Magnesium 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:

Calcium

(Ca)

6 atoms

The binding sites of Magnesium atom in the Crystal Structure of T2R-Ttl-KXO1 Complex (pdb code 6knz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of T2R-Ttl-KXO1 Complex, PDB code: 6knz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of T2R-Ttl-KXO1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of T2R-Ttl-KXO1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:40.5 occ:1.00 O A:HOH624 1.9 44.8 1.0 O A:HOH613 1.9 41.1 1.0 O A:HOH638 2.0 47.1 1.0 O A:HOH609 2.0 48.2 1.0 O2G A:GTP501 2.1 29.0 1.0 O1B A:GTP501 2.3 34.3 1.0 HZ1 B:LYS254 3.2 68.2 1.0 PG A:GTP501 3.3 49.6 1.0 HB2 A:GLN11 3.4 49.6 1.0 PB A:GTP501 3.4 45.6 1.0 HG2 A:GLU71 3.5 70.7 1.0 OE2 A:GLU71 3.5 65.7 1.0 O3B A:GTP501 3.7 49.4 1.0 HG3 A:GLU71 3.7 70.7 1.0 HB2 A:ASP98 3.7 57.2 1.0 H A:GLN11 3.7 50.9 1.0 OD1 A:ASP69 3.8 47.5 1.0 HZ3 B:LYS254 3.8 68.2 1.0 O1G A:GTP501 3.9 40.2 1.0 NZ B:LYS254 3.9 56.7 1.0 CG A:GLU71 3.9 58.8 1.0 HB3 A:ASP98 4.0 57.2 1.0 O3A A:GTP501 4.0 39.0 1.0 OD2 A:ASP69 4.1 51.6 1.0 HD21 B:ASN249 4.1 92.0 1.0 CD A:GLU71 4.2 59.3 1.0 CB A:GLN11 4.2 41.2 1.0 OD2 A:ASP98 4.2 48.9 1.0 CB A:ASP98 4.2 47.5 1.0 HB3 A:GLN11 4.2 49.6 1.0 HG1 A:THR145 4.3 47.9 1.0 CG A:ASP69 4.3 50.0 1.0 HZ2 B:LYS254 4.3 68.2 1.0 N A:GLN11 4.4 42.3 1.0 ND2 B:ASN249 4.4 76.5 1.0 HD22 B:ASN249 4.5 92.0 1.0 O3G A:GTP501 4.5 38.0 1.0 CG A:ASP98 4.6 46.9 1.0 O1A A:GTP501 4.7 46.4 1.0 O2B A:GTP501 4.7 41.8 1.0 HA2 A:GLY10 4.7 48.7 1.0 OE1 A:GLN11 4.7 51.5 1.0 HB A:THR145 4.8 56.9 1.0 HG21 A:VAL74 4.8 67.7 1.0 CA A:GLN11 4.9 44.3 1.0 OG1 A:THR145 4.9 39.8 1.0 PA A:GTP501 4.9 49.4 1.0 HE3 B:LYS254 4.9 60.3 1.0 CE B:LYS254 5.0 50.1 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of T2R-Ttl-KXO1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of T2R-Ttl-KXO1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:39.8 occ:1.00 O B:HOH605 2.1 52.0 1.0 O C:HOH654 2.2 49.5 1.0 OE1 B:GLN11 2.3 58.0 1.0 O B:HOH621 2.3 45.2 1.0 O1A B:GDP501 2.3 42.8 1.0 O B:HOH637 2.8 49.0 1.0 CD B:GLN11 3.4 59.1 1.0 PA B:GDP501 3.6 54.0 1.0 HB3 B:GLN11 3.7 52.0 1.0 OD2 B:ASP179 3.7 50.9 1.0 O3A B:GDP501 3.9 40.8 1.0 H8 B:GDP501 4.0 54.6 1.0 HB2 B:GLN11 4.0 52.0 1.0 C5' B:GDP501 4.0 50.1 1.0 OD1 B:ASN101 4.2 40.9 1.0 CB B:GLN11 4.2 43.2 1.0 O5' B:GDP501 4.2 40.5 1.0 HE22 B:GLN11 4.3 81.8 1.0 HD21 B:ASN101 4.3 47.5 1.0 NE2 B:GLN11 4.3 68.0 1.0 CG B:GLN11 4.4 52.3 1.0 O1B B:GDP501 4.5 41.4 1.0 OE1 C:GLU254 4.5 54.9 1.0 HG2 B:GLN11 4.6 62.9 1.0 O2A B:GDP501 4.8 39.9 1.0 CG B:ASP179 4.8 48.9 1.0 PB B:GDP501 4.8 47.0 1.0 HB3 B:ASP179 4.9 59.6 1.0 ND2 B:ASN101 5.0 39.4 1.0 C8 B:GDP501 5.0 45.4 1.0 CG B:ASN101 5.0 41.2 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of T2R-Ttl-KXO1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of T2R-Ttl-KXO1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:42.4 occ:1.00 O C:HOH611 2.0 38.1 1.0 O C:HOH625 2.0 43.0 1.0 O C:HOH631 2.0 42.0 1.0 O1B C:GTP501 2.1 32.7 1.0 O1G C:GTP501 2.2 30.8 1.0 O C:HOH627 2.2 47.5 1.0 HG2 C:GLU71 3.3 55.1 1.0 PG C:GTP501 3.3 45.0 1.0 HB2 C:GLN11 3.4 46.6 1.0 PB C:GTP501 3.4 39.9 1.0 HZ1 D:LYS254 3.4 74.2 1.0 OE2 C:GLU71 3.6 53.8 1.0 H C:GLN11 3.6 43.6 1.0 HG3 C:GLU71 3.7 55.1 1.0 O3B C:GTP501 3.7 36.0 1.0 O2G C:GTP501 3.8 38.9 1.0 OD1 C:ASP69 3.8 38.1 1.0 HB2 C:ASP98 3.8 50.8 1.0 OD2 C:ASP69 3.8 36.1 1.0 CG C:GLU71 3.9 45.7 1.0 O3A C:GTP501 4.0 42.6 1.0 HE21 C:GLN11 4.0 67.6 1.0 HZ3 D:LYS254 4.0 74.2 1.0 NZ D:LYS254 4.1 61.6 1.0 CB C:GLN11 4.2 38.7 1.0 HB3 C:GLN11 4.2 46.6 1.0 CD C:GLU71 4.2 48.2 1.0 CG C:ASP69 4.2 44.7 1.0 HB3 C:ASP98 4.3 50.8 1.0 OD2 C:ASP98 4.3 40.4 1.0 N C:GLN11 4.3 36.2 1.0 CB C:ASP98 4.4 42.1 1.0 HZ2 D:LYS254 4.5 74.2 1.0 NE2 C:GLN11 4.6 56.2 1.0 O2B C:GTP501 4.6 38.8 1.0 O3G C:GTP501 4.6 32.2 1.0 HA2 C:GLY10 4.7 46.9 1.0 HG1 C:THR145 4.7 50.7 1.0 HG21 C:VAL74 4.7 56.4 1.0 O1A C:GTP501 4.8 36.6 1.0 CG C:ASP98 4.8 41.6 1.0 CA C:GLN11 4.8 39.4 1.0 HB3 D:ASN249 4.9 0.9 1.0 HE22 C:GLN11 4.9 67.6 1.0 PA C:GTP501 4.9 40.0 1.0 HB C:THR145 5.0 47.5 1.0 H C:GLU71 5.0 60.0 1.0 HG23 C:VAL74 5.0 56.4 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of T2R-Ttl-KXO1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of T2R-Ttl-KXO1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:74.8 occ:1.00 O2G D:GTP503 2.6 83.8 1.0 O2B D:GTP503 2.7 71.2 1.0 O3G D:GTP503 2.8 76.7 1.0 HB2 D:GLN11 2.9 92.0 1.0 PG D:GTP503 3.2 89.6 1.0 HG3 D:GLU71 3.2 0.7 1.0 H D:GLN11 3.5 97.8 1.0 CB D:GLN11 3.7 76.5 1.0 HB3 D:GLN11 3.8 92.0 1.0 HB2 D:GLU71 3.8 0.1 1.0 PB D:GTP503 3.9 78.0 1.0 O3B D:GTP503 4.0 77.0 1.0 CG D:GLU71 4.1 0.6 1.0 N D:GLN11 4.1 81.4 1.0 HG21 D:THR74 4.2 0.6 1.0 OD2 D:ASP69 4.2 72.0 1.0 HG23 D:THR74 4.2 0.6 1.0 OE1 D:GLN11 4.4 80.7 1.0 OD1 D:ASP69 4.4 70.0 1.0 CB D:GLU71 4.5 87.5 1.0 CA D:GLN11 4.5 82.1 1.0 CD D:GLU71 4.5 0.8 1.0 O3A D:GTP503 4.5 70.1 1.0 O1G D:GTP503 4.5 76.3 1.0 O2A D:GTP503 4.6 83.5 1.0 CG2 D:THR74 4.6 86.2 1.0 HA2 D:GLY10 4.6 91.7 1.0 HG22 D:THR74 4.7 0.6 1.0 HA D:GLN11 4.7 98.7 1.0 CG D:ASP69 4.8 72.2 1.0 CG D:GLN11 4.8 77.2 1.0 OE2 D:GLU71 4.8 88.0 1.0 HG3 D:GLN11 4.8 92.9 1.0 HG2 D:GLU71 4.8 0.7 1.0 HG1 D:THR145 4.8 96.9 1.0 HB3 D:GLU71 4.8 0.1 1.0 OE1 D:GLU71 4.9 1.0 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of T2R-Ttl-KXO1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of T2R-Ttl-KXO1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:98.8 occ:1.00 O1G F:ACP402 2.3 0.8 1.0 OE1 F:GLU331 2.7 98.3 1.0 OD1 F:ASN333 2.8 94.5 1.0 HE3 F:LYS74 2.9 0.6 1.0 O1B F:ACP402 3.0 0.8 1.0 HZ1 F:LYS74 3.1 0.1 1.0 OE2 F:GLU331 3.4 0.6 1.0 CD F:GLU331 3.4 0.4 1.0 NZ F:LYS74 3.6 94.9 1.0 HZ2 F:LYS74 3.6 0.1 1.0 CE F:LYS74 3.7 87.0 1.0 PG F:ACP402 3.8 0.4 1.0 CG F:ASN333 3.9 87.4 1.0 HE2 F:LYS74 4.0 0.6 1.0 PB F:ACP402 4.2 0.5 1.0 O2G F:ACP402 4.4 0.3 1.0 HB3 F:ASN333 4.4 91.8 1.0 HA F:ASN333 4.4 85.0 1.0 HZ3 F:LYS74 4.5 0.1 1.0 C3B F:ACP402 4.6 0.8 1.0 CB F:ASN333 4.6 76.3 1.0 O3G F:ACP402 4.8 0.3 1.0 HD22 F:ASN333 4.8 0.9 1.0 ND2 F:ASN333 4.8 90.6 1.0 HB2 F:GLU331 4.9 96.0 1.0 CG F:GLU331 4.9 82.6 1.0 HD2 F:LYS74 4.9 0.2 1.0 CD F:LYS74 4.9 100.0 1.0 HA F:SER152 5.0 0.1 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