Magnesium in PDB 7e4p: Crystal Structure of Tubulin in Complex with Ansamitocin P3

The structure of Crystal Structure of Tubulin in Complex with Ansamitocin P3, PDB code: 7e4p was solved by Y.Wang, W.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.25 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.399, 158.569, 181.76, 90, 90, 90
R / Rfree (%)	21.3 / 22.9

The structure of Crystal Structure of Tubulin in Complex with Ansamitocin P3 also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of Tubulin in Complex with Ansamitocin P3 (pdb code 7e4p). 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 Tubulin in Complex with Ansamitocin P3, PDB code: 7e4p:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of Tubulin in Complex with Ansamitocin P3


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 Tubulin in Complex with Ansamitocin P3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:25.2 occ:1.00 O A:HOH727 2.0 24.6 1.0 O A:HOH654 2.1 23.5 1.0 O A:HOH711 2.1 26.7 1.0 O A:HOH635 2.1 25.7 1.0 O2G A:GTP501 2.1 25.0 1.0 O1B A:GTP501 2.1 22.2 1.0 HZ1 B:LYS252 3.2 38.1 1.0 PB A:GTP501 3.3 22.0 1.0 PG A:GTP501 3.3 22.8 1.0 HB2 A:GLN11 3.4 34.1 1.0 O3A A:GTP501 3.6 28.2 1.0 O1G A:GTP501 3.7 25.8 1.0 O3B A:GTP501 3.7 27.1 1.0 H A:GLN11 3.8 31.0 1.0 HB2 A:ASP98 3.9 40.1 1.0 NZ B:LYS252 3.9 31.8 1.0 HZ2 B:LYS252 4.0 38.1 1.0 OE1 A:GLU71 4.0 49.4 1.0 HB3 A:GLN11 4.1 34.1 1.0 CB A:GLN11 4.2 28.4 1.0 HZ3 B:LYS252 4.2 38.1 1.0 OD1 A:ASP69 4.2 35.9 1.0 HB3 A:ASP98 4.3 40.1 1.0 HB3 A:GLU71 4.3 50.1 1.0 OD2 A:ASP69 4.3 34.7 1.0 O A:HOH621 4.4 31.0 1.0 CB A:ASP98 4.5 33.4 1.0 N A:GLN11 4.5 25.9 1.0 OD2 A:ASP98 4.5 34.0 1.0 O3G A:GTP501 4.5 25.8 1.0 O2B A:GTP501 4.6 26.4 1.0 O1A A:GTP501 4.6 26.2 1.0 PA A:GTP501 4.7 22.4 1.0 CG A:ASP69 4.7 37.8 1.0 HG1 A:THR145 4.7 32.5 1.0 OE1 A:GLN11 4.8 37.5 1.0 CG A:ASP98 4.8 32.4 1.0 CD A:GLU71 4.8 51.2 1.0 CA A:GLN11 4.9 28.4 1.0 HG21 A:VAL74 4.9 59.0 1.0 HA2 A:GLY10 5.0 32.4 1.0 O B:HOH691 5.0 23.7 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of Tubulin in Complex with Ansamitocin P3


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 Tubulin in Complex with Ansamitocin P3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:24.0 occ:1.00 O B:HOH676 2.0 31.7 1.0 OE1 B:GLN11 2.1 33.3 1.0 O1A B:GDP501 2.1 24.4 1.0 O B:HOH661 2.6 41.4 1.0 O C:HOH613 2.7 32.1 1.0 O B:HOH671 2.7 31.3 1.0 CD B:GLN11 3.3 34.2 1.0 PA B:GDP501 3.5 19.8 1.0 HB3 B:GLN11 3.5 35.2 1.0 H8 B:GDP501 3.6 34.2 1.0 OD2 B:ASP177 3.7 36.9 1.0 HB2 B:GLN11 3.9 35.2 1.0 CB B:GLN11 4.0 29.3 1.0 O3A B:GDP501 4.1 24.6 1.0 OE1 C:GLU254 4.1 49.4 1.0 HE22 B:GLN11 4.2 40.5 1.0 CG B:GLN11 4.2 32.0 1.0 NE2 B:GLN11 4.2 33.8 1.0 C5' B:GDP501 4.3 23.4 1.0 OD1 B:ASN99 4.3 25.3 1.0 O5' B:GDP501 4.4 20.3 1.0 O1B B:GDP501 4.4 25.0 1.0 HG2 B:GLN11 4.5 38.4 1.0 O2A B:GDP501 4.5 22.2 1.0 HD21 B:ASN99 4.6 27.7 1.0 C8 B:GDP501 4.6 28.5 1.0 CG B:ASP177 4.7 33.9 1.0 PB B:GDP501 4.9 18.5 1.0 HG3 B:GLN11 5.0 38.4 1.0 HB3 B:ASP177 5.0 39.6 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of Tubulin in Complex with Ansamitocin P3


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 Tubulin in Complex with Ansamitocin P3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:27.3 occ:1.00 O C:HOH687 2.0 29.7 1.0 O C:HOH667 2.0 29.2 1.0 O C:HOH648 2.1 31.5 1.0 O1B C:GTP501 2.1 25.9 1.0 O1G C:GTP501 2.3 23.9 1.0 PB C:GTP501 3.4 18.8 1.0 HB2 C:GLN11 3.4 27.3 1.0 HZ1 D:LYS252 3.4 35.6 1.0 PG C:GTP501 3.5 22.9 1.0 OE1 C:GLU71 3.5 37.9 1.0 H C:GLN11 3.6 23.9 1.0 O C:HOH602 3.8 40.1 1.0 OD1 C:ASP69 3.8 22.0 1.0 O3B C:GTP501 3.8 23.3 1.0 HB2 C:ASP98 3.8 37.6 1.0 O3A C:GTP501 3.9 24.7 1.0 OD2 C:ASP69 3.9 25.0 1.0 O2G C:GTP501 4.0 26.2 1.0 HB3 C:ASP98 4.1 37.6 1.0 HB3 C:GLU71 4.1 40.0 1.0 CB C:GLN11 4.2 22.7 1.0 NZ D:LYS252 4.2 29.7 1.0 HZ2 D:LYS252 4.2 35.6 1.0 HB3 C:GLN11 4.2 27.3 1.0 CG C:ASP69 4.3 24.5 1.0 N C:GLN11 4.4 19.9 1.0 CB C:ASP98 4.4 31.4 1.0 HZ3 D:LYS252 4.5 35.6 1.0 O2B C:GTP501 4.6 23.4 1.0 OD2 C:ASP98 4.6 36.4 1.0 CD C:GLU71 4.7 37.5 1.0 HA2 C:GLY10 4.7 27.7 1.0 O3G C:GTP501 4.7 22.6 1.0 OE1 C:GLN11 4.7 40.3 1.0 HG1 C:THR145 4.7 29.2 1.0 HG21 C:VAL74 4.7 39.8 1.0 CA C:GLN11 4.8 23.4 1.0 HB C:THR145 4.9 28.5 1.0 O1A C:GTP501 4.9 24.7 1.0 PA C:GTP501 4.9 21.4 1.0 CG C:ASP98 4.9 30.9 1.0 O C:HOH636 4.9 29.8 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of Tubulin in Complex with Ansamitocin P3


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 Tubulin in Complex with Ansamitocin P3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:69.8 occ:1.00 O D:HOH624 2.1 55.0 1.0 O2G D:GTP501 2.1 69.7 1.0 O D:HOH601 2.2 60.5 1.0 O D:HOH608 2.4 46.7 1.0 OE2 D:GLU69 2.6 92.9 1.0 O2B D:GTP501 2.7 58.2 1.0 PG D:GTP501 3.1 79.5 1.0 O3G D:GTP501 3.1 71.5 1.0 HB2 D:GLN11 3.2 70.4 1.0 PB D:GTP501 3.6 53.0 1.0 CD D:GLU69 3.6 84.6 1.0 H D:GLN11 3.7 59.9 1.0 O3A D:GTP501 3.8 56.5 1.0 O3B D:GTP501 3.8 60.0 1.0 HB3 D:GLN11 3.8 70.4 1.0 CB D:GLN11 3.9 58.7 1.0 HG2 D:GLU69 4.0 83.4 1.0 O1G D:GTP501 4.3 67.2 1.0 N D:GLN11 4.3 49.9 1.0 CG D:GLU69 4.4 69.5 1.0 OE1 D:GLU69 4.5 86.8 1.0 OD2 D:ASP67 4.5 51.6 1.0 OD1 D:ASP67 4.6 46.8 1.0 OE1 D:GLN11 4.6 83.3 1.0 CA D:GLN11 4.7 54.7 1.0 O2A D:GTP501 4.7 61.6 1.0 PA D:GTP501 4.8 46.7 1.0 HA2 D:GLY10 4.8 58.6 1.0 HG3 D:GLU69 4.8 83.4 1.0 HG1 D:THR143 4.9 63.1 1.0 CD D:GLN11 4.9 72.6 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of Tubulin in Complex with Ansamitocin P3


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 Tubulin in Complex with Ansamitocin P3 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:69.0 occ:1.00 HD21 F:ASN333 2.2 93.4 1.0 O1B F:ACP401 2.2 79.5 1.0 ND2 F:ASN333 2.8 77.8 1.0 O2G F:ACP401 2.8 80.7 1.0 OE2 F:GLU331 2.8 77.5 1.0 OE1 F:GLU331 2.9 63.5 1.0 HD22 F:ASN333 3.0 93.4 1.0 HZ1 F:LYS74 3.1 89.8 1.0 CD F:GLU331 3.3 67.1 1.0 HZ2 F:LYS74 3.6 89.8 1.0 PB F:ACP401 3.6 92.9 1.0 NZ F:LYS74 3.6 74.9 1.0 HZ3 F:LYS74 3.7 89.8 1.0 CG F:ASN333 3.9 63.1 1.0 PG F:ACP401 4.1 116.9 1.0 OD1 F:ASN333 4.2 65.2 1.0 O2B F:ACP401 4.4 95.9 1.0 C3B F:ACP401 4.5 83.4 1.0 O3A F:ACP401 4.6 78.3 1.0 CG F:GLU331 4.8 61.8 1.0 HA F:ASN333 4.8 55.8 1.0 O1G F:ACP401 4.8 81.2 1.0 O1A F:ACP401 4.9 80.3 1.0

Y.Wang, W.Li. C3 Ester Side Chain Plays A Pivotal Role in the Antitumor Activity of Maytansinoids To Be Published.