Calcium in PDB 5cb4: Crystal Structure of T2R-Ttl-Tivantinib Complex

The structure of Crystal Structure of T2R-Ttl-Tivantinib Complex, PDB code: 5cb4 was solved by Y.Wang, Y.Yu, Q.Chen, J.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.82 / 2.19
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.060, 158.444, 181.825, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 23.2

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

Magnesium

(Mg)

3 atoms

The binding sites of Calcium atom in the Crystal Structure of T2R-Ttl-Tivantinib Complex (pdb code 5cb4). 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-Tivantinib Complex, PDB code: 5cb4:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of T2R-Ttl-Tivantinib 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-Tivantinib Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:56.4 occ:1.00 OD2 A:ASP39 2.4 61.4 1.0 OD1 A:ASP39 2.4 46.6 1.0 O A:GLY44 2.4 45.4 1.0 OG1 A:THR41 2.5 62.6 1.0 OE2 A:GLU55 2.5 46.9 1.0 O A:HOH610 2.5 45.4 1.0 CG A:ASP39 2.7 49.9 1.0 O A:THR41 2.7 56.4 1.0 OE1 A:GLU55 2.9 52.9 1.0 CD A:GLU55 3.0 65.8 1.0 HZ A:PHE49 3.3 78.2 1.0 HB A:THR41 3.4 71.2 1.0 HA3 A:GLY45 3.5 81.6 1.0 CB A:THR41 3.5 59.4 1.0 C A:GLY44 3.5 57.7 1.0 C A:THR41 3.7 70.7 1.0 H A:THR41 3.8 80.1 1.0 H A:GLY44 3.8 75.2 1.0 HD21 A:ASN50 3.8 53.0 1.0 CA A:THR41 4.0 56.4 1.0 CZ A:PHE49 4.1 65.2 1.0 CB A:ASP39 4.2 49.7 1.0 N A:GLY45 4.3 44.9 1.0 N A:THR41 4.3 66.8 1.0 CA A:GLY45 4.3 68.0 1.0 O A:HOH614 4.3 48.8 1.0 HE1 A:PHE49 4.4 70.3 1.0 NE2 A:HIS61 4.4 64.8 1.0 CA A:GLY44 4.4 60.9 1.0 OD1 A:ASN50 4.4 44.6 1.0 N A:GLY44 4.5 62.6 1.0 CG A:GLU55 4.5 53.7 1.0 HA2 A:GLY44 4.6 73.1 1.0 HB2 A:ASP39 4.6 59.6 1.0 ND2 A:ASN50 4.6 44.2 1.0 HB3 A:ASP39 4.6 59.6 1.0 CE1 A:PHE49 4.7 58.6 1.0 CG2 A:THR41 4.8 59.5 1.0 HG21 A:THR41 4.9 71.4 1.0 O A:HOH609 4.9 54.9 1.0 HG3 A:GLU55 4.9 64.4 1.0 HA2 A:GLY45 4.9 81.6 1.0 HG2 A:GLU55 4.9 64.4 1.0 N A:ILE42 4.9 68.5 1.0 HA A:ASP39 4.9 61.6 1.0 HA A:THR41 4.9 67.7 1.0 CG A:ASN50 5.0 48.5 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of T2R-Ttl-Tivantinib 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-Tivantinib Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:44.5 occ:1.00 O C:THR41 2.4 49.4 1.0 OD2 C:ASP39 2.4 43.6 1.0 OG1 C:THR41 2.4 45.8 1.0 O C:GLY44 2.4 42.9 1.0 OE2 C:GLU55 2.5 44.6 1.0 O C:HOH609 2.5 37.0 1.0 OE1 C:GLU55 2.5 44.1 1.0 OD1 C:ASP39 2.6 43.9 1.0 CD C:GLU55 2.8 41.3 1.0 CG C:ASP39 2.9 37.6 1.0 HA3 C:GLY45 3.3 72.9 1.0 C C:THR41 3.5 63.5 1.0 C C:GLY44 3.5 46.0 1.0 CB C:THR41 3.5 57.4 1.0 HB C:THR41 3.7 68.8 1.0 H C:THR41 3.8 63.3 1.0 H C:GLY44 3.9 58.4 1.0 CA C:THR41 3.9 58.3 1.0 HD21 C:ASN50 4.0 46.8 1.0 HZ C:PHE49 4.0 40.8 1.0 CA C:GLY45 4.1 60.7 1.0 O C:HOH612 4.2 46.6 1.0 HE1 C:PHE49 4.2 50.4 1.0 N C:THR41 4.2 52.8 1.0 N C:GLY45 4.2 48.6 1.0 CG C:GLU55 4.4 37.5 1.0 CB C:ASP39 4.4 36.4 1.0 OD2 C:ASP47 4.4 56.1 1.0 N C:GLY44 4.5 48.7 1.0 NE2 C:HIS61 4.5 35.9 1.0 CA C:GLY44 4.5 36.7 1.0 HA2 C:GLY45 4.6 72.9 1.0 OD1 C:ASN50 4.6 35.1 1.0 HA C:ILE42 4.7 60.5 1.0 N C:ILE42 4.7 52.5 1.0 CZ C:PHE49 4.7 34.0 1.0 HB3 C:ASP39 4.7 43.6 1.0 HG2 C:GLU55 4.7 45.0 1.0 HG3 C:GLU55 4.7 45.0 1.0 ND2 C:ASN50 4.8 39.0 1.0 O C:HOH752 4.8 46.3 1.0 CE1 C:PHE49 4.8 42.0 1.0 HB2 C:ASP39 4.8 43.6 1.0 CG2 C:THR41 4.8 51.2 1.0 HA2 C:GLY44 4.8 44.0 1.0 HA C:THR41 4.9 69.9 1.0 H C:GLY43 4.9 51.3 1.0 HG21 C:THR41 5.0 61.5 1.0

Y.Wang, H.Zhang, B.Gigant, Y.Yu, Y.Wu, X.Chen, Q.Lai, Z.Yang, Q.Chen, J.Yang. Structures of A Diverse Set of Colchicine Binding Site Inhibitors in Complex with Tubulin Provide A Rationale For Drug Discovery. Febs J. V. 283 102 2016.
ISSN: ISSN 1742-464X
PubMed: 26462166
DOI: 10.1111/FEBS.13555