Calcium in PDB 5yz3: Crystal Structure of T2R-Ttl-28 Complex

The structure of Crystal Structure of T2R-Ttl-28 Complex, PDB code: 5yz3 was solved by Y.Yu, Q.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.62 / 2.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.887, 157.496, 180.904, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 23.4

The structure of Crystal Structure of T2R-Ttl-28 Complex also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Chlorine	(Cl)	1 atom
Sodium	(Na)	1 atom

The binding sites of Calcium atom in the Crystal Structure of T2R-Ttl-28 Complex (pdb code 5yz3). 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-28 Complex, PDB code: 5yz3:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of T2R-Ttl-28 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-28 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:50.1 occ:1.00 O A:GLY44 2.3 57.5 1.0 OD2 A:ASP39 2.3 55.1 1.0 O A:THR41 2.4 65.9 1.0 OE2 A:GLU55 2.4 56.6 1.0 OG1 A:THR41 2.4 72.3 1.0 OD1 A:ASP39 2.5 58.7 1.0 OE1 A:GLU55 2.5 64.6 1.0 CG A:ASP39 2.7 54.5 1.0 CD A:GLU55 2.8 59.9 1.0 HA3 A:GLY45 3.0 78.1 1.0 HB A:THR41 3.2 75.4 1.0 C A:GLY44 3.2 60.9 1.0 CB A:THR41 3.3 62.9 1.0 C A:THR41 3.4 64.8 1.0 HD21 A:ASN50 3.6 77.8 1.0 H A:GLY44 3.6 75.7 1.0 CA A:GLY45 3.8 65.1 1.0 HZ A:PHE49 3.8 63.4 1.0 CA A:THR41 3.8 65.1 1.0 HE1 A:HIS61 3.9 74.5 1.0 N A:GLY45 3.9 60.3 1.0 H A:THR41 4.0 71.8 1.0 HA2 A:GLY45 4.1 78.1 1.0 CB A:ASP39 4.2 53.4 1.0 N A:THR41 4.3 59.8 1.0 CA A:GLY44 4.3 66.5 1.0 N A:GLY44 4.3 63.1 1.0 CG A:GLU55 4.3 59.8 1.0 ND2 A:ASN50 4.4 64.8 1.0 HB2 A:ASP39 4.4 64.0 1.0 HA2 A:GLY44 4.5 79.7 1.0 CZ A:PHE49 4.6 52.9 1.0 OD2 A:ASP47 4.6 58.9 1.0 N A:ILE42 4.6 61.8 1.0 HB3 A:ASP39 4.6 64.0 1.0 OD1 A:ASN50 4.6 56.5 1.0 HE1 A:PHE49 4.6 60.9 1.0 HA A:ILE42 4.7 66.9 1.0 H A:GLY45 4.7 72.4 1.0 CG2 A:THR41 4.7 56.0 1.0 HG3 A:GLU55 4.7 71.8 1.0 HG2 A:GLU55 4.7 71.8 1.0 HA A:THR41 4.7 78.2 1.0 CE1 A:HIS61 4.7 62.1 1.0 HG21 A:THR41 4.8 67.1 1.0 CG A:ASN50 5.0 57.4 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of T2R-Ttl-28 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-28 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:37.4 occ:1.00 O C:THR41 2.3 41.0 1.0 OG1 C:THR41 2.4 41.9 1.0 O C:GLY44 2.4 39.4 1.0 OE2 C:GLU55 2.4 36.1 1.0 O C:HOH623 2.5 31.4 1.0 OD2 C:ASP39 2.5 34.8 1.0 OE1 C:GLU55 2.6 34.1 1.0 OD1 C:ASP39 2.8 39.4 1.0 CD C:GLU55 2.8 33.7 1.0 CG C:ASP39 3.0 37.5 1.0 HA3 C:GLY45 3.2 52.1 1.0 C C:GLY44 3.3 41.5 1.0 C C:THR41 3.4 38.7 1.0 CB C:THR41 3.5 40.6 1.0 HB C:THR41 3.7 48.8 1.0 H C:GLY44 3.9 55.8 1.0 CA C:THR41 3.9 40.3 1.0 H C:THR41 4.0 49.4 1.0 HD21 C:ASN50 4.0 35.9 1.0 CA C:GLY45 4.0 43.4 1.0 N C:GLY45 4.0 39.5 1.0 HZ C:PHE49 4.0 42.0 1.0 HE1 C:PHE49 4.2 43.2 1.0 O C:HOH637 4.2 29.9 1.0 O C:HOH635 4.3 41.8 1.0 OD2 C:ASP47 4.3 40.1 1.0 CA C:GLY44 4.3 44.2 1.0 N C:THR41 4.3 41.1 1.0 CG C:GLU55 4.4 30.3 1.0 N C:GLY44 4.4 46.5 1.0 HA2 C:GLY44 4.4 53.0 1.0 HA2 C:GLY45 4.5 52.1 1.0 OD1 C:ASN50 4.5 29.0 1.0 HA C:ILE42 4.5 47.3 1.0 CB C:ASP39 4.5 41.6 1.0 NE2 C:HIS61 4.6 34.0 1.0 N C:ILE42 4.6 40.0 1.0 HG3 C:GLU55 4.7 36.3 1.0 CZ C:PHE49 4.7 35.0 1.0 CG2 C:THR41 4.8 41.0 1.0 ND2 C:ASN50 4.8 29.9 1.0 HG2 C:GLU55 4.8 36.3 1.0 H C:GLY45 4.8 47.4 1.0 CE1 C:PHE49 4.8 36.0 1.0 HA C:THR41 4.8 48.4 1.0 HB3 C:ASP39 4.9 50.0 1.0 HG21 C:THR41 4.9 49.1 1.0 HB2 C:ASP39 4.9 50.0 1.0 CA C:ILE42 5.0 39.4 1.0 HG23 C:THR41 5.0 49.1 1.0

N.Ning, Y.Yu, M.Wu, R.Zhang, T.Zhang, C.Zhu, L.Huang, C.H.Yun, C.H.Benes, J.Zhang, X.Deng, Q.Chen, R.Ren. A Novel Microtubule Inhibitor Overcomes Multidrug Resistance in Tumors. Cancer Res. V. 78 5949 2018.
ISSN: ESSN 1538-7445
PubMed: 30135190
DOI: 10.1158/0008-5472.CAN-18-0455