Calcium in PDB 6adu: Crystal Structure of An Enzyme in Complex with Ligand C

The structure of Crystal Structure of An Enzyme in Complex with Ligand C, PDB code: 6adu was solved by X.K.Tan, W.D.Liu, C.C.Chen, R.T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.67 / 1.96
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	87.773, 256.546, 36.043, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 24.7

The structure of Crystal Structure of An Enzyme in Complex with Ligand C also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Crystal Structure of An Enzyme in Complex with Ligand C (pdb code 6adu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of An Enzyme in Complex with Ligand C, PDB code: 6adu:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structure of An Enzyme in Complex with Ligand C


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 An Enzyme in Complex with Ligand C within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:25.4 occ:1.00 O A:ASN98 2.2 25.0 1.0 OE2 A:GLU95 2.3 31.3 1.0 O A:GLY37 2.4 21.0 1.0 O A:GLU95 2.4 23.1 1.0 OE2 A:GLU39 2.4 24.4 1.0 OD1 A:ASP216 2.4 27.7 1.0 OD2 A:ASP216 2.7 24.9 1.0 CG A:ASP216 2.9 24.8 1.0 C A:ASN98 3.3 22.8 1.0 C A:GLY37 3.4 22.0 1.0 C A:GLU95 3.4 27.1 1.0 CD A:GLU95 3.5 29.4 1.0 CD A:GLU39 3.6 29.1 1.0 CA A:GLY37 3.7 25.0 1.0 N A:ASN98 3.9 25.3 1.0 CB A:GLU95 4.1 28.5 1.0 CA A:ASN98 4.1 24.3 1.0 CG A:GLU39 4.1 29.4 1.0 CA A:GLU95 4.2 26.2 1.0 CG A:GLU95 4.3 28.9 1.0 N A:GLY96 4.4 28.2 1.0 CB A:ASP216 4.4 24.0 1.0 N A:GLU95 4.4 26.4 1.0 OE1 A:GLU95 4.4 34.5 1.0 N A:ILE99 4.4 24.7 1.0 CB A:ASN98 4.5 23.7 1.0 CA A:GLY96 4.6 28.3 1.0 N A:PHE38 4.6 24.7 1.0 OE1 A:GLU39 4.6 28.4 1.0 N A:ARG97 4.6 24.2 1.0 C A:GLY96 4.6 27.9 1.0 CB A:ALA93 4.7 28.4 1.0 CA A:ILE99 4.7 25.3 1.0 C A:ARG97 4.9 26.1 1.0 N A:GLU39 4.9 24.6 1.0 C A:PHE38 4.9 22.7 1.0 N A:ASN217 5.0 23.8 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of An Enzyme in Complex with Ligand C


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 An Enzyme in Complex with Ligand C within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:51.0 occ:1.00 O A:GLY149 2.3 25.7 1.0 O A:LEU138 2.3 31.5 1.0 OD1 A:ASN137 2.4 26.6 1.0 O A:PHE147 2.4 28.4 1.0 OE1 A:GLU175 2.7 51.6 1.0 CD A:GLU175 3.4 48.0 1.0 C A:GLY149 3.4 28.4 1.0 C A:LEU138 3.5 29.0 1.0 OE2 A:GLU175 3.5 50.0 1.0 CG A:ASN137 3.5 25.2 1.0 N A:GLY149 3.5 25.3 1.0 C A:PHE147 3.6 30.8 1.0 N A:LEU138 3.8 26.6 1.0 C A:ALA148 3.9 26.8 1.0 CA A:ALA148 4.0 31.6 1.0 CA A:GLY149 4.1 27.1 1.0 CA A:LEU138 4.1 30.9 1.0 C A:ASN137 4.2 30.2 1.0 ND2 A:ASN137 4.2 29.4 1.0 N A:ALA148 4.3 30.1 1.0 CD2 A:PHE210 4.4 34.2 1.0 N A:PHE150 4.5 29.0 1.0 N A:ALA139 4.5 30.7 1.0 CB A:LEU138 4.6 36.9 1.0 O A:ALA148 4.6 29.0 1.0 CA A:ASN137 4.6 24.3 1.0 CB A:ASN137 4.7 22.5 1.0 O A:ASN137 4.7 29.4 1.0 CA A:ALA139 4.7 32.7 1.0 CA A:PHE147 4.7 30.9 1.0 CA A:PHE150 4.8 26.5 1.0 CG A:GLU175 4.8 42.5 1.0 CB A:PHE147 4.8 30.1 1.0 CB A:PHE210 4.9 33.6 1.0 CB A:PHE150 4.9 26.6 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of An Enzyme in Complex with Ligand C


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 An Enzyme in Complex with Ligand C within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:29.7 occ:1.00 O B:GLY37 2.3 30.0 1.0 OD1 B:ASP216 2.4 26.1 1.0 O B:GLU95 2.4 33.9 1.0 O B:ASN98 2.4 25.0 1.0 OE2 B:GLU39 2.4 32.1 1.0 OE2 B:GLU95 2.5 32.0 1.0 OD2 B:ASP216 2.6 28.0 1.0 CG B:ASP216 2.8 25.6 1.0 C B:GLU95 3.3 34.3 1.0 C B:GLY37 3.4 26.9 1.0 C B:ASN98 3.5 31.2 1.0 CD B:GLU39 3.6 34.9 1.0 CD B:GLU95 3.6 34.8 1.0 CA B:GLY37 3.8 25.8 1.0 CB B:GLU95 3.9 34.6 1.0 N B:ASN98 3.9 30.8 1.0 CA B:GLU95 4.0 33.5 1.0 CG B:GLU39 4.2 33.8 1.0 CA B:ASN98 4.3 30.9 1.0 N B:GLU95 4.3 31.0 1.0 CB B:ASP216 4.3 25.5 1.0 N B:GLY96 4.3 30.8 1.0 CG B:GLU95 4.3 35.8 1.0 CA B:GLY96 4.5 29.2 1.0 OE1 B:GLU95 4.5 36.1 1.0 OE1 B:GLU39 4.6 34.9 1.0 N B:PHE38 4.6 26.1 1.0 N B:ILE99 4.6 35.3 1.0 C B:GLY96 4.6 28.9 1.0 N B:ARG97 4.7 29.9 1.0 CB B:ASN98 4.7 28.9 1.0 N B:ASN217 4.8 27.2 1.0 CB B:ALA93 4.8 35.1 1.0 CA B:ILE99 4.9 30.6 1.0 C B:ARG97 4.9 33.6 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of An Enzyme in Complex with Ligand C


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 An Enzyme in Complex with Ligand C within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:55.4 occ:1.00 O B:GLY149 2.2 28.0 1.0 O B:PHE147 2.3 31.9 1.0 O B:LEU138 2.4 37.4 1.0 OD1 B:ASN137 2.4 27.1 1.0 OE1 B:GLU175 2.6 57.3 1.0 C B:GLY149 3.3 29.8 1.0 CD B:GLU175 3.3 48.4 1.0 N B:GLY149 3.3 30.8 1.0 C B:PHE147 3.5 36.9 1.0 OE2 B:GLU175 3.5 50.4 1.0 C B:LEU138 3.5 38.2 1.0 CG B:ASN137 3.5 30.8 1.0 C B:ALA148 3.8 32.9 1.0 CA B:GLY149 3.9 32.5 1.0 N B:LEU138 3.9 34.2 1.0 CA B:ALA148 4.0 35.0 1.0 ND2 B:ASN137 4.1 28.9 1.0 CA B:LEU138 4.2 40.4 1.0 N B:ALA148 4.2 33.6 1.0 C B:ASN137 4.3 35.3 1.0 N B:PHE150 4.4 28.2 1.0 CD2 B:PHE210 4.4 31.8 1.0 CB B:LEU138 4.5 45.6 1.0 N B:ALA139 4.6 40.1 1.0 O B:ALA148 4.6 31.1 1.0 CA B:PHE147 4.6 37.2 1.0 CG B:GLU175 4.6 46.4 1.0 CB B:PHE210 4.7 33.1 1.0 CB B:ASN137 4.7 26.1 1.0 CA B:PHE150 4.8 28.8 1.0 CA B:ALA139 4.8 36.6 1.0 CB B:PHE147 4.8 38.9 1.0 O B:ASN137 4.8 31.6 1.0 CA B:ASN137 4.8 27.5 1.0 O B:HOH467 4.9 51.0 1.0 CB B:PHE150 5.0 30.4 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of An Enzyme in Complex with Ligand C


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 An Enzyme in Complex with Ligand C within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca303 b:29.9 occ:1.00 O C:GLY37 2.2 26.8 1.0 O C:ASN98 2.2 29.9 1.0 OE2 C:GLU95 2.4 36.7 1.0 O C:GLU95 2.4 31.0 1.0 OD1 C:ASP216 2.4 31.4 1.0 OE2 C:GLU39 2.4 31.9 1.0 OD2 C:ASP216 2.9 29.4 1.0 CG C:ASP216 2.9 31.6 1.0 C C:GLY37 3.3 28.2 1.0 C C:ASN98 3.4 31.1 1.0 C C:GLU95 3.4 32.5 1.0 CD C:GLU39 3.6 36.4 1.0 CD C:GLU95 3.6 39.1 1.0 CA C:GLY37 3.7 31.2 1.0 N C:ASN98 3.9 30.2 1.0 CB C:GLU95 4.1 33.1 1.0 CA C:ASN98 4.1 32.0 1.0 CG C:GLU39 4.2 35.2 1.0 CA C:GLU95 4.2 32.6 1.0 N C:GLY96 4.4 31.2 1.0 CB C:ASP216 4.4 29.7 1.0 CG C:GLU95 4.4 40.1 1.0 N C:GLU95 4.5 30.4 1.0 N C:ILE99 4.5 29.4 1.0 N C:PHE38 4.5 28.1 1.0 OE1 C:GLU95 4.5 36.1 1.0 OE1 C:GLU39 4.5 36.0 1.0 CB C:ASN98 4.5 30.5 1.0 N C:ARG97 4.6 28.1 1.0 C C:GLY96 4.6 29.3 1.0 CA C:GLY96 4.7 28.1 1.0 CA C:ILE99 4.7 30.1 1.0 CB C:ALA93 4.8 33.7 1.0 N C:GLU39 4.9 32.1 1.0 C C:ARG97 4.9 31.8 1.0 N C:ASN217 4.9 29.3 1.0 C C:PHE38 4.9 32.2 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of An Enzyme in Complex with Ligand C


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 An Enzyme in Complex with Ligand C within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca304 b:52.6 occ:1.00 OD1 C:ASN137 2.3 30.6 1.0 O C:LEU138 2.3 30.0 1.0 O C:GLY149 2.4 27.6 1.0 O C:PHE147 2.4 36.3 1.0 OE1 C:GLU175 2.7 58.3 1.0 C C:LEU138 3.5 34.3 1.0 CG C:ASN137 3.5 33.2 1.0 C C:GLY149 3.5 33.7 1.0 C C:PHE147 3.6 37.2 1.0 N C:LEU138 3.7 30.1 1.0 CD C:GLU175 3.8 53.8 1.0 N C:GLY149 3.8 32.3 1.0 C C:ALA148 4.0 33.6 1.0 C C:ASN137 4.0 27.7 1.0 CA C:LEU138 4.1 34.0 1.0 OE2 C:GLU175 4.2 56.2 1.0 CA C:ALA148 4.2 35.7 1.0 ND2 C:ASN137 4.2 28.2 1.0 CA C:GLY149 4.3 32.7 1.0 N C:ALA148 4.3 33.9 1.0 CB C:LEU138 4.4 35.3 1.0 O C:ASN137 4.5 29.8 1.0 CA C:ASN137 4.5 26.9 1.0 O C:ALA148 4.5 31.6 1.0 N C:PHE150 4.6 29.6 1.0 CB C:ASN137 4.6 26.5 1.0 N C:ALA139 4.6 35.2 1.0 CB C:PHE147 4.6 36.4 1.0 CA C:PHE147 4.6 38.5 1.0 CD2 C:PHE210 4.7 35.5 1.0 CA C:PHE150 4.7 28.3 1.0 CB C:PHE150 4.8 25.5 1.0 CA C:ALA139 4.9 40.0 1.0 CB C:PHE210 4.9 34.0 1.0 O C:HOH450 5.0 37.5 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of An Enzyme in Complex with Ligand C


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of An Enzyme in Complex with Ligand C within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca303 b:35.1 occ:1.00 OE1 D:GLU95 2.4 38.2 1.0 O D:ASN98 2.4 38.6 1.0 O D:GLY37 2.4 33.8 1.0 O D:GLU95 2.4 36.1 1.0 OE2 D:GLU39 2.4 38.0 1.0 OD1 D:ASP216 2.5 30.8 1.0 OD2 D:ASP216 2.7 38.4 1.0 CG D:ASP216 2.9 32.9 1.0 C D:GLU95 3.3 36.6 1.0 C D:GLY37 3.4 32.1 1.0 C D:ASN98 3.5 37.0 1.0 CD D:GLU95 3.5 41.4 1.0 CD D:GLU39 3.5 44.7 1.0 CA D:GLY37 3.8 34.6 1.0 N D:ASN98 3.9 40.3 1.0 CB D:GLU95 3.9 39.0 1.0 CA D:GLU95 4.1 36.4 1.0 CG D:GLU39 4.1 37.9 1.0 CA D:ASN98 4.2 37.9 1.0 N D:GLY96 4.3 37.0 1.0 CG D:GLU95 4.3 42.0 1.0 N D:GLU95 4.4 35.5 1.0 CB D:ASP216 4.4 31.3 1.0 OE2 D:GLU95 4.5 41.5 1.0 CA D:GLY96 4.5 35.6 1.0 N D:ILE99 4.6 34.5 1.0 OE1 D:GLU39 4.6 44.4 1.0 C D:GLY96 4.6 35.4 1.0 N D:PHE38 4.6 31.1 1.0 N D:ARG97 4.6 39.0 1.0 CB D:ASN98 4.7 37.8 1.0 CB D:ALA93 4.7 37.2 1.0 CA D:ILE99 4.8 32.9 1.0 C D:ARG97 4.9 44.2 1.0 C D:PHE38 5.0 33.8 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of An Enzyme in Complex with Ligand C


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of An Enzyme in Complex with Ligand C within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca304 b:52.3 occ:1.00 O D:GLY149 2.3 26.9 1.0 OD1 D:ASN137 2.3 26.2 1.0 O D:LEU138 2.4 34.5 1.0 O D:PHE147 2.4 34.7 1.0 OE1 D:GLU175 3.0 55.0 1.0 C D:GLY149 3.5 30.0 1.0 CG D:ASN137 3.5 28.2 1.0 C D:LEU138 3.5 35.2 1.0 C D:PHE147 3.6 34.2 1.0 N D:GLY149 3.7 32.4 1.0 N D:LEU138 3.8 34.2 1.0 CD D:GLU175 3.9 50.8 1.0 C D:ALA148 4.0 33.0 1.0 C D:ASN137 4.1 33.9 1.0 ND2 D:ASN137 4.2 27.4 1.0 CA D:LEU138 4.2 35.3 1.0 CA D:GLY149 4.2 32.9 1.0 CA D:ALA148 4.3 33.6 1.0 OE2 D:GLU175 4.3 52.3 1.0 N D:ALA148 4.4 35.2 1.0 O D:ASN137 4.4 30.5 1.0 N D:PHE150 4.5 32.5 1.0 CB D:LEU138 4.5 37.5 1.0 O D:ALA148 4.5 28.6 1.0 CD2 D:PHE210 4.5 35.7 1.0 CA D:ASN137 4.6 26.6 1.0 CB D:ASN137 4.6 27.9 1.0 N D:ALA139 4.6 33.9 1.0 CA D:PHE150 4.6 32.1 1.0 CA D:PHE147 4.6 34.1 1.0 CB D:PHE147 4.7 32.8 1.0 O D:HOH432 4.8 47.2 1.0 CB D:PHE210 4.8 34.4 1.0 CB D:PHE150 4.8 30.2 1.0 O D:HOH460 4.9 37.2 1.0 O D:PHE210 4.9 30.9 1.0 CA D:ALA139 5.0 35.0 1.0

X.K.Tan, W.D.Liu, C.C.Chen, R.T.Guo. Crystal Structure of An Enzyme in Complex with Ligand C To Be Published.