Calcium in PDB 1nkq: Crystal Structure of Yeast YNQ8, A Fumarylacetoacetate Hydrolase Family Protein

The structure of Crystal Structure of Yeast YNQ8, A Fumarylacetoacetate Hydrolase Family Protein, PDB code: 1nkq was solved by S.Eswaramoorthy, D.Kumaran, B.Daniels, F.W.Studier, S.Swaminathan, S.K.Burley, New York Sgx Research Center For Structural Genomics(Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.705, 85.990, 316.704, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 26.2

The binding sites of Calcium atom in the Crystal Structure of Yeast YNQ8, A Fumarylacetoacetate Hydrolase Family Protein (pdb code 1nkq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Yeast YNQ8, A Fumarylacetoacetate Hydrolase Family Protein, PDB code: 1nkq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Yeast YNQ8, A Fumarylacetoacetate Hydrolase Family Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Yeast YNQ8, A Fumarylacetoacetate Hydrolase Family Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca260 b:15.1 occ:1.00 OD2 A:ASP121 2.1 19.9 1.0 OXT A:ACY701 2.1 33.8 1.0 OE2 A:GLU89 2.2 17.1 1.0 O A:HOH833 2.4 31.8 1.0 OE1 A:GLU87 2.7 26.7 1.0 C A:ACY701 2.8 34.1 1.0 O A:ACY701 3.0 36.9 1.0 CD A:GLU89 3.1 16.6 1.0 CG A:ASP121 3.2 19.7 1.0 OE1 A:GLU89 3.4 16.2 1.0 CB A:ASP121 3.6 17.3 1.0 CZ A:PHE37 3.7 11.7 1.0 CD A:GLU87 3.8 28.7 1.0 NZ A:LYS142 4.0 17.0 1.0 CH3 A:ACY701 4.3 34.7 1.0 O A:ILE15 4.3 15.9 1.0 OD1 A:ASP121 4.3 22.1 1.0 OE2 A:GLU87 4.4 31.7 1.0 CE2 A:PHE37 4.5 13.9 1.0 CG A:GLU89 4.5 16.4 1.0 CB A:GLU87 4.6 21.6 1.0 CE1 A:PHE37 4.7 14.4 1.0 CG A:GLU87 4.8 25.5 1.0 CA A:GLY215 4.9 11.6 1.0 CG2 A:THR216 5.0 15.7 1.0 N A:THR216 5.0 14.4 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Yeast YNQ8, A Fumarylacetoacetate Hydrolase Family Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Yeast YNQ8, A Fumarylacetoacetate Hydrolase Family Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca560 b:15.7 occ:1.00 OD2 B:ASP421 2.2 8.8 1.0 OE2 B:GLU389 2.3 19.4 1.0 O B:ACY703 2.3 33.8 1.0 OE1 B:GLU387 2.3 28.3 1.0 O B:HOH854 2.4 30.7 1.0 C B:ACY703 2.9 34.7 1.0 OXT B:ACY703 3.0 35.6 1.0 CG B:ASP421 3.3 13.6 1.0 CD B:GLU389 3.3 18.9 1.0 CD B:GLU387 3.5 27.9 1.0 OE1 B:GLU389 3.7 21.6 1.0 CB B:ASP421 3.7 13.8 1.0 NZ B:LYS442 4.1 14.5 1.0 CZ B:PHE337 4.1 13.2 1.0 O B:ILE315 4.3 20.2 1.0 OE2 B:GLU387 4.3 31.6 1.0 CH3 B:ACY703 4.3 35.1 1.0 CB B:GLU387 4.4 21.6 1.0 OD1 B:ASP421 4.4 14.4 1.0 CG B:GLU387 4.5 24.7 1.0 CE2 B:PHE337 4.6 14.0 1.0 CG B:GLU389 4.6 18.7 1.0 CG2 B:THR516 4.7 12.1 1.0 N B:THR516 4.8 15.6 1.0 CB B:THR516 4.8 15.5 1.0 CA B:GLY515 4.9 15.4 1.0 O B:ASP421 4.9 15.9 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Yeast YNQ8, A Fumarylacetoacetate Hydrolase Family Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Yeast YNQ8, A Fumarylacetoacetate Hydrolase Family Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca260 b:22.5 occ:1.00 OXT C:ACY705 2.1 35.8 1.0 OE2 C:GLU89 2.2 14.2 1.0 OD2 C:ASP121 2.3 17.5 1.0 O C:HOH867 2.5 18.4 1.0 OE1 C:GLU87 2.5 24.2 1.0 C C:ACY705 2.9 34.8 1.0 CD C:GLU89 3.0 14.2 1.0 O C:ACY705 3.1 35.6 1.0 CG C:ASP121 3.3 17.5 1.0 OE1 C:GLU89 3.4 12.2 1.0 CB C:ASP121 3.7 16.3 1.0 CD C:GLU87 3.7 26.7 1.0 CZ C:PHE37 4.3 16.4 1.0 CH3 C:ACY705 4.3 37.2 1.0 CB C:GLU87 4.3 18.1 1.0 CG C:GLU89 4.3 14.2 1.0 OD1 C:ASP121 4.4 15.3 1.0 O C:ILE15 4.5 11.2 1.0 CG C:GLU87 4.5 23.3 1.0 OE2 C:GLU87 4.6 30.5 1.0 CG2 C:THR216 4.6 11.6 1.0 CB C:THR216 4.7 11.5 1.0 N C:THR216 4.8 12.8 1.0 CE2 C:PHE37 4.8 15.7 1.0 CA C:GLY215 4.8 13.2 1.0 C C:GLY215 4.9 13.6 1.0 O C:ASP121 5.0 15.7 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Yeast YNQ8, A Fumarylacetoacetate Hydrolase Family Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Yeast YNQ8, A Fumarylacetoacetate Hydrolase Family Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca560 b:17.5 occ:1.00 OE2 D:GLU389 2.2 19.2 1.0 O D:ACY707 2.4 33.8 1.0 OD2 D:ASP421 2.4 10.8 1.0 OE1 D:GLU387 2.5 18.1 1.0 O D:HOH784 2.7 20.2 1.0 C D:ACY707 3.0 33.9 1.0 OXT D:ACY707 3.0 33.5 1.0 CD D:GLU389 3.2 19.4 1.0 CG D:ASP421 3.4 10.1 1.0 OE1 D:GLU389 3.6 18.7 1.0 CB D:ASP421 3.7 10.3 1.0 CD D:GLU387 3.8 22.0 1.0 CZ D:PHE337 4.0 6.3 1.0 O D:ILE315 4.3 15.1 1.0 CG2 D:THR516 4.3 14.4 1.0 CH3 D:ACY707 4.4 35.0 1.0 CB D:GLU387 4.4 13.2 1.0 CG D:GLU389 4.5 17.3 1.0 OD1 D:ASP421 4.6 12.4 1.0 OE2 D:GLU387 4.6 25.8 1.0 CE2 D:PHE337 4.6 6.7 1.0 CG D:GLU387 4.7 18.0 1.0 CA D:GLY515 4.7 13.0 1.0 NZ D:LYS442 4.8 4.4 1.0 N D:THR516 4.8 13.3 1.0 CB D:THR516 4.8 14.9 1.0 C D:GLY515 4.9 13.0 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Yeast YNQ8, A Fumarylacetoacetate Hydrolase Family Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Yeast YNQ8, A Fumarylacetoacetate Hydrolase Family Protein within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca260 b:21.1 occ:1.00 OE2 E:GLU89 2.2 22.5 1.0 OXT E:ACY709 2.3 34.6 1.0 OD2 E:ASP121 2.3 15.0 1.0 O E:HOH882 2.5 22.4 1.0 OE1 E:GLU87 2.7 26.4 1.0 C E:ACY709 2.9 33.9 1.0 O E:ACY709 3.1 34.2 1.0 CD E:GLU89 3.2 21.7 1.0 CG E:ASP121 3.3 16.0 1.0 OE1 E:GLU89 3.5 21.5 1.0 CD E:GLU87 3.5 25.4 1.0 CB E:ASP121 3.6 14.7 1.0 OE2 E:GLU87 4.1 27.9 1.0 CZ E:PHE37 4.1 9.3 1.0 CB E:GLU87 4.2 20.0 1.0 NZ E:LYS142 4.2 14.2 1.0 CH3 E:ACY709 4.3 36.8 1.0 CG E:GLU89 4.4 19.3 1.0 OD1 E:ASP121 4.4 15.0 1.0 CG E:GLU87 4.5 23.9 1.0 O E:ILE15 4.5 17.2 1.0 CG2 E:THR216 4.6 18.6 1.0 CE2 E:PHE37 4.7 10.1 1.0 CB E:THR216 4.8 18.4 1.0 O E:ASP121 5.0 13.6 1.0 N E:THR216 5.0 16.0 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Yeast YNQ8, A Fumarylacetoacetate Hydrolase Family Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Yeast YNQ8, A Fumarylacetoacetate Hydrolase Family Protein within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca560 b:17.3 occ:1.00 OE2 F:GLU389 2.1 18.6 1.0 OD2 F:ASP421 2.3 18.7 1.0 OE2 F:GLU387 2.4 30.1 1.0 O F:ACY711 2.4 34.6 1.0 O F:HOH789 2.4 20.9 1.0 OXT F:ACY711 2.9 32.4 1.0 C F:ACY711 2.9 33.8 1.0 CD F:GLU389 3.1 19.2 1.0 CG F:ASP421 3.3 16.2 1.0 OE1 F:GLU389 3.6 19.8 1.0 CD F:GLU387 3.6 28.8 1.0 CB F:ASP421 3.6 16.3 1.0 CZ F:PHE337 4.1 11.2 1.0 CH3 F:ACY711 4.3 35.4 1.0 NZ F:LYS442 4.3 15.9 1.0 O F:ILE315 4.3 20.2 1.0 CB F:GLU387 4.4 22.2 1.0 OE1 F:GLU387 4.4 31.0 1.0 CG F:GLU389 4.4 18.3 1.0 OD1 F:ASP421 4.4 16.3 1.0 CG2 F:THR516 4.5 17.7 1.0 CE2 F:PHE337 4.6 8.6 1.0 CG F:GLU387 4.6 25.7 1.0 CB F:THR516 4.7 18.1 1.0 N F:THR516 4.8 16.1 1.0 CA F:GLY515 4.8 16.8 1.0 C F:GLY515 4.9 17.2 1.0

S.Eswaramoorthy, D.Kumaran, B.Daniels, F.W.Studier, S.Swaminathan. Crtystal Structure of Yeast Hypothetical Protein YNQ8_YEAST To Be Published.