Calcium in PDB 5yl4: Crystal Structure of T2R-Ttl-8WR Complex

The structure of Crystal Structure of T2R-Ttl-8WR Complex, PDB code: 5yl4 was solved by Z.Y.Fu, W.B.Li, Y.Y.Chu, Y.W.Hou, C.P.Ji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.23 / 2.64
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.461, 157.730, 182.147, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 25.6

The structure of Crystal Structure of T2R-Ttl-8WR Complex also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Calcium atom in the Crystal Structure of T2R-Ttl-8WR Complex (pdb code 5yl4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of T2R-Ttl-8WR Complex, PDB code: 5yl4:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of T2R-Ttl-8WR Complex


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 T2R-Ttl-8WR Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:63.2 occ:1.00 OE2 A:GLU55 2.4 56.5 1.0 O A:GLY44 2.4 62.2 1.0 OD1 A:ASP39 2.6 50.2 1.0 OD2 A:ASP39 2.6 51.3 1.0 O A:THR41 2.6 68.9 1.0 OG1 A:THR41 2.8 67.2 1.0 CG A:ASP39 3.0 52.3 1.0 CD A:GLU55 3.2 59.5 1.0 OE1 A:GLU55 3.3 58.7 1.0 C A:GLY44 3.5 65.2 1.0 CB A:THR41 3.6 66.7 1.0 C A:THR41 3.7 67.2 1.0 CA A:GLY45 4.0 64.9 1.0 CA A:THR41 4.1 66.6 1.0 N A:GLY45 4.1 64.2 1.0 OD1 A:ASN50 4.1 62.1 1.0 N A:THR41 4.4 64.6 1.0 OD2 A:ASP47 4.4 57.0 1.0 CZ A:PHE49 4.5 63.3 1.0 CB A:ASP39 4.5 52.6 1.0 CA A:GLY44 4.6 65.2 1.0 N A:GLY44 4.6 64.2 1.0 CG A:GLU55 4.6 59.4 1.0 ND2 A:ASN50 4.7 57.2 1.0 NE2 A:HIS61 4.8 67.4 1.0 N A:ILE42 4.9 65.4 1.0 CG A:ASN50 4.9 56.5 1.0 CE1 A:PHE49 5.0 63.5 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of T2R-Ttl-8WR Complex


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 T2R-Ttl-8WR Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:76.3 occ:1.00 OE1 B:GLU111 2.6 57.2 1.0 CD B:GLU111 3.5 56.9 1.0 OE2 B:GLU111 3.7 63.9 1.0 OE1 B:GLU108 4.3 39.2 1.0 CG B:GLU111 4.9 52.1 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of T2R-Ttl-8WR Complex


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 T2R-Ttl-8WR Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:49.2 occ:1.00 OE2 C:GLU55 2.4 41.0 1.0 OG1 C:THR41 2.4 53.5 1.0 OD1 C:ASP39 2.5 39.7 1.0 O C:THR41 2.6 50.6 1.0 OD2 C:ASP39 2.7 37.0 1.0 OE1 C:GLU55 2.7 40.7 1.0 O C:GLY44 2.7 48.4 1.0 CD C:GLU55 2.9 40.1 1.0 CG C:ASP39 3.0 40.8 1.0 C C:GLY44 3.5 49.1 1.0 C C:THR41 3.6 49.2 1.0 CB C:THR41 3.6 51.1 1.0 OD2 C:ASP47 3.8 47.7 1.0 CA C:GLY45 3.9 47.4 1.0 N C:GLY45 4.0 48.0 1.0 CA C:THR41 4.1 50.5 1.0 OD1 C:ASN50 4.3 33.6 1.0 N C:THR41 4.4 51.5 1.0 CG C:GLU55 4.5 38.4 1.0 CA C:GLY44 4.5 51.6 1.0 CB C:ASP39 4.5 42.9 1.0 N C:GLY44 4.6 52.1 1.0 CZ C:PHE49 4.7 32.2 1.0 ND2 C:ASN50 4.8 32.3 1.0 N C:ILE42 4.8 49.7 1.0 CG2 C:THR41 4.9 50.0 1.0 CE1 C:PHE49 4.9 32.6 1.0 NE2 C:HIS61 5.0 37.4 1.0

Z.Y.Fu, W.B.Li. Design, Synthesis and Biological Activity Evaluation of Plinabulin Derivatives Based on Co-Crystal Structure To Be Published.