Mercury in the structure of Crystal Structure of Human PPPDE1 (pdb 3ebq)

The binding sites of Mercury atom in the structure of Crystal Structure of Human PPPDE1 (pdb code 3ebq). This binding sites where shown with 5.0 Angstroms radius around Mercury atom. The 3ebq structure was solved by J.R.WALKER, M.AKUTSU, L.QIU, Y.LI, Y.SLESSAREV, C.BOUNTRA, J.WEIGELT, C.H.ARROWSMITH, A.M.EDWARDS, A.BOTCHKAREV, S.DHE-PAGANON, STRUCTURAL GENOMICS CONSORTIUM (SGC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 28.0-1.9 Space group P43212 a (A) 41.625 b (A) 41.625 c (A) 184.239 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 22.4 Rfree (%) 27.3 Mercury Binding Sites: Mercury binding site 1 out of 3 in 3ebq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Mercury in the PDB 3ebq. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Mercury atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Cys58, A: Pro59, A: Gly62, A: Thr63, conact list: Atom Atom Distance (A) Hg CB A:Cys58 3.13 Hg SG A:Cys58 2.46 Hg CA A:Cys58 4.24 Hg CD A:Pro59 4.89 Hg O A:Gly62 3.05 Hg C A:Gly62 3.97 Hg N A:Thr63 4.32 Hg CB A:Thr63 4.86 Hg C A:Thr63 4.76 Hg CA A:Thr63 3.96 interactive model: Mercury binding site 2 out of 3 in 3ebq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Mercury in the PDB 3ebq. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Mercury atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Trp37, A: His38, A: Tyr101, A: Asn107, A: Cys108, A: Asn109, A: Hg202, conact list: Atom Atom Distance (A) Hg O A:Trp37 4.20 Hg N A:His38 4.99 Hg CB A:His38 4.21 Hg ND1 A:His38 3.96 Hg CG A:His38 4.55 Hg CA A:His38 4.20 Hg OH A:Tyr101 4.13 Hg CB A:Asn107 4.02 Hg ND2 A:Asn107 4.44 Hg C A:Asn107 4.66 Hg OD1 A:Asn107 4.33 Hg CG A:Asn107 4.08 Hg CA A:Asn107 4.90 Hg N A:Cys108 3.66 Hg N A:Cys108 3.66 Hg CB A:Cys108 3.49 Hg CB A:Cys108 3.49 Hg SG A:Cys108 4.54 Hg SG A:Cys108 2.35 Hg C A:Cys108 4.55 Hg C A:Cys108 4.59 Hg CA A:Cys108 4.06 Hg CA A:Cys108 4.08 Hg N A:Asn109 4.18 Hg ND2 A:Asn109 3.86 Hg OD1 A:Asn109 4.51 Hg CG A:Asn109 4.30 Hg HG A:Hg202 0.00 Hg HG A:Hg202 3.86 interactive model: Mercury binding site 3 out of 3 in 3ebq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Mercury in the PDB 3ebq. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Mercury atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: His38, A: Phe50, A: Gly51, A: Tyr101, A: Cys108, A: Hg202, conact list: Atom Atom Distance (A) Hg NE2 A:His38 4.91 Hg ND1 A:His38 3.43 Hg CE1 A:His38 3.68 Hg CG A:His38 4.67 Hg O A:Phe50 3.88 Hg C A:Phe50 4.57 Hg CA A:Gly51 4.71 Hg CD1 A:Tyr101 4.96 Hg CZ A:Tyr101 4.30 Hg CE1 A:Tyr101 3.90 Hg OH A:Tyr101 3.99 Hg N A:Cys108 4.29 Hg N A:Cys108 4.28 Hg CB A:Cys108 3.15 Hg CB A:Cys108 3.18 Hg SG A:Cys108 2.29 Hg SG A:Cys108 3.72 Hg CA A:Cys108 4.26 Hg CA A:Cys108 4.25 Hg HG A:Hg202 3.86 Hg HG A:Hg202 0.00 interactive model: