Asn697 2.48 Ca CG C:Asn697 3.25 Ca CA C:Asn697 4.19 Ca O C:Glu706 2.27 Ca N C:Glu706 4.25 Ca CB C:Glu706 4.76 Ca C C:Glu706 3.32 Ca CA C:Glu706 4.31 Ca N C:Asp707 4.07 Ca CB C:Asp707 4.43 Ca OD2 C:Asp707 4.60 Ca OD1 C:Asp707 2.56 Ca CG C:Asp707 3.70 Ca CA C:Asp707 4.01 Ca OD2 C:Asp719 4.44 interactive model: Calcium binding site 2 out of 6 in 2ox8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Calcium in the PDB 2ox8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Gln694, C: Asp696, C: Asn697, C: Trp698, C: Glu706, C: Asn718, C: Asp719, C: Phe720, conact list: Atom Atom Distance (A) Ca NE2 C:Gln694 4.77 Ca OE1 C:Gln694 2.98 Ca CD C:Gln694 4.15 Ca N C:Asp696 4.41 Ca CB C:Asp696 4.68 Ca OD2 C:Asp696 3.84 Ca OD1 C:Asp696 2.31 Ca CG C:Asp696 3.41 Ca CA C:Asp696 4.98 Ca N C:Asn697 4.50 Ca N C:Trp698 4.76 Ca CB C:Trp698 4.96 Ca OE1 C:Glu706 2.68 Ca CB C:Glu706 4.73 Ca OE2 C:Glu706 3.55 Ca CD C:Glu706 3.37 Ca CG C:Glu706 4.62 Ca CB C:Asn718 4.80 Ca ND2 C:Asn718 3.97 Ca C C:Asn718 4.73 Ca OD1 C:Asn718 2.46 Ca CG C:Asn718 3.51 Ca O C:Asp719 2.67 Ca N C:Asp719 3.69 Ca CB C:Asp719 4.05 Ca OD2 C:Asp719 3.17 Ca C C:Asp719 3.62 Ca OD1 C:Asp719 2.86 Ca CG C:Asp719 3.06 Ca CA C:Asp719 3.99 Ca N C:Phe720 4.80 interactive model: Calcium binding site 3 out of 6 in 2ox8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Calcium in the PDB 2ox8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Asp670, C: Ser671, C: Glu674, C: Pro704, C: Asp707, conact list: Atom Atom Distance (A) Ca O C:Asp670 4.86 Ca O C:Ser671 4.77 Ca CA C:Ser671 4.88 Ca OE1 C:Glu674 2.63 Ca OE2 C:Glu674 4.41 Ca CD C:Glu674 3.77 Ca CG C:Glu674 4.80 Ca O C:Pro704 3.60 Ca C C:Pro704 4.77 Ca CB C:Asp707 4.42 Ca OD2 C:Asp707 2.20 Ca OD1 C:Asp707 3.51 Ca CG C:Asp707 3.15 interactive model: Calcium binding site 4 out of 6 in 2ox8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Calcium in the PDB 2ox8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Asp670, D: Glu674, D: Asn675, D: Trp677, D: Asn697, D: Glu706, D: Asp707, D: Asp719, conact list: Atom Atom Distance (A) Ca CB D:Asp670 4.74 Ca OD2 D:Asp670 2.74 Ca OD1 D:Asp670 3.20 Ca CG D:Asp670 3.31 Ca OE1 D:Glu674 4.21 Ca OE2 D:Glu674 2.13 Ca CD D:Glu674 3.36 Ca CG D:Glu674 4.24 Ca N D:Asn675 4.63 Ca CZ2 D:Trp677 3.96 Ca CE2 D:Trp677 4.72 Ca NE1 D:Trp677 4.96 Ca CH2 D:Trp677 4.60 Ca N D:Asn697 4.90 Ca CB D:Asn697 3.82 Ca ND2 D:Asn697 4.75 Ca OD1 D:Asn697 2.70 Ca CG D:Asn697 3.56 Ca CA D:Asn697 4.11 Ca O D:Glu706 2.25 Ca N D:Glu706 4.39 Ca CB D:Glu706 4.75 Ca C D:Glu706 3.45 Ca CA D:Glu706 4.41 Ca N D:Asp707 4.31 Ca CB D:Asp707 4.74 Ca OD2 D:Asp707 4.96 Ca OD1 D:Asp707 2.87 Ca CG D:Asp707 4.04 Ca CA D:Asp707 4.27 Ca OD2 D:Asp719 4.41 interactive model: Calcium binding site 5 out of 6 in 2ox8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Calcium in the PDB 2ox8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Gln694, D: Asp696, D: Asn697, D: Trp698, D: Glu706, D: Asn718, D: Asp719, conact list: Atom Atom Distance (A) Ca NE2 D:Gln694 4.93 Ca OE1 D:Gln694 2.94 Ca CD D:Gln694 4.17 Ca N D:Asp696 4.01 Ca CB D:Asp696 4.06 Ca OD2 D:Asp696 2.55 Ca C D:Asp696 4.81 Ca OD1 D:Asp696 2.30 Ca CG D:Asp696 2.66 Ca CA D:Asp696 4.50 Ca N D:Asn697 4.27 Ca N D:Trp698 4.39 Ca CB D:Trp698 4.39 Ca OE1 D:Glu706 2.19 Ca CB D:Glu706 4.91 Ca OE2 D:Glu706 3.21 Ca CD D:Glu706 3.05 Ca CG D:Glu706 4.48 Ca ND2 D:Asn718 3.82 Ca OD1 D:Asn718 3.42 Ca CG D:Asn718 3.98 Ca O D:Asp719 2.95 Ca N D:Asp719 4.36 Ca CB D:Asp719 4.44 Ca OD2 D:Asp719 3.36 Ca C D:Asp719 4.04 Ca OD1 D:Asp719 2.89 Ca CG D:Asp719 3.29 Ca CA D:Asp719 4.53 interactive model: Calcium binding site 6 out of 6 in 2ox8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Calcium in the PDB 2ox8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Asp670, D: Ser671, D: Glu674, D: Pro704, D: Asp707, conact list: Atom Atom Distance (A) Ca O D:Asp670 4.43 Ca CA D:Ser671 4.78 Ca OE1 D:Glu674 2.31 Ca CB D:Glu674 4.85 Ca OE2 D:Glu674 4.16 Ca CD D:Glu674 3.52 Ca CG D:Glu674 4.62 Ca O D:Pro704 3.77 Ca C D:Pro704 4.96 Ca CB D:Asp707 4.44 Ca OD2 D:Asp707 2.15 Ca OD1 D:Asp707 3.48 Ca CG D:Asp707 3.13 interactive model: