Zinc in the structure of Crystal Structure of A Two-Domain Protein Containing Predicted Php- Like Metal-Dependent Phosphoesterase (BVU_3505) From Bacteroides Vulgatus Atcc 8482 At 2.20 A Resolution (pdb 3e38)

The binding sites of Zinc atom in the structure of Crystal Structure of A Two-Domain Protein Containing Predicted Php- Like Metal-Dependent Phosphoesterase (BVU_3505) From Bacteroides Vulgatus Atcc 8482 At 2.20 A Resolution (pdb code 3e38). This binding sites where shown with 5.0 Angstroms radius around Zinc atom. The 3e38 structure was solved by JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 29.6-2.2 Space group P21212 a (A) 95.680 b (A) 117.820 c (A) 79.560 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.2 Rfree (%) 22.5 Zinc Binding Sites: Zinc binding site 1 out of 6 in 3e38 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 3e38. 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: A: His44, A: His76, A: Glu113, A: His122, A: Asn156, A: His157, A: Asp214, A: Zn2, A: Cac7, A: Hoh378, conact list: Atom Atom Distance (A) Zn NE2 A:His44 4.44 Zn CE1 A:His44 4.49 Zn ND1 A:His76 4.77 Zn CE1 A:His76 4.09 Zn OE1 A:Glu113 3.51 Zn OE2 A:Glu113 2.22 Zn CD A:Glu113 3.16 Zn CG A:Glu113 4.44 Zn NE2 A:His122 4.29 Zn CB A:His122 3.63 Zn ND1 A:His122 2.28 Zn CD2 A:His122 4.39 Zn CE1 A:His122 3.16 Zn CG A:His122 3.30 Zn CB A:Asn156 4.75 Zn ND2 A:Asn156 4.46 Zn NE2 A:His157 2.18 Zn ND1 A:His157 4.27 Zn CD2 A:His157 3.17 Zn CE1 A:His157 3.15 Zn CG A:His157 4.32 Zn OD2 A:Asp214 4.22 Zn ZN A:Zn2 3.59 Zn O1 A:Cac7 3.26 Zn O2 A:Cac7 2.07 Zn AS A:Cac7 3.16 Zn C2 A:Cac7 4.74 Zn C1 A:Cac7 4.06 Zn O A:Hoh378 2.08 interactive model: Zinc binding site 2 out of 6 in 3e38 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 3e38. 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: A: His44, A: His46, A: His76, A: Glu113, A: Asp214, A: His216, A: Zn1, A: Zn3, A: Cac7, A: Hoh378, conact list: Atom Atom Distance (A) Zn NE2 A:His44 2.32 Zn ND1 A:His44 4.39 Zn CD2 A:His44 3.13 Zn CE1 A:His44 3.36 Zn CG A:His44 4.31 Zn NE2 A:His46 2.02 Zn ND1 A:His46 4.00 Zn CD2 A:His46 3.12 Zn CE1 A:His46 2.84 Zn CG A:His46 4.16 Zn NE2 A:His76 4.05 Zn ND1 A:His76 4.76 Zn CE1 A:His76 3.91 Zn OE1 A:Glu113 2.25 Zn CB A:Glu113 4.86 Zn OE2 A:Glu113 3.45 Zn CD A:Glu113 3.18 Zn CG A:Glu113 4.54 Zn CB A:Asp214 4.49 Zn OD2 A:Asp214 3.22 Zn OD1 A:Asp214 2.40 Zn CG A:Asp214 3.11 Zn CA A:Asp214 4.89 Zn NE2 A:His216 4.39 Zn CE1 A:His216 4.05 Zn ZN A:Zn1 3.59 Zn ZN A:Zn3 4.16 Zn O1 A:Cac7 1.89 Zn O2 A:Cac7 4.22 Zn AS A:Cac7 3.51 Zn C2 A:Cac7 4.99 Zn C1 A:Cac7 4.25 Zn O A:Hoh378 1.81 interactive model: Zinc binding site 3 out of 6 in 3e38 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 3e38. 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: A: His46, A: Asp51, A: His76, A: Tyr79, A: Glu113, A: Asp214, A: His216, A: Zn2, A: Cac7, A: Hoh378, conact list: Atom Atom Distance (A) Zn NE2 A:His46 3.94 Zn ND1 A:His46 4.15 Zn CD2 A:His46 4.18 Zn CE1 A:His46 3.94 Zn CG A:His46 4.31 Zn CB A:Asp51 4.10 Zn OD2 A:Asp51 2.10 Zn OD1 A:Asp51 2.53 Zn CG A:Asp51 2.62 Zn NE2 A:His76 2.12 Zn ND1 A:His76 4.12 Zn CD2 A:His76 3.22 Zn CE1 A:His76 2.95 Zn CG A:His76 4.28 Zn CD2 A:Tyr79 4.85 Zn OE1 A:Glu113 4.85 Zn OD1 A:Asp214 4.88 Zn NE2 A:His216 2.06 Zn ND1 A:His216 4.17 Zn CD2 A:His216 3.00 Zn CE1 A:His216 3.08 Zn CG A:His216 4.17 Zn ZN A:Zn2 4.16 Zn O1 A:Cac7 2.63 Zn O2 A:Cac7 4.20 Zn AS A:Cac7 2.81 Zn C2 A:Cac7 2.13 Zn C1 A:Cac7 4.20 Zn O A:Hoh378 4.78 interactive model: Zinc binding site 4 out of 6 in 3e38 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 3e38. 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: His44, B: His76, B: Glu113, B: His122, B: Asn156, B: His157, B: Asp214, B: Zn5, B: Cac8, B: Hoh403, conact list: Atom Atom Distance (A) Zn NE2 B:His44 4.53 Zn CE1 B:His44 4.43 Zn ND1 B:His76 4.90 Zn CE1 B:His76 4.08 Zn OE1 B:Glu113 3.54 Zn OE2 B:Glu113 2.20 Zn CD B:Glu113 3.16 Zn CG B:Glu113 4.37 Zn NE2 B:His122 4.32 Zn CB B:His122 3.56 Zn ND1 B:His122 2.29 Zn CD2 B:His122 4.38 Zn CE1 B:His122 3.21 Zn CG B:His122 3.27 Zn CB B:Asn156 4.69 Zn ND2 B:Asn156 4.62 Zn NE2 B:His157 2.21 Zn ND1 B:His157 4.19 Zn CD2 B:His157 3.35 Zn CE1 B:His157 2.99 Zn CG B:His157 4.39 Zn OD2 B:Asp214 4.31 Zn ZN B:Zn5 3.55 Zn O1 B:Cac8 3.52 Zn O2 B:Cac8 1.91 Zn AS B:Cac8 3.23 Zn C2 B:Cac8 4.78 Zn C1 B:Cac8 4.02 Zn O B:Hoh403 1.81 interactive model: Zinc binding site 5 out of 6 in 3e38 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Zinc in the PDB 3e38. 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: His44, B: His46, B: His76, B: Glu113, B: His157, B: Asp214, B: His216, B: Zn4, B: Zn6, B: Cac8, B: Hoh403, conact list: Atom Atom Distance (A) Zn NE2 B:His44 2.19 Zn ND1 B:His44 4.23 Zn CD2 B:His44 3.15 Zn CE1 B:His44 3.14 Zn CG B:His44 4.27 Zn NE2 B:His46 2.22 Zn ND1 B:His46 4.20 Zn CD2 B:His46 3.32 Zn CE1 B:His46 3.03 Zn CG B:His46 4.37 Zn NE2 B:His76 4.12 Zn ND1 B:His76 4.84 Zn CE1 B:His76 3.97 Zn OE1 B:Glu113 2.22 Zn CB B:Glu113 4.85 Zn OE2 B:Glu113 3.20 Zn CD B:Glu113 3.03 Zn CG B:Glu113 4.38 Zn NE2 B:His157 4.91 Zn CB B:Asp214 4.58 Zn OD2 B:Asp214 3.36 Zn OD1 B:Asp214 2.46 Zn CG B:Asp214 3.23 Zn CA B:Asp214 4.90 Zn NE2 B:His216 4.55 Zn CE1 B:His216 4.22 Zn ZN B:Zn4 3.55 Zn ZN B:Zn6 4.20 Zn O1 B:Cac8 1.94 Zn O2 B:Cac8 3.91 Zn AS B:Cac8 3.40 Zn C1 B:Cac8 4.07 Zn O B:Hoh403 2.11 interactive model: Zinc binding site 6 out of 6 in 3e38 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Zinc in the PDB 3e38. 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: His46, B: Asp51, B: His76, B: Tyr79, B: Glu113, B: His216, B: Zn5, B: Cac8, conact list: Atom Atom Distance (A) Zn NE2 B:His46 3.87 Zn ND1 B:His46 4.10 Zn CD2 B:His46 4.17 Zn CE1 B:His46 3.85 Zn CG B:His46 4.28 Zn CB B:Asp51 3.97 Zn OD2 B:Asp51 1.80 Zn OD1 B:Asp51 2.51 Zn CG B:Asp51 2.48 Zn CA B:Asp51 4.98 Zn NE2 B:His76 2.14 Zn ND1 B:His76 4.26 Zn CD2 B:His76 3.07 Zn CE1 B:His76 3.17 Zn CG B:His76 4.24 Zn CD2 B:Tyr79 4.90 Zn OE1 B:Glu113 4.65 Zn NE2 B:His216 2.10 Zn ND1 B:His216 4.22 Zn CD2 B:His216 3.06 Zn CE1 B:His216 3.12 Zn CG B:His216 4.23 Zn ZN B:Zn5 4.20 Zn O1 B:Cac8 2.46 Zn O2 B:Cac8 4.26 Zn AS B:Cac8 2.87 Zn C2 B:Cac8 2.43 Zn C1 B:Cac8 4.28 interactive model: