Magnesium in PDB 5ca0: Crystal Structure of T2R-Ttl-Lexibulin Complex

The structure of Crystal Structure of T2R-Ttl-Lexibulin Complex, PDB code: 5ca0 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)	38.70 / 2.50
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 (%)	19.8 / 23.7

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

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of T2R-Ttl-Lexibulin Complex (pdb code 5ca0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of T2R-Ttl-Lexibulin Complex, PDB code: 5ca0:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of T2R-Ttl-Lexibulin 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-Lexibulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:48.1 occ:1.00 O A:HOH607 2.1 55.8 1.0 O A:HOH606 2.1 46.7 1.0 O A:HOH608 2.1 51.9 1.0 O A:HOH630 2.1 55.6 1.0 O1G A:GTP501 2.1 39.3 1.0 O1B A:GTP501 2.2 41.5 1.0 HZ1 B:LYS252 3.1 71.8 1.0 HB2 A:GLN11 3.3 74.0 1.0 PB A:GTP501 3.3 51.5 1.0 PG A:GTP501 3.4 53.2 1.0 OE1 A:GLU71 3.5 76.1 1.0 H A:GLN11 3.7 61.1 1.0 O3A A:GTP501 3.7 53.4 1.0 O3B A:GTP501 3.8 67.7 1.0 NZ B:LYS252 3.9 59.8 1.0 HB2 A:ASP98 4.0 56.1 1.0 HZ2 B:LYS252 4.0 71.8 1.0 HB3 A:GLN11 4.0 74.0 1.0 O2G A:GTP501 4.0 46.5 1.0 CB A:GLN11 4.1 61.7 1.0 OD1 A:ASP69 4.1 57.0 1.0 HZ3 B:LYS252 4.1 71.8 1.0 HB3 A:GLU71 4.1 85.2 1.0 HB3 A:ASP98 4.2 56.1 1.0 OD2 A:ASP69 4.2 43.8 1.0 N A:GLN11 4.3 51.0 1.0 OE1 A:GLN11 4.4 69.4 1.0 HD22 B:ASN247 4.5 1.0 1.0 CB A:ASP98 4.5 46.8 1.0 O3G A:GTP501 4.6 51.2 1.0 CG A:ASP69 4.6 61.6 1.0 OD2 A:ASP98 4.6 62.7 1.0 O2B A:GTP501 4.6 63.6 1.0 CD A:GLU71 4.7 76.6 1.0 HG1 A:THR145 4.7 55.2 1.0 HA2 A:GLY10 4.7 47.7 1.0 PA A:GTP501 4.7 51.1 1.0 CA A:GLN11 4.8 66.2 1.0 O1A A:GTP501 4.8 53.3 1.0 HD21 B:ASN247 4.9 1.0 1.0 CB A:GLU71 5.0 71.0 1.0 HA A:GLN11 5.0 79.5 1.0 HB A:THR145 5.0 62.4 1.0 CG A:ASP98 5.0 64.2 1.0 HB2 A:GLU71 5.0 85.2 1.0 HG21 A:VAL74 5.0 88.1 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of T2R-Ttl-Lexibulin 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-Lexibulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:56.5 occ:1.00 O1A B:GDP501 2.1 90.4 1.0 OE1 B:GLN11 2.2 82.2 1.0 O C:HOH609 2.2 56.6 1.0 O B:HOH618 2.5 47.7 1.0 CD B:GLN11 3.4 75.4 1.0 PA B:GDP501 3.5 52.1 1.0 OD2 B:ASP177 3.7 79.5 1.0 HB3 B:GLN11 3.8 90.2 1.0 H8 B:GDP501 3.9 64.1 1.0 O2A B:GDP501 3.9 53.7 1.0 OE1 C:GLU254 4.0 0.4 1.0 OD1 B:ASN99 4.1 62.5 1.0 HE22 B:GLN11 4.1 83.6 1.0 HB2 B:GLN11 4.1 90.2 1.0 NE2 B:GLN11 4.2 69.6 1.0 CB B:GLN11 4.3 75.2 1.0 C5' B:GDP501 4.3 48.3 1.0 O5' B:GDP501 4.4 50.6 1.0 HD21 B:ASN99 4.4 58.1 1.0 O1B B:GDP501 4.4 64.3 1.0 CG B:GLN11 4.4 64.7 1.0 CG B:ASP177 4.5 65.3 1.0 HB3 B:ASP177 4.6 66.0 1.0 O3A B:GDP501 4.7 64.5 1.0 HG2 B:GLN11 4.8 77.6 1.0 C8 B:GDP501 4.9 53.5 1.0 PB B:GDP501 4.9 58.6 1.0 CD C:GLU254 4.9 76.2 1.0 CG B:ASN99 4.9 44.9 1.0 O3B B:GDP501 5.0 59.9 1.0 ND2 B:ASN99 5.0 48.5 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of T2R-Ttl-Lexibulin 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-Lexibulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:46.3 occ:1.00 O C:HOH607 2.0 50.7 1.0 O C:HOH628 2.1 52.4 1.0 O C:HOH612 2.1 44.7 1.0 O1B C:GTP501 2.1 49.9 1.0 O1G C:GTP501 2.2 44.6 1.0 O C:HOH617 2.2 45.5 1.0 PB C:GTP501 3.3 39.6 1.0 HB2 C:GLN11 3.3 50.9 1.0 HZ1 D:LYS252 3.4 77.6 1.0 PG C:GTP501 3.4 49.1 1.0 H C:GLN11 3.5 46.8 1.0 O3B C:GTP501 3.7 49.0 1.0 O3A C:GTP501 3.7 57.4 1.0 OD1 C:ASP69 3.8 42.9 1.0 OE1 C:GLU71 3.8 65.0 1.0 OD2 C:ASP69 3.9 43.2 1.0 HB3 C:GLU71 4.0 71.0 1.0 CB C:GLN11 4.1 42.5 1.0 HB3 C:GLN11 4.1 50.9 1.0 HB2 C:ASP98 4.1 68.3 1.0 N C:GLN11 4.2 39.0 1.0 O2G C:GTP501 4.2 49.0 1.0 NZ D:LYS252 4.2 64.7 1.0 HB3 C:ASP98 4.3 68.3 1.0 CG C:ASP69 4.3 47.6 1.0 HZ2 D:LYS252 4.3 77.6 1.0 HA2 C:GLY10 4.5 63.2 1.0 O2B C:GTP501 4.5 51.7 1.0 O3G C:GTP501 4.5 53.9 1.0 HG21 C:VAL74 4.6 82.5 1.0 HZ3 D:LYS252 4.6 77.6 1.0 OE1 C:GLN11 4.6 67.3 1.0 HG1 C:THR145 4.7 57.8 1.0 CB C:ASP98 4.7 56.9 1.0 CA C:GLN11 4.7 41.2 1.0 PA C:GTP501 4.8 48.2 1.0 CD C:GLU71 4.8 47.5 1.0 CB C:GLU71 4.9 59.2 1.0 O1A C:GTP501 4.9 55.1 1.0 HB C:THR145 4.9 53.5 1.0 HA C:GLN11 4.9 49.5 1.0 OD2 C:ASP98 4.9 64.3 1.0 OG1 C:THR145 5.0 48.2 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