Magnesium in PDB 7e4y: Crystal Structure of Tubulin in Complex with L-DM4-Sme

The structure of Crystal Structure of Tubulin in Complex with L-DM4-Sme, PDB code: 7e4y 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)	39.51 / 2.71
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	103.991, 156.034, 182.357, 90, 90, 90
R / Rfree (%)	19.6 / 23.9

The structure of Crystal Structure of Tubulin in Complex with L-DM4-Sme also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Crystal Structure of Tubulin in Complex with L-DM4-Sme (pdb code 7e4y). 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 L-DM4-Sme, PDB code: 7e4y:
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 L-DM4-Sme


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 L-DM4-Sme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:39.7 occ:1.00 O3G A:GTP501 2.0 35.2 1.0 O A:HOH611 2.1 33.0 1.0 O A:HOH613 2.2 41.8 1.0 O1B A:GTP501 2.2 27.8 1.0 PG A:GTP501 2.9 42.5 1.0 HZ1 B:LYS254 3.1 52.4 1.0 O1G A:GTP501 3.1 30.7 1.0 PB A:GTP501 3.3 23.2 1.0 O3B A:GTP501 3.5 45.2 1.0 HB2 A:ASP98 3.5 57.2 1.0 O3A A:GTP501 3.8 50.3 1.0 HB2 A:GLN11 3.8 53.9 1.0 HB3 A:ASP98 3.8 57.2 1.0 NZ B:LYS254 3.9 43.7 1.0 H A:GLN11 4.1 45.5 1.0 HZ2 B:LYS254 4.1 52.4 1.0 OD1 A:ASP69 4.1 39.0 1.0 HB3 A:GLU71 4.1 67.9 1.0 CB A:ASP98 4.1 47.7 1.0 OE1 A:GLU71 4.2 76.0 1.0 O2G A:GTP501 4.3 33.1 1.0 HZ3 B:LYS254 4.4 52.4 1.0 HG1 A:THR145 4.4 59.3 1.0 OD2 A:ASP98 4.5 71.0 1.0 OD2 A:ASP69 4.5 49.0 1.0 HB3 A:GLN11 4.5 53.9 1.0 CB A:GLN11 4.6 44.9 1.0 CG A:ASP98 4.6 57.6 1.0 O2B A:GTP501 4.6 45.4 1.0 HE3 B:LYS254 4.7 51.8 1.0 N A:GLN11 4.8 38.0 1.0 CG A:ASP69 4.8 42.6 1.0 HB A:THR145 4.8 47.9 1.0 OG1 A:THR145 4.8 49.4 1.0 CE B:LYS254 4.8 43.2 1.0 HB2 A:GLU71 4.9 67.9 1.0 CB A:GLU71 4.9 56.5 1.0 H A:ALA99 4.9 46.0 1.0 HA2 A:GLY10 4.9 47.1 1.0 PA A:GTP501 5.0 48.9 1.0 OE1 A:GLN11 5.0 51.5 1.0 HE2 B:LYS254 5.0 51.8 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of Tubulin in Complex with L-DM4-Sme


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 L-DM4-Sme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:39.3 occ:1.00 O B:HOH616 1.9 48.4 1.0 O1A B:GDP501 2.1 42.5 1.0 O B:HOH624 2.5 46.3 1.0 OE1 B:GLN11 2.7 56.5 1.0 PA B:GDP501 3.6 58.6 1.0 CD B:GLN11 3.8 55.1 1.0 HB3 B:GLN11 3.9 57.1 1.0 OD2 B:ASP179 3.9 69.4 1.0 H8 B:GDP501 4.0 40.0 1.0 OD1 B:ASN101 4.2 36.8 1.0 OE1 C:GLU254 4.2 67.0 1.0 O3A B:GDP501 4.2 34.5 1.0 HB2 B:GLN11 4.2 57.1 1.0 HD21 B:ASN101 4.4 56.0 1.0 CB B:GLN11 4.4 47.6 1.0 C5' B:GDP501 4.5 35.5 1.0 O2A B:GDP501 4.5 23.8 1.0 O5' B:GDP501 4.5 27.8 1.0 HE22 B:GLN11 4.6 83.1 1.0 O3B B:GDP501 4.6 41.0 1.0 NE2 B:GLN11 4.7 69.2 1.0 CG B:GLN11 4.7 52.4 1.0 CG B:ASP179 4.7 73.8 1.0 PB B:GDP501 4.9 36.4 1.0 C8 B:GDP501 5.0 33.3 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of Tubulin in Complex with L-DM4-Sme


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 L-DM4-Sme within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:34.9 occ:1.00 O C:HOH618 1.9 37.0 1.0 O C:HOH611 1.9 34.5 1.0 O1B C:GTP501 2.0 35.7 1.0 O C:HOH623 2.0 45.3 1.0 O1G C:GTP501 2.2 28.9 1.0 O C:HOH622 2.3 34.8 1.0 HZ1 D:LYS254 3.1 57.2 1.0 PB C:GTP501 3.3 30.7 1.0 PG C:GTP501 3.4 26.9 1.0 HG2 C:GLU71 3.4 51.8 1.0 HB2 C:GLN11 3.5 48.2 1.0 O3B C:GTP501 3.7 33.4 1.0 OE1 C:GLU71 3.7 57.1 1.0 NZ D:LYS254 3.9 47.7 1.0 O2G C:GTP501 3.9 28.4 1.0 HZ2 D:LYS254 3.9 57.2 1.0 O3A C:GTP501 4.0 38.9 1.0 H C:GLN11 4.0 26.4 1.0 HG3 C:GLU71 4.0 51.8 1.0 HB2 C:ASP98 4.1 50.4 1.0 CG C:GLU71 4.1 43.1 1.0 OD1 C:ASP69 4.2 31.5 1.0 HZ3 D:LYS254 4.2 57.2 1.0 OD2 C:ASP69 4.2 31.2 1.0 CB C:GLN11 4.3 40.2 1.0 CD C:GLU71 4.4 55.6 1.0 HB3 C:GLN11 4.4 48.2 1.0 HB3 C:ASP98 4.4 50.4 1.0 O2B C:GTP501 4.5 27.8 1.0 O3G C:GTP501 4.6 26.9 1.0 OE1 C:GLN11 4.6 50.9 1.0 OD2 C:ASP98 4.6 61.9 1.0 CB C:ASP98 4.6 42.0 1.0 N C:GLN11 4.6 22.0 1.0 CG C:ASP69 4.7 33.8 1.0 HG1 C:THR145 4.7 37.1 1.0 HG21 C:VAL74 4.7 48.4 1.0 O1A C:GTP501 4.8 29.4 1.0 PA C:GTP501 4.9 27.4 1.0 HE3 D:LYS254 5.0 49.5 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of Tubulin in Complex with L-DM4-Sme


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 L-DM4-Sme within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:78.5 occ:1.00 O D:HOH606 2.1 80.9 1.0 O2G D:GTP501 2.4 92.1 1.0 O D:HOH603 2.5 80.5 1.0 O D:HOH601 2.5 92.2 1.0 O1B D:GTP501 2.5 84.5 1.0 HB2 D:GLN11 2.9 106.6 1.0 O1G D:GTP501 3.0 87.1 1.0 OE2 D:GLU71 3.0 88.5 1.0 PG D:GTP501 3.1 95.5 1.0 PB D:GTP501 3.5 67.7 1.0 H D:GLN11 3.7 95.3 1.0 O3A D:GTP501 3.8 83.7 1.0 HE21 D:GLN11 3.8 94.9 1.0 CB D:GLN11 3.8 88.8 1.0 O3B D:GTP501 3.8 80.6 1.0 CD D:GLU71 3.8 96.1 1.0 HB3 D:GLN11 3.8 106.6 1.0 HG2 D:GLU71 4.0 114.6 1.0 NE2 D:GLN11 4.1 79.1 1.0 N D:GLN11 4.3 79.5 1.0 HE22 D:GLN11 4.4 94.9 1.0 CG D:GLU71 4.4 95.5 1.0 O3G D:GTP501 4.5 76.9 1.0 HG3 D:GLU71 4.6 114.6 1.0 CA D:GLN11 4.6 78.3 1.0 OD1 D:ASP69 4.6 68.7 1.0 CD D:GLN11 4.7 86.0 1.0 OE1 D:GLU71 4.7 90.0 1.0 HG1 D:THR74 4.7 125.2 1.0 HG1 D:THR145 4.8 103.0 1.0 OD2 D:ASP69 4.8 72.2 1.0 CG D:GLN11 4.8 88.8 1.0 HD21 D:ASN101 4.9 118.1 1.0 O D:HOH602 4.9 57.5 1.0 HA D:GLN11 4.9 94.0 1.0 O2B D:GTP501 4.9 90.1 1.0 HA2 D:GLY10 4.9 89.2 1.0 PA D:GTP501 4.9 58.1 1.0 O1A D:GTP501 5.0 74.2 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of Tubulin in Complex with L-DM4-Sme


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 L-DM4-Sme within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:90.8 occ:1.00 HD21 F:ASN333 2.0 115.4 1.0 O1B F:ACP402 2.0 145.7 1.0 OE2 F:GLU331 2.3 115.8 1.0 O2G F:ACP402 2.5 130.1 1.0 ND2 F:ASN333 2.6 96.2 1.0 OE1 F:GLU331 2.7 115.5 1.0 HD22 F:ASN333 2.7 115.4 1.0 CD F:GLU331 2.8 114.8 1.0 HZ2 F:LYS74 3.2 121.2 1.0 PB F:ACP402 3.3 175.1 1.0 HZ1 F:LYS74 3.4 121.2 1.0 NZ F:LYS74 3.7 101.0 1.0 PG F:ACP402 3.7 158.5 1.0 CG F:ASN333 3.8 86.5 1.0 HZ3 F:LYS74 4.1 121.2 1.0 C3B F:ACP402 4.1 158.8 1.0 O1A F:ACP402 4.2 136.4 1.0 O2B F:ACP402 4.2 149.0 1.0 O1G F:ACP402 4.3 121.9 1.0 CG F:GLU331 4.3 93.3 1.0 OD1 F:ASN333 4.3 87.5 1.0 O3A F:ACP402 4.4 162.9 1.0 HG3 F:GLU331 4.5 111.9 1.0 HG2 F:GLU331 4.8 111.9 1.0 HB2 F:GLU331 4.8 100.1 1.0 HE3 F:LYS74 4.8 113.7 1.0 PA F:ACP402 4.9 168.5 1.0 HA F:ASN333 4.9 79.6 1.0 H3B1 F:ACP402 4.9 190.6 1.0 CE F:LYS74 4.9 94.8 1.0 H3B2 F:ACP402 4.9 190.6 1.0

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