Zinc in the structure of Alkaline Phosphatase (H412Q) (pdb 1hqa)

The binding sites of Zinc atom in the structure of Alkaline Phosphatase (H412Q) (pdb code 1hqa). This binding sites where shown with 5.0 Angstroms radius around Zinc atom. The 1hqa structure was solved by L.MA, E.R.KANTROWITZ, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 8.0-2.2 Space group I222 a (A) 194.900 b (A) 167.000 c (A) 76.800 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16.1 Rfree (%) n/a Zinc Binding Sites: Zinc binding site 1 out of 6 in 1hqa Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 1hqa. 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: Asp51, A: Ser102, A: Asp327, A: His331, A: His370, A: His372, A: Gln412, A: Zn451, A: Hoh619, A: Hoh646, A: Hoh647, A: Hoh668, A: Hoh669, conact list: Atom Atom Distance (A) Zn OD1 A:Asp51 4.56 Zn OG A:Ser102 4.01 Zn CB A:Asp327 4.22 Zn OD2 A:Asp327 2.41 Zn OD1 A:Asp327 2.39 Zn CG A:Asp327 2.72 Zn NE2 A:His331 2.22 Zn ND1 A:His331 4.36 Zn CD2 A:His331 3.18 Zn CE1 A:His331 3.25 Zn CG A:His331 4.36 Zn NE2 A:His370 4.22 Zn CE1 A:His370 4.20 Zn NE2 A:His372 4.16 Zn CD2 A:His372 4.89 Zn NE2 A:Gln412 4.94 Zn OE1 A:Gln412 3.15 Zn CD A:Gln412 4.27 Zn ZN A:Zn451 4.17 Zn O A:Hoh619 4.40 Zn O A:Hoh646 2.74 Zn O A:Hoh647 3.51 Zn O A:Hoh668 3.27 Zn O A:Hoh669 4.55 interactive model: Zinc binding site 2 out of 6 in 1hqa Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 1hqa. 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: Asp51, A: Gly52, A: Asp101, A: Ser102, A: Asp327, A: Asp369, A: His370, A: Zn450, A: Zn452, A: Hoh453, A: Hoh496, A: Hoh646, A: Hoh647, conact list: Atom Atom Distance (A) Zn CB A:Asp51 4.19 Zn OD2 A:Asp51 2.81 Zn C A:Asp51 4.76 Zn OD1 A:Asp51 1.97 Zn CG A:Asp51 2.72 Zn CA A:Asp51 4.65 Zn N A:Gly52 4.48 Zn C A:Asp101 4.78 Zn N A:Ser102 3.92 Zn CB A:Ser102 3.04 Zn OG A:Ser102 2.15 Zn C A:Ser102 4.89 Zn CA A:Ser102 3.51 Zn CB A:Asp327 4.59 Zn OD2 A:Asp327 4.53 Zn OD1 A:Asp327 3.79 Zn CG A:Asp327 4.12 Zn CB A:Asp369 4.22 Zn OD2 A:Asp369 1.90 Zn OD1 A:Asp369 3.21 Zn CG A:Asp369 2.89 Zn NE2 A:His370 1.97 Zn ND1 A:His370 4.06 Zn CD2 A:His370 2.94 Zn CE1 A:His370 2.97 Zn CG A:His370 4.06 Zn ZN A:Zn450 4.17 Zn ZN A:Zn452 4.64 Zn O A:Hoh453 4.31 Zn O A:Hoh496 4.16 Zn O A:Hoh646 3.77 Zn O A:Hoh647 4.12 interactive model: Zinc binding site 3 out of 6 in 1hqa Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 1hqa. 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: Asp51, A: Ser102, A: Asp153, A: Thr155, A: Glu322, A: Ala324, A: Asp369, A: Zn451, A: Hoh453, A: Hoh454, A: Hoh455, A: Hoh496, A: Hoh619, A: Hoh647, conact list: Atom Atom Distance (A) Zn CB A:Asp51 3.66 Zn OD2 A:Asp51 2.07 Zn OD1 A:Asp51 4.08 Zn CG A:Asp51 3.08 Zn CB A:Ser102 4.43 Zn OG A:Ser102 4.38 Zn OD2 A:Asp153 3.61 Zn CG A:Asp153 4.61 Zn N A:Thr155 4.08 Zn CB A:Thr155 3.23 Zn CG2 A:Thr155 4.18 Zn OG1 A:Thr155 2.25 Zn CA A:Thr155 4.29 Zn OE1 A:Glu322 3.58 Zn OE2 A:Glu322 2.04 Zn CD A:Glu322 3.12 Zn CG A:Glu322 4.37 Zn O A:Ala324 4.72 Zn CB A:Ala324 4.49 Zn CA A:Ala324 4.81 Zn OD2 A:Asp369 4.94 Zn ZN A:Zn451 4.64 Zn O A:Hoh453 2.33 Zn O A:Hoh454 2.19 Zn O A:Hoh455 2.17 Zn O A:Hoh496 4.17 Zn O A:Hoh619 4.00 Zn O A:Hoh647 4.57 interactive model: Zinc binding site 4 out of 6 in 1hqa Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 1hqa. 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: Asp51, B: Ser102, B: Asp327, B: His331, B: His370, B: His372, B: Gln412, B: Zn451, B: Hoh596, B: Hoh597, B: Hoh598, B: Hoh600, conact list: Atom Atom Distance (A) Zn OD1 B:Asp51 4.66 Zn OG B:Ser102 4.09 Zn O B:Asp327 4.93 Zn CB B:Asp327 4.31 Zn OD2 B:Asp327 2.52 Zn OD1 B:Asp327 2.44 Zn CG B:Asp327 2.81 Zn NE2 B:His331 2.10 Zn ND1 B:His331 4.26 Zn CD2 B:His331 3.06 Zn CE1 B:His331 3.16 Zn CG B:His331 4.24 Zn NE2 B:His370 4.37 Zn CE1 B:His370 4.35 Zn NE2 B:His372 4.26 Zn NE2 B:Gln412 4.94 Zn OE1 B:Gln412 3.21 Zn CD B:Gln412 4.33 Zn ZN B:Zn451 4.27 Zn O B:Hoh596 3.98 Zn O B:Hoh597 2.96 Zn O B:Hoh598 3.39 Zn O B:Hoh600 2.71 interactive model: Zinc binding site 5 out of 6 in 1hqa Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Zinc in the PDB 1hqa. 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: Asp51, B: Gly52, B: Asp101, B: Ser102, B: Asp327, B: Asp369, B: His370, B: Zn450, B: Zn452, B: Hoh508, B: Hoh547, B: Hoh596, B: Hoh598, B: Hoh600, conact list: Atom Atom Distance (A) Zn CB B:Asp51 4.21 Zn OD2 B:Asp51 2.95 Zn C B:Asp51 4.75 Zn OD1 B:Asp51 1.99 Zn CG B:Asp51 2.79 Zn CA B:Asp51 4.63 Zn N B:Gly52 4.47 Zn C B:Asp101 4.80 Zn N B:Ser102 3.94 Zn CB B:Ser102 3.01 Zn OG B:Ser102 2.15 Zn C B:Ser102 4.90 Zn CA B:Ser102 3.54 Zn CB B:Asp327 4.57 Zn OD2 B:Asp327 3.69 Zn OD1 B:Asp327 4.59 Zn CG B:Asp327 4.08 Zn CB B:Asp369 4.25 Zn OD2 B:Asp369 1.96 Zn OD1 B:Asp369 3.23 Zn CG B:Asp369 2.92 Zn NE2 B:His370 2.02 Zn ND1 B:His370 4.08 Zn CD2 B:His370 2.98 Zn CE1 B:His370 2.99 Zn CG B:His370 4.10 Zn ZN B:Zn450 4.27 Zn ZN B:Zn452 4.70 Zn O B:Hoh508 4.23 Zn O B:Hoh547 4.01 Zn O B:Hoh596 4.99 Zn O B:Hoh598 4.49 Zn O B:Hoh600 3.96 interactive model: Zinc binding site 6 out of 6 in 1hqa Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Zinc in the PDB 1hqa. 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: Asp51, B: Ser102, B: Asp153, B: Thr155, B: Glu322, B: Ala324, B: Asp369, B: Zn451, B: Hoh508, B: Hoh509, B: Hoh510, B: Hoh547, B: Hoh596, conact list: Atom Atom Distance (A) Zn CB B:Asp51 3.71 Zn OD2 B:Asp51 2.06 Zn OD1 B:Asp51 4.03 Zn CG B:Asp51 3.08 Zn CB B:Ser102 4.46 Zn OG B:Ser102 4.48 Zn OD2 B:Asp153 3.53 Zn CG B:Asp153 4.58 Zn N B:Thr155 4.09 Zn CB B:Thr155 3.16 Zn CG2 B:Thr155 4.11 Zn OG1 B:Thr155 2.22 Zn CA B:Thr155 4.27 Zn OE1 B:Glu322 3.48 Zn OE2 B:Glu322 2.03 Zn CD B:Glu322 3.09 Zn CG B:Glu322 4.36 Zn O B:Ala324 4.76 Zn CB B:Ala324 4.52 Zn CA B:Ala324 4.80 Zn OD2 B:Asp369 4.93 Zn ZN B:Zn451 4.70 Zn O B:Hoh508 2.25 Zn O B:Hoh509 2.07 Zn O B:Hoh510 2.23 Zn O B:Hoh547 4.14 Zn O B:Hoh596 4.23 interactive model: