Magnesium in PDB 7cld: Crystal Structure of T2R-Ttl-Cevipabulin Complex

The structure of Crystal Structure of T2R-Ttl-Cevipabulin Complex, PDB code: 7cld was solved by L.J.Chen, Q.Chen, Y.Yu, J.H.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.03 / 2.61
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.422, 160.778, 174.764, 90, 90, 90
R / Rfree (%)	20.7 / 25.8

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

Chlorine	(Cl)	2 atoms
Calcium	(Ca)	7 atoms
Fluorine	(F)	10 atoms

The binding sites of Magnesium atom in the Crystal Structure of T2R-Ttl-Cevipabulin Complex (pdb code 7cld). 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-Cevipabulin Complex, PDB code: 7cld:
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-Cevipabulin 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-Cevipabulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:23.8 occ:1.00 O2G A:GTP501 1.9 16.8 1.0 O A:HOH635 2.1 20.3 1.0 O A:HOH623 2.1 19.3 1.0 O A:HOH609 2.2 19.4 1.0 O A:HOH652 2.2 18.7 1.0 O1B A:GTP501 2.3 10.7 1.0 PG A:GTP501 3.2 23.0 1.0 HZ1 B:LYS252 3.2 52.5 1.0 HZ3 B:LYS252 3.3 52.5 1.0 PB A:GTP501 3.4 23.6 1.0 HB2 A:GLN11 3.5 45.2 1.0 O1G A:GTP501 3.6 22.3 1.0 HG2 A:GLU71 3.6 55.8 1.0 HB2 A:ASP98 3.6 27.5 1.0 NZ B:LYS252 3.7 44.0 1.0 O3B A:GTP501 3.7 24.0 1.0 HG3 A:GLU71 3.9 55.8 1.0 O3A A:GTP501 3.9 22.3 1.0 OE2 A:GLU71 3.9 45.3 1.0 OD2 A:ASP98 4.0 25.1 1.0 HB3 A:ASP98 4.1 27.5 1.0 H A:GLN11 4.1 30.0 1.0 OD2 A:ASP69 4.1 28.9 1.0 CG A:GLU71 4.2 46.7 1.0 HZ2 B:LYS252 4.2 52.5 1.0 OD1 A:ASP69 4.2 28.3 1.0 CB A:ASP98 4.2 23.1 1.0 CB A:GLN11 4.3 37.9 1.0 HB3 A:GLN11 4.4 45.2 1.0 O3G A:GTP501 4.4 17.9 1.0 CG A:ASP98 4.4 23.5 1.0 OE1 A:GLN11 4.5 42.7 1.0 CD A:GLU71 4.5 45.2 1.0 HG1 A:THR145 4.6 26.8 1.0 CG A:ASP69 4.6 26.2 1.0 O1A A:GTP501 4.7 15.6 1.0 N A:GLN11 4.7 25.2 1.0 O2B A:GTP501 4.7 25.6 1.0 HE3 B:LYS252 4.8 56.6 1.0 CE B:LYS252 4.8 47.3 1.0 PA A:GTP501 5.0 27.7 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of T2R-Ttl-Cevipabulin 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-Cevipabulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:44.8 occ:1.00 O B:HOH636 2.2 29.4 1.0 O C:HOH668 2.6 33.5 1.0 O B:HOH625 2.6 63.2 1.0 O C:HOH635 2.8 66.7 1.0 OE1 B:GLN11 3.1 41.9 1.0 OE2 B:GLU69 3.4 54.7 1.0 O1A B:GDP501 3.9 23.0 1.0 HB2 B:GLN11 4.1 34.6 1.0 CD B:GLN11 4.2 40.2 1.0 HB3 B:GLN11 4.5 34.6 1.0 CD B:GLU69 4.6 53.9 1.0 CB B:GLN11 4.7 29.0 1.0 HD21 B:ASN99 4.7 37.8 1.0 O1B B:GDP501 4.7 17.6 1.0 OE1 C:GLU254 4.7 40.4 1.0 O B:HOH618 4.8 40.8 1.0 H C:ASN249 4.9 29.7 1.0 HB2 C:ASN249 4.9 41.1 1.0 OE1 B:GLU69 5.0 57.5 1.0 O B:HOH647 5.0 29.2 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of T2R-Ttl-Cevipabulin 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-Cevipabulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:19.3 occ:1.00 O C:HOH643 2.0 20.7 1.0 O C:HOH672 2.0 22.9 1.0 O C:HOH616 2.0 16.9 1.0 O1G C:GTP501 2.0 15.8 1.0 O C:HOH651 2.2 14.1 1.0 O1B C:GTP501 2.3 19.9 1.0 HZ1 D:LYS252 3.0 38.7 1.0 PG C:GTP501 3.3 23.1 1.0 PB C:GTP501 3.4 27.0 1.0 HB2 C:GLN11 3.5 37.5 1.0 HG2 C:GLU71 3.6 53.1 1.0 O3B C:GTP501 3.7 33.3 1.0 O3A C:GTP501 3.8 34.4 1.0 HZ2 D:LYS252 3.8 38.7 1.0 NZ D:LYS252 3.8 32.4 1.0 HB2 C:ASP98 3.8 40.2 1.0 O2G C:GTP501 3.9 16.9 1.0 OE2 C:GLU71 4.0 50.9 1.0 H C:GLN11 4.1 21.0 1.0 OD2 C:ASP98 4.2 43.8 1.0 HZ3 D:LYS252 4.3 38.7 1.0 OD1 C:ASP69 4.3 17.6 1.0 OD2 C:ASP69 4.4 21.1 1.0 CB C:GLN11 4.4 31.4 1.0 CG C:GLU71 4.4 44.5 1.0 HB3 C:GLN11 4.5 37.5 1.0 HB3 C:ASP98 4.5 40.2 1.0 CB C:ASP98 4.5 33.7 1.0 O3G C:GTP501 4.5 15.1 1.0 HE3 D:LYS252 4.5 36.4 1.0 HG1 C:THR145 4.5 27.7 1.0 CD C:GLU71 4.6 49.5 1.0 CE D:LYS252 4.7 30.5 1.0 O2B C:GTP501 4.7 29.1 1.0 HG3 C:GLU71 4.7 53.1 1.0 CG C:ASP98 4.7 40.8 1.0 N C:GLN11 4.7 17.7 1.0 O1A C:GTP501 4.8 33.7 1.0 HE2 D:LYS252 4.8 36.4 1.0 CG C:ASP69 4.8 18.4 1.0 PA C:GTP501 4.8 41.8 1.0 OE1 C:GLN11 4.8 39.2 1.0 HE22 D:GLN245 5.0 111.7 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of T2R-Ttl-Cevipabulin 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-Cevipabulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:59.2 occ:1.00 O2B D:GTP503 2.3 49.3 1.0 O2G D:GTP503 3.0 43.8 1.0 HB2 D:GLN11 3.0 73.5 1.0 O3G D:GTP503 3.4 38.5 1.0 PB D:GTP503 3.6 49.9 1.0 PG D:GTP503 3.6 45.2 1.0 H D:GLN11 3.7 65.3 1.0 OD2 D:ASP67 3.7 37.2 1.0 OD1 D:ASP67 3.9 35.7 1.0 CB D:GLN11 3.9 61.5 1.0 O3B D:GTP503 4.0 48.0 1.0 HB3 D:GLN11 4.1 73.5 1.0 N D:GLN11 4.1 54.6 1.0 HB3 D:GLU69 4.2 101.7 1.0 CG D:ASP67 4.2 37.0 1.0 O3A D:GTP503 4.3 44.3 1.0 HE21 D:GLN11 4.4 83.2 1.0 HA2 D:GLY10 4.5 60.8 1.0 CA D:GLN11 4.5 55.8 1.0 HG1 D:THR143 4.5 56.3 1.0 HA D:GLN11 4.6 66.7 1.0 O2A D:GTP503 4.6 45.5 1.0 HB2 D:GLU69 4.7 101.7 1.0 O1B D:GTP503 4.7 58.2 1.0 NE2 D:GLN11 4.8 69.5 1.0 OE2 D:GLU69 4.8 87.7 1.0 HG1 D:THR72 4.8 134.1 1.0 CB D:GLU69 4.9 84.9 1.0 HB D:THR143 4.9 51.2 1.0 CG D:GLN11 4.9 64.3 1.0 C D:GLY10 4.9 53.4 1.0 PA D:GTP503 4.9 41.4 1.0 HG3 D:GLN11 5.0 77.0 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of T2R-Ttl-Cevipabulin 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-Cevipabulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:89.4 occ:1.00 O1B F:ACP402 2.2 92.5 1.0 HZ3 F:LYS74 2.5 87.7 1.0 OE2 F:GLU331 2.9 74.9 1.0 O3G F:ACP402 2.9 111.6 1.0 HZ1 F:LYS74 3.2 87.7 1.0 NZ F:LYS74 3.2 73.3 1.0 OE1 F:GLU331 3.3 76.9 1.0 HD21 F:ASN333 3.4 87.3 1.0 PB F:ACP402 3.4 94.8 1.0 CD F:GLU331 3.5 76.3 1.0 HZ2 F:LYS74 3.5 87.7 1.0 O2B F:ACP402 3.8 95.6 1.0 ND2 F:ASN333 4.0 73.0 1.0 PG F:ACP402 4.0 109.9 1.0 HD22 F:ASN333 4.2 87.3 1.0 C3B F:ACP402 4.3 102.3 1.0 H3B2 F:ACP402 4.4 122.5 1.0 CE F:LYS74 4.4 73.4 1.0 HE2 F:LYS74 4.4 87.8 1.0 O1G F:ACP402 4.6 110.5 1.0 O3A F:ACP402 4.7 92.6 1.0 HE3 F:LYS74 4.7 87.8 1.0 HA F:SER152 4.9 138.8 1.0 CG F:GLU331 5.0 73.9 1.0

J.Yang, Y.Yu, Y.Li, W.Yan, H.Ye, L.Niu, M.Tang, Z.Wang, Z.Yang, H.Pei, H.Wei, M.Zhao, J.Wen, L.Yang, L.Ouyang, Y.Wei, Q.Chen, W.Li, L.Chen. Cevipabulin-Tubulin Complex Reveals A Novel Agent Binding Site on Alpha-Tubulin with Tubulin Degradation Effect. Sci Adv V. 7 2021.
ISSN: ESSN 2375-2548
PubMed: 34138737
DOI: 10.1126/SCIADV.ABG4168