Magnesium in PDB 7dp8: Crystal Structure of T2R-Ttl-Cevipabulin-Eribulin Complex

The structure of Crystal Structure of T2R-Ttl-Cevipabulin-Eribulin Complex, PDB code: 7dp8 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)	59.46 / 2.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	103.937, 159.071, 176.236, 90, 90, 90
R / Rfree (%)	22.7 / 26.4

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

Calcium	(Ca)	6 atoms
Chlorine	(Cl)	2 atoms
Fluorine	(F)	10 atoms

The binding sites of Magnesium atom in the Crystal Structure of T2R-Ttl-Cevipabulin-Eribulin Complex (pdb code 7dp8). 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-Eribulin Complex, PDB code: 7dp8:
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-Eribulin 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-Eribulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:47.4 occ:1.00 O2G A:GTP501 2.0 43.2 1.0 O A:HOH610 2.1 43.7 1.0 O A:HOH602 2.1 51.6 1.0 O A:HOH608 2.1 50.0 1.0 O A:HOH612 2.2 52.3 1.0 O1B A:GTP501 2.5 43.9 1.0 PG A:GTP501 3.3 47.4 1.0 HG2 A:GLU71 3.3 71.5 1.0 HZ1 B:LYS252 3.3 64.8 1.0 HB2 A:GLN11 3.4 63.6 1.0 HZ3 B:LYS252 3.4 64.8 1.0 PB A:GTP501 3.6 82.6 1.0 O1G A:GTP501 3.7 44.1 1.0 OE2 A:GLU71 3.7 63.7 1.0 HB2 A:ASP98 3.8 59.3 1.0 O3B A:GTP501 3.8 55.4 1.0 NZ B:LYS252 3.8 53.8 1.0 HG3 A:GLU71 3.8 71.5 1.0 H A:GLN11 3.9 61.4 1.0 CG A:GLU71 4.0 59.4 1.0 OD1 A:ASP69 4.0 54.7 1.0 OD2 A:ASP69 4.0 57.9 1.0 OD2 A:ASP98 4.1 53.5 1.0 O3A A:GTP501 4.1 54.2 1.0 HB3 A:ASP98 4.2 59.3 1.0 CB A:GLN11 4.3 52.9 1.0 HZ2 B:LYS252 4.3 64.8 1.0 CB A:ASP98 4.3 49.3 1.0 CD A:GLU71 4.3 58.9 1.0 HB3 A:GLN11 4.4 63.6 1.0 CG A:ASP98 4.4 47.6 1.0 CG A:ASP69 4.4 55.4 1.0 O3G A:GTP501 4.5 44.2 1.0 OE1 A:GLN11 4.6 57.9 1.0 N A:GLN11 4.6 51.0 1.0 HG1 A:THR145 4.7 58.9 1.0 O1A A:GTP501 4.7 55.3 1.0 HG21 A:VAL74 4.9 74.6 1.0 O2B A:GTP501 4.9 53.8 1.0 HE3 B:LYS252 4.9 62.3 1.0 HA2 A:GLY10 5.0 58.4 1.0 CE B:LYS252 5.0 51.8 1.0 CA A:GLN11 5.0 60.1 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of T2R-Ttl-Cevipabulin-Eribulin 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-Eribulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:65.0 occ:1.00 O B:HOH602 1.8 69.5 1.0 O B:HOH608 2.0 74.6 1.0 O B:HOH605 2.1 65.2 1.0 O C:HOH734 2.6 60.4 1.0 O B:HOH611 2.7 61.4 1.0 OE2 B:GLU69 3.4 72.0 1.0 HE21 B:GLN11 3.5 80.7 1.0 HE22 B:GLN11 3.7 80.7 1.0 O1A B:GDP501 3.8 59.9 1.0 NE2 B:GLN11 3.8 67.1 1.0 HD21 B:ASN99 4.1 54.5 1.0 O1B B:GDP501 4.3 51.3 1.0 HB2 B:GLN11 4.4 69.2 1.0 OE1 C:GLU254 4.5 57.9 1.0 CD B:GLU69 4.5 75.9 1.0 HB3 B:GLN11 4.7 69.2 1.0 O3A B:GDP501 4.8 53.1 1.0 ND2 B:ASN99 4.8 45.3 1.0 HD22 B:ASN99 4.8 54.5 1.0 OE2 C:GLU254 4.8 51.1 1.0 PA B:GDP501 4.9 38.8 1.0 CD B:GLN11 4.9 60.0 1.0 OE1 B:GLU69 4.9 81.5 1.0 PB B:GDP501 5.0 31.4 1.0 CB B:GLN11 5.0 57.5 1.0 O B:HOH606 5.0 49.1 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of T2R-Ttl-Cevipabulin-Eribulin 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-Eribulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg603 b:40.7 occ:1.00 O1G C:GTP602 1.9 50.3 1.0 O C:HOH738 2.1 58.2 1.0 O1B C:GTP602 2.1 51.5 1.0 O C:HOH719 2.1 59.1 1.0 O C:HOH709 2.2 36.9 1.0 O C:HOH707 2.3 52.1 1.0 HZ1 D:LYS252 3.0 63.0 1.0 PG C:GTP602 3.1 34.9 1.0 PB C:GTP602 3.2 31.1 1.0 HB2 C:GLN11 3.5 54.0 1.0 O3B C:GTP602 3.5 54.8 1.0 O2G C:GTP602 3.7 52.3 1.0 HG2 C:GLU71 3.7 65.4 1.0 HB2 C:ASP98 3.8 56.0 1.0 O3A C:GTP602 3.8 54.3 1.0 NZ D:LYS252 3.8 52.3 1.0 H C:GLN11 3.8 52.3 1.0 HZ2 D:LYS252 3.9 63.0 1.0 HE22 D:GLN245 4.0 78.7 1.0 OE1 C:GLU71 4.2 56.7 1.0 HG3 C:GLU71 4.2 65.4 1.0 OD1 C:ASP69 4.2 46.8 1.0 OD2 C:ASP69 4.2 43.7 1.0 OD2 C:ASP98 4.3 53.5 1.0 CB C:GLN11 4.3 44.9 1.0 HZ3 D:LYS252 4.3 63.0 1.0 CG C:GLU71 4.4 54.4 1.0 HB3 C:ASP98 4.4 56.0 1.0 HB3 C:GLN11 4.4 54.0 1.0 O3G C:GTP602 4.4 38.4 1.0 CB C:ASP98 4.4 46.5 1.0 O2B C:GTP602 4.5 49.2 1.0 N C:GLN11 4.6 43.4 1.0 HG1 C:THR145 4.6 53.5 1.0 O1A C:GTP602 4.6 54.7 1.0 NE2 D:GLN245 4.6 65.4 1.0 HE3 D:LYS252 4.6 56.8 1.0 CG C:ASP69 4.7 48.4 1.0 CE D:LYS252 4.7 47.2 1.0 PA C:GTP602 4.7 55.5 1.0 CG C:ASP98 4.7 49.1 1.0 CD C:GLU71 4.8 57.2 1.0 HE2 D:LYS252 4.8 56.8 1.0 HB C:THR145 4.8 58.8 1.0 HA2 C:GLY10 4.9 56.7 1.0 OE1 C:GLN11 5.0 57.8 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of T2R-Ttl-Cevipabulin-Eribulin 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-Eribulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:63.7 occ:1.00 O D:HOH601 2.3 63.6 1.0 O2G D:GTP502 2.7 62.2 1.0 O2B D:GTP502 2.8 57.0 1.0 OE2 D:GLU69 3.1 78.6 1.0 HB2 D:GLN11 3.2 82.7 1.0 O3G D:GTP502 3.4 58.9 1.0 HB2 D:GLU69 3.5 90.7 1.0 PG D:GTP502 3.5 67.9 1.0 HB3 D:GLU69 3.7 90.7 1.0 OD2 D:ASP67 3.7 64.9 1.0 H D:GLN11 3.9 77.2 1.0 PB D:GTP502 4.0 56.1 1.0 CD D:GLU69 4.0 84.8 1.0 CB D:GLU69 4.0 75.4 1.0 CB D:GLN11 4.1 68.8 1.0 OD1 D:ASP67 4.1 61.9 1.0 HB3 D:GLN11 4.2 82.7 1.0 O3B D:GTP502 4.2 62.0 1.0 HE21 D:GLN11 4.3 88.5 1.0 CG D:ASP67 4.3 58.7 1.0 N D:GLN11 4.4 64.2 1.0 OG1 D:THR72 4.5 79.8 1.0 CG D:GLU69 4.6 78.7 1.0 O3A D:GTP502 4.6 59.0 1.0 NE2 D:GLN11 4.7 73.6 1.0 HA2 D:GLY10 4.7 72.5 1.0 HG1 D:THR143 4.8 74.4 1.0 OE1 D:GLU69 4.8 77.4 1.0 CA D:GLN11 4.8 65.7 1.0 HG2 D:GLU69 4.8 94.6 1.0 HG1 D:THR72 4.8 96.0 1.0 O2A D:GTP502 4.8 66.9 1.0 H D:GLU69 4.8 84.1 1.0 O1G D:GTP502 4.9 57.7 1.0 HA D:GLN11 5.0 79.0 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of T2R-Ttl-Cevipabulin-Eribulin 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-Eribulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:79.2 occ:1.00 O1B F:ACP402 2.2 94.7 1.0 O3G F:ACP402 2.6 89.3 1.0 OE2 F:GLU331 2.8 86.9 1.0 HD21 F:ASN333 3.0 95.2 1.0 HZ3 F:LYS74 3.0 106.4 1.0 PB F:ACP402 3.4 93.5 1.0 CD F:GLU331 3.6 85.5 1.0 ND2 F:ASN333 3.6 79.2 1.0 OE1 F:GLU331 3.6 84.7 1.0 HZ1 F:LYS74 3.7 106.4 1.0 HD22 F:ASN333 3.7 95.2 1.0 NZ F:LYS74 3.7 88.5 1.0 PG F:ACP402 3.8 101.0 1.0 O2B F:ACP402 3.9 95.1 1.0 C3B F:ACP402 4.1 93.7 1.0 HZ2 F:LYS74 4.1 106.4 1.0 H3B2 F:ACP402 4.2 112.7 1.0 O1G F:ACP402 4.3 96.4 1.0 O3A F:ACP402 4.8 84.0 1.0 CG F:ASN333 4.8 78.8 1.0 HA F:SER152 4.9 123.8 1.0 CE F:LYS74 4.9 90.5 1.0 O2G F:ACP402 5.0 85.0 1.0 HE2 F:LYS74 5.0 108.8 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