Calcium in PDB 6knz: Crystal Structure of T2R-Ttl-KXO1 Complex

The structure of Crystal Structure of T2R-Ttl-KXO1 Complex, PDB code: 6knz was solved by Q.Chen, Y.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.23 / 2.48
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.928, 157.059, 182.210, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 26.1

The structure of Crystal Structure of T2R-Ttl-KXO1 Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Crystal Structure of T2R-Ttl-KXO1 Complex (pdb code 6knz). 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-KXO1 Complex, PDB code: 6knz:
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-KXO1 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-KXO1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:72.6 occ:1.00 O A:GLY44 2.3 88.9 1.0 OD1 A:ASP39 2.4 82.9 1.0 O A:THR41 2.4 85.8 1.0 OD2 A:ASP39 2.4 90.5 1.0 O A:HOH608 2.4 0.1 1.0 OE2 A:GLU55 2.6 91.4 1.0 OG1 A:THR41 2.6 0.0 1.0 HG1 A:THR41 2.7 0.2 1.0 CG A:ASP39 2.7 85.9 1.0 OE1 A:GLU55 2.8 85.4 1.0 CD A:GLU55 3.1 84.7 1.0 HA3 A:GLY45 3.4 0.6 1.0 C A:THR41 3.5 85.0 1.0 C A:GLY44 3.5 89.2 1.0 H A:GLY44 3.6 96.3 1.0 CB A:THR41 3.6 94.6 1.0 HZ A:PHE49 3.6 0.3 1.0 HB A:THR41 3.6 0.7 1.0 HD22 A:ASN50 3.6 0.6 1.0 H A:THR41 3.7 0.9 1.0 CA A:THR41 3.9 90.0 1.0 N A:THR41 4.1 88.1 1.0 CB A:ASP39 4.2 83.1 1.0 CA A:GLY45 4.3 0.4 1.0 N A:GLY45 4.3 89.5 1.0 N A:GLY44 4.3 80.1 1.0 OD2 A:ASP47 4.4 97.7 1.0 ND2 A:ASN50 4.4 87.0 1.0 CZ A:PHE49 4.4 88.4 1.0 CA A:GLY44 4.6 87.3 1.0 CG A:GLU55 4.6 82.5 1.0 HB2 A:ASP39 4.6 99.9 1.0 HB3 A:ASP39 4.6 99.9 1.0 NE2 A:HIS61 4.6 81.6 1.0 N A:ILE42 4.6 82.7 1.0 HA A:ILE42 4.6 94.4 1.0 HA2 A:GLY45 4.7 0.6 1.0 H A:GLY43 4.8 96.3 1.0 HE1 A:PHE49 4.9 0.7 1.0 HA A:ASP39 4.9 0.7 1.0 HA A:THR41 4.9 0.2 1.0 HD21 A:ASN50 4.9 0.6 1.0 HG2 A:GLU55 4.9 99.2 1.0 CG2 A:THR41 4.9 81.8 1.0 HG3 A:GLU55 4.9 99.2 1.0 OD1 A:ASN50 5.0 87.7 1.0 CA A:ASP39 5.0 86.3 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of T2R-Ttl-KXO1 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-KXO1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:1.0 occ:1.00 O B:HOH612 2.6 70.7 1.0 HB3 B:ASP116 3.6 78.7 1.0 OD2 B:ASP116 4.0 70.1 1.0 OD1 B:ASP120 4.2 61.7 1.0 OD2 B:ASP120 4.3 68.2 1.0 CB B:ASP116 4.4 65.4 1.0 CG B:ASP116 4.5 66.8 1.0 CG B:ASP120 4.7 65.8 1.0 HB2 B:ASP116 4.9 78.7 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of T2R-Ttl-KXO1 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-KXO1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca505 b:93.1 occ:1.00 OE1 B:GLU113 2.7 75.1 1.0 OE2 B:GLU113 3.4 75.8 1.0 CD B:GLU113 3.4 72.1 1.0 OE1 B:GLU110 4.6 50.0 1.0 CG B:GLU113 4.9 67.4 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of T2R-Ttl-KXO1 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-KXO1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:65.0 occ:1.00 O C:THR41 2.3 64.5 1.0 OD2 C:ASP39 2.4 61.7 1.0 OE2 C:GLU55 2.4 62.6 1.0 OG1 C:THR41 2.5 61.0 1.0 O C:GLY44 2.5 63.2 1.0 O C:HOH604 2.5 55.4 1.0 OE1 C:GLU55 2.6 57.8 1.0 OD1 C:ASP39 2.6 58.6 1.0 CG C:ASP39 2.8 61.8 1.0 CD C:GLU55 2.8 60.6 1.0 C C:THR41 3.3 59.8 1.0 HA3 C:GLY45 3.4 73.1 1.0 CB C:THR41 3.4 58.1 1.0 C C:GLY44 3.5 63.8 1.0 HB C:THR41 3.5 69.9 1.0 H C:THR41 3.7 71.7 1.0 HZ C:PHE49 3.7 61.6 1.0 H C:GLY44 3.8 77.0 1.0 CA C:THR41 3.8 60.0 1.0 N C:THR41 4.1 59.6 1.0 CA C:GLY45 4.2 60.8 1.0 HD21 C:ASN50 4.2 63.8 1.0 N C:GLY45 4.2 60.9 1.0 OD2 C:ASP47 4.2 63.7 1.0 CB C:ASP39 4.3 66.6 1.0 CG C:GLU55 4.3 58.7 1.0 HE1 C:PHE49 4.4 61.5 1.0 N C:GLY44 4.4 64.0 1.0 CA C:GLY44 4.5 69.1 1.0 N C:ILE42 4.5 59.2 1.0 CZ C:PHE49 4.5 51.2 1.0 HA C:ILE42 4.6 68.4 1.0 OD1 C:ASN50 4.6 48.4 1.0 HB3 C:ASP39 4.6 80.1 1.0 HA2 C:GLY45 4.6 73.1 1.0 NE2 C:HIS61 4.7 55.3 1.0 HG3 C:GLU55 4.7 70.7 1.0 HG2 C:GLU55 4.7 70.7 1.0 HB2 C:ASP39 4.7 80.1 1.0 HA2 C:GLY44 4.7 83.1 1.0 HA C:THR41 4.7 72.2 1.0 CG2 C:THR41 4.8 60.2 1.0 CE1 C:PHE49 4.9 51.1 1.0 ND2 C:ASN50 4.9 53.0 1.0 HG21 C:THR41 4.9 72.4 1.0 CA C:ILE42 5.0 56.8 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of T2R-Ttl-KXO1 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-KXO1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca502 b:0.1 occ:1.00 O D:PRO222 3.7 82.6 1.0 HG13 D:VAL177 3.7 93.8 1.0 H D:TYR224 3.9 0.2 1.0 HA D:THR223 3.9 1.0 1.0 N D:TYR224 4.0 89.2 1.0 CD2 D:TYR224 4.1 75.3 1.0 CE2 D:TYR224 4.1 75.9 1.0 CG D:TYR224 4.2 83.2 1.0 C D:THR223 4.2 90.5 1.0 CZ D:TYR224 4.2 73.5 1.0 CD1 D:TYR224 4.3 75.6 1.0 CE1 D:TYR224 4.3 76.4 1.0 HD2 D:TYR224 4.4 90.5 1.0 HE2 D:TYR224 4.5 91.3 1.0 CA D:THR223 4.5 89.0 1.0 CG1 D:VAL177 4.5 78.0 1.0 HA D:TYR224 4.6 93.5 1.0 O D:THR223 4.6 89.3 1.0 HG12 D:VAL177 4.6 93.8 1.0 O D:VAL177 4.7 83.0 1.0 HD1 D:TYR224 4.7 90.9 1.0 C D:PRO222 4.7 91.3 1.0 HE1 D:TYR224 4.7 91.8 1.0 CA D:TYR224 4.8 77.8 1.0 HH D:TYR224 4.8 94.2 1.0 OH D:TYR224 4.9 78.3 1.0 HB2 D:TYR224 4.9 95.2 1.0 HG11 D:VAL177 4.9 93.8 1.0 CB D:TYR224 4.9 79.2 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of T2R-Ttl-KXO1 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-KXO1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:83.4 occ:1.00 O A:HOH647 2.5 53.9 1.0 OD2 E:ASP44 3.3 85.3 1.0 HZ3 A:LYS166 3.6 67.1 1.0 OG A:SER158 3.6 63.7 1.0 HZ1 A:LYS166 3.8 67.1 1.0 HG A:SER158 3.9 76.6 1.0 HA A:HIS197 3.9 68.0 1.0 HB3 A:SER158 4.1 75.6 1.0 NZ A:LYS166 4.1 55.8 1.0 O A:GLU196 4.4 65.2 1.0 O A:GLY162 4.4 89.5 1.0 CB A:SER158 4.4 62.8 1.0 CG E:ASP44 4.4 88.5 1.0 HZ2 A:LYS166 4.5 67.1 1.0 HA A:SER158 4.5 79.1 1.0 CA A:HIS197 4.8 56.5 1.0 HA2 A:GLY162 4.8 0.6 1.0 O A:HIS197 4.9 51.0 1.0 OD1 E:ASP44 5.0 86.0 1.0

L.Niu, J.Yang, W.Yan, Y.Yu, Y.Zheng, H.Ye, Q.Chen, L.Chen. Reversible Binding of the Anticancer Drug KXO1 (Tirbanibulin) to the Colchicine-Binding Site of Beta-Tubulin Explains KXO1'S Low Clinical Toxicity. J.Biol.Chem. 2019.
ISSN: ESSN 1083-351X
PubMed: 31628188
DOI: 10.1074/JBC.RA119.010732