Calcium in PDB 8jjb: Crystal Structure of T2R-Ttl-Y61 Complex

The structure of Crystal Structure of T2R-Ttl-Y61 Complex, PDB code: 8jjb was solved by J.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.06 / 2.68
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.287, 157.915, 181.748, 90, 90, 90
R / Rfree (%)	22.7 / 26

The structure of Crystal Structure of T2R-Ttl-Y61 Complex also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Magnesium	(Mg)	5 atoms

The binding sites of Calcium atom in the Crystal Structure of T2R-Ttl-Y61 Complex (pdb code 8jjb). 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 T2R-Ttl-Y61 Complex, PDB code: 8jjb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of T2R-Ttl-Y61 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-Y61 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:84.2 occ:0.00 HZ A:PHE49 2.0 91.2 1.0 HG1 A:THR41 2.0 121.2 1.0 OG1 A:THR41 2.3 100.9 1.0 OE2 A:GLU55 2.5 90.8 1.0 OD1 A:ASP39 2.6 75.0 1.0 CZ A:PHE49 2.7 75.9 1.0 OD2 A:ASP39 2.8 90.1 1.0 OD2 A:ASP47 2.9 68.8 1.0 CG A:ASP39 2.9 82.4 1.0 OD1 A:ASN50 3.4 85.1 1.0 HE2 A:PHE49 3.5 97.9 1.0 CE2 A:PHE49 3.5 81.5 1.0 HD21 A:ASN50 3.5 90.6 1.0 CD A:GLU55 3.6 94.5 1.0 CE1 A:PHE49 3.6 76.4 1.0 HE1 A:PHE49 3.6 91.7 1.0 HA3 A:GLY45 3.7 97.4 1.0 CB A:THR41 3.7 107.0 1.0 HB2 A:ASP47 3.8 82.7 1.0 O A:GLY44 3.8 73.2 1.0 HG23 A:THR41 3.9 105.2 1.0 CG A:ASP47 4.0 71.6 1.0 OE1 A:GLU55 4.1 98.6 1.0 O A:THR41 4.1 102.8 1.0 HG21 A:THR41 4.1 105.2 1.0 H A:THR41 4.1 108.8 1.0 CG2 A:THR41 4.1 87.6 1.0 HB A:THR41 4.2 128.5 1.0 ND2 A:ASN50 4.2 75.5 1.0 CG A:ASN50 4.2 73.4 1.0 CB A:ASP39 4.2 75.2 1.0 HB2 A:ASP39 4.3 90.3 1.0 CB A:ASP47 4.4 68.8 1.0 H A:ASP47 4.5 97.6 1.0 NE2 A:HIS61 4.6 90.2 1.0 CA A:GLY45 4.6 81.1 1.0 CA A:THR41 4.6 92.1 1.0 HA A:ASP39 4.7 95.0 1.0 C A:GLY44 4.7 82.6 1.0 N A:THR41 4.8 90.6 1.0 CD2 A:PHE49 4.8 72.7 1.0 CG A:GLU55 4.8 88.0 1.0 C A:THR41 4.8 99.5 1.0 CD1 A:PHE49 4.8 75.8 1.0 HD2 A:HIS61 4.9 106.2 1.0 HG3 A:GLU55 4.9 105.7 1.0 HB3 A:ASP39 4.9 90.3 1.0 HD22 A:ASN50 5.0 90.6 1.0 HG2 A:GLU55 5.0 105.7 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of T2R-Ttl-Y61 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-Y61 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:70.7 occ:0.00 HB3 B:ASP114 3.2 57.7 1.0 CB B:ASP114 4.1 48.0 1.0 OD2 B:ASP114 4.1 78.7 1.0 CG B:ASP114 4.3 64.6 1.0 OD1 B:ASP118 4.3 58.8 1.0 OD2 B:ASP118 4.5 67.1 1.0 HH22 B:ARG121 4.5 99.7 1.0 HB2 B:ASP114 4.6 57.7 1.0 CG B:ASP118 4.9 64.1 1.0 HH21 B:ARG121 4.9 99.7 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of T2R-Ttl-Y61 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-Y61 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:76.6 occ:0.00 OE1 B:GLU111 2.7 85.6 1.0 OE2 B:GLU111 3.2 100.1 1.0 CD B:GLU111 3.3 92.0 1.0 OE1 B:GLU108 4.6 64.0 1.0 CG B:GLU111 4.7 56.9 1.0 HB2 B:GLU111 4.9 81.0 1.0 HG3 B:GLU111 4.9 68.4 1.0 OE2 B:GLU108 5.0 63.8 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of T2R-Ttl-Y61 Complex


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 T2R-Ttl-Y61 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:66.1 occ:0.00 OG1 C:THR41 2.3 84.0 1.0 OE2 C:GLU55 2.4 72.7 1.0 HA3 C:GLY45 2.6 88.5 1.0 O C:GLY44 2.7 66.4 1.0 OD2 C:ASP47 2.9 78.9 1.0 OD1 C:ASP39 3.0 61.4 1.0 OD2 C:ASP39 3.0 63.3 1.0 HZ C:PHE49 3.1 64.4 1.0 OD1 C:ASN50 3.2 65.7 1.0 CG C:ASP39 3.3 63.5 1.0 CD C:GLU55 3.4 65.2 1.0 CA C:GLY45 3.5 73.7 1.0 O C:THR41 3.6 76.3 1.0 HD21 C:ASN50 3.6 66.8 1.0 C C:GLY44 3.7 69.1 1.0 CB C:THR41 3.7 67.5 1.0 CZ C:PHE49 3.8 53.6 1.0 OE1 C:GLU55 3.8 73.5 1.0 HE2 C:PHE49 3.9 65.1 1.0 CG C:ASP47 4.0 59.6 1.0 N C:GLY45 4.0 68.5 1.0 HB C:THR41 4.0 81.0 1.0 HA2 C:GLY45 4.0 88.5 1.0 HB2 C:ASP47 4.0 75.6 1.0 CG C:ASN50 4.1 57.2 1.0 H C:ASP47 4.1 66.0 1.0 CE2 C:PHE49 4.2 54.2 1.0 ND2 C:ASN50 4.2 55.6 1.0 H C:THR41 4.4 64.9 1.0 C C:GLY45 4.4 65.6 1.0 HG21 C:THR41 4.4 61.6 1.0 C C:THR41 4.5 65.6 1.0 CG2 C:THR41 4.6 51.3 1.0 CB C:ASP47 4.6 63.0 1.0 CA C:THR41 4.6 62.8 1.0 H C:GLY44 4.6 81.3 1.0 HG3 C:GLU55 4.7 68.2 1.0 HG23 C:THR41 4.7 61.6 1.0 CG C:GLU55 4.7 56.8 1.0 CB C:ASP39 4.7 64.6 1.0 H C:ASP46 4.7 91.9 1.0 CE1 C:PHE49 4.8 57.5 1.0 H C:GLY45 4.8 82.3 1.0 N C:ASP46 4.8 76.5 1.0 HB2 C:ASP39 4.9 77.6 1.0 HE1 C:PHE49 4.9 69.1 1.0 N C:THR41 4.9 54.0 1.0 OD1 C:ASP47 4.9 60.0 1.0 CA C:GLY44 4.9 68.1 1.0 N C:ASP47 5.0 54.9 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of T2R-Ttl-Y61 Complex


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 T2R-Ttl-Y61 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca502 b:74.5 occ:0.00 HG13 D:VAL175 3.1 109.7 1.0 CZ D:TYR222 3.9 63.4 1.0 O D:VAL175 3.9 84.5 1.0 CE1 D:TYR222 3.9 72.8 1.0 CG1 D:VAL175 4.0 91.4 1.0 HG12 D:VAL175 4.0 109.7 1.0 O D:PRO220 4.1 81.3 1.0 HA D:THR221 4.1 103.8 1.0 CE2 D:TYR222 4.1 69.8 1.0 HE1 D:TYR222 4.2 87.5 1.0 CD1 D:TYR222 4.2 66.0 1.0 OH D:TYR222 4.3 69.4 1.0 H D:TYR222 4.4 92.6 1.0 HG11 D:VAL175 4.4 109.7 1.0 HA D:VAL175 4.4 98.8 1.0 CD2 D:TYR222 4.4 77.8 1.0 CG D:TYR222 4.5 73.9 1.0 HE2 D:TYR222 4.5 83.9 1.0 HH D:TYR222 4.5 83.4 1.0 HD1 D:TYR222 4.6 79.3 1.0 N D:TYR222 4.7 77.1 1.0 C D:VAL175 4.9 89.2 1.0 HD2 D:TYR222 4.9 93.4 1.0 CA D:THR221 5.0 86.4 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of T2R-Ttl-Y61 Complex


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 T2R-Ttl-Y61 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:75.2 occ:0.00 OD2 E:ASP44 3.4 104.1 1.0 HZ1 A:LYS166 3.4 96.1 1.0 HG A:SER158 3.6 84.4 1.0 HZ3 A:LYS166 3.8 96.1 1.0 HA A:HIS197 3.9 68.8 1.0 OG A:SER158 3.9 70.2 1.0 HB3 A:SER158 4.0 70.5 1.0 NZ A:LYS166 4.0 80.0 1.0 O A:GLY162 4.2 94.4 1.0 O A:GLU196 4.4 65.2 1.0 CB A:SER158 4.4 58.7 1.0 CG E:ASP44 4.5 99.5 1.0 HZ2 A:LYS166 4.5 96.1 1.0 HA A:SER158 4.6 78.6 1.0 CA A:HIS197 4.8 57.3 1.0 HA2 A:GLY162 4.8 91.9 1.0 O A:HIS197 4.9 55.4 1.0 OD1 A:ASP199 4.9 55.2 1.0 HE2 A:LYS166 4.9 75.8 1.0 OD1 E:ASP44 4.9 82.9 1.0

C.Zhang, W.Yan, Y.Liu, M.Tang, Y.Teng, F.Wang, X.Hu, M.Zhao, J.Yang, Y.Li. Structure-Based Design and Synthesis of BML284 Derivatives: A Novel Class of Colchicine-Site Noncovalent Tubulin Degradation Agents. Eur.J.Med.Chem. V. 268 16265 2024.
ISSN: ISSN 0223-5234
PubMed: 38430854
DOI: 10.1016/J.EJMECH.2024.116265