Calcium in PDB 7exc: Crystal Structure of T2R-Ttl-1129A2 Complex

The structure of Crystal Structure of T2R-Ttl-1129A2 Complex, PDB code: 7exc was solved by J.H.Yang, W.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.85 / 2.39
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.248, 157.375, 181.974, 90, 90, 90
R / Rfree (%)	21.8 / 26.4

The structure of Crystal Structure of T2R-Ttl-1129A2 Complex also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Calcium atom in the Crystal Structure of T2R-Ttl-1129A2 Complex (pdb code 7exc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of T2R-Ttl-1129A2 Complex, PDB code: 7exc:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of T2R-Ttl-1129A2 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-1129A2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:60.6 occ:0.00 OG1 A:THR41 2.4 68.2 1.0 HZ A:PHE49 2.4 73.3 1.0 OE2 A:GLU55 2.5 60.6 1.0 OD1 A:ASN50 2.6 61.3 1.0 HD21 A:ASN50 2.7 69.3 1.0 OD2 A:ASP47 2.9 67.1 1.0 HA3 A:GLY45 2.9 77.7 1.0 CZ A:PHE49 2.9 61.0 1.0 OD2 A:ASP39 3.1 62.9 1.0 ND2 A:ASN50 3.3 57.7 1.0 O A:GLY44 3.3 53.9 1.0 HE1 A:PHE49 3.3 74.7 1.0 CG A:ASN50 3.3 54.7 1.0 CE1 A:PHE49 3.4 62.1 1.0 HB2 A:ASP47 3.5 69.4 1.0 CG A:ASP47 3.5 64.0 1.0 H A:ASP47 3.6 73.8 1.0 CB A:THR41 3.6 79.0 1.0 OD1 A:ASP39 3.6 67.2 1.0 CG A:ASP39 3.6 65.5 1.0 HG21 A:THR41 3.6 86.4 1.0 CD A:GLU55 3.7 56.2 1.0 HG23 A:THR41 3.7 86.4 1.0 CE2 A:PHE49 3.8 60.8 1.0 CA A:GLY45 3.8 64.7 1.0 CG2 A:THR41 3.9 71.9 1.0 HB A:THR41 3.9 94.9 1.0 HE2 A:PHE49 3.9 73.1 1.0 CB A:ASP47 4.0 57.8 1.0 C A:GLY44 4.1 60.2 1.0 HD22 A:ASN50 4.1 69.3 1.0 OD1 A:ASP47 4.2 76.9 1.0 O A:THR41 4.3 69.0 1.0 OE1 A:GLU55 4.3 63.3 1.0 C A:GLY45 4.3 64.2 1.0 N A:GLY45 4.4 49.4 1.0 N A:ASP47 4.4 61.4 1.0 HA2 A:GLY45 4.4 77.7 1.0 CD1 A:PHE49 4.5 58.7 1.0 HG3 A:GLU55 4.6 73.7 1.0 H A:THR41 4.7 88.0 1.0 N A:ASP46 4.7 67.5 1.0 H A:ASP46 4.7 81.1 1.0 HB3 A:ASP47 4.7 69.4 1.0 CA A:THR41 4.8 74.0 1.0 CG A:GLU55 4.8 61.3 1.0 CD2 A:PHE49 4.8 51.2 1.0 HB2 A:ASP39 4.8 66.2 1.0 CB A:ASN50 4.8 53.5 1.0 HG22 A:THR41 4.8 86.4 1.0 CA A:ASP47 4.8 65.3 1.0 CB A:ASP39 4.9 55.0 1.0 O A:GLY45 5.0 49.1 1.0 C A:THR41 5.0 72.4 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of T2R-Ttl-1129A2 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-1129A2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:48.2 occ:0.00 OG1 C:THR41 2.2 59.3 1.0 OE2 C:GLU55 2.2 48.6 1.0 O C:THR41 2.3 53.7 1.0 OD2 C:ASP39 2.3 50.2 1.0 O C:GLY44 2.5 53.2 1.0 OD1 C:ASP39 2.5 49.3 1.0 CG C:ASP39 2.7 41.0 1.0 OE1 C:GLU55 2.8 43.3 1.0 CD C:GLU55 2.9 47.2 1.0 HA3 C:GLY45 3.2 59.4 1.0 CB C:THR41 3.3 48.4 1.0 C C:THR41 3.3 39.1 1.0 C C:GLY44 3.3 44.0 1.0 HB C:THR41 3.4 58.2 1.0 H C:THR41 3.6 52.0 1.0 CA C:THR41 3.7 44.7 1.0 H C:GLY44 3.7 59.0 1.0 OD2 C:ASP47 3.9 60.2 1.0 CA C:GLY45 3.9 49.4 1.0 N C:GLY45 3.9 44.3 1.0 HZ C:PHE49 4.0 43.5 1.0 O C:HOH612 4.0 54.5 1.0 N C:THR41 4.0 43.2 1.0 CB C:ASP39 4.3 46.0 1.0 HA2 C:GLY45 4.3 59.4 1.0 HD21 C:ASN50 4.3 42.5 1.0 CA C:GLY44 4.3 43.3 1.0 CG C:GLU55 4.3 33.5 1.0 N C:GLY44 4.4 49.1 1.0 N C:ILE42 4.5 52.8 1.0 HA2 C:GLY44 4.5 52.0 1.0 CG2 C:THR41 4.6 46.9 1.0 HB3 C:ASP39 4.6 55.3 1.0 HG3 C:GLU55 4.6 40.3 1.0 HA C:THR41 4.6 53.7 1.0 HA C:ILE42 4.6 63.3 1.0 OD1 C:ASN50 4.7 38.0 1.0 H C:GLY45 4.7 53.3 1.0 O C:HOH617 4.7 38.1 1.0 HE1 C:PHE49 4.7 51.4 1.0 HB2 C:ASP39 4.7 55.3 1.0 HG21 C:THR41 4.7 56.4 1.0 HG2 C:GLU55 4.8 40.3 1.0 CZ C:PHE49 4.8 36.2 1.0 HG23 C:THR41 4.8 56.4 1.0 NE2 C:HIS61 4.9 38.2 1.0 HA C:ASP39 5.0 59.6 1.0

Y.Li, Y.Liu, Z.Zhu, W.Yan, C.Zhang, Z.Yang, P.Bai, M.Tang, M.Shi, W.He, S.Fu, J.Liu, K.Han, J.Li, L.Xie, H.Ye, J.Yang, L.Chen. Structure-Based Design and Synthesis of N-Substituted 3-Amino-Beta-Carboline Derivatives As Potent Alpha Beta-Tubulin Degradation Agents J.Med.Chem. V. 65 2675 2022.
ISSN: ISSN 0022-2623
DOI: 10.1021/ACS.JMEDCHEM.1C02159