Magnesium in PDB 6ls4: A Novel Anti-Tumor Agent S-40 in Complex with Tubulin

The structure of A Novel Anti-Tumor Agent S-40 in Complex with Tubulin, PDB code: 6ls4 was solved by T.Du, S.Lin, M.Ji, N.Xue, Y.Liu, K.Zhang, D.Lu, X.Chen, H.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.73 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.68, 102.2, 131.5, 90, 107.42, 90
R / Rfree (%)	22.2 / 24

The binding sites of Magnesium atom in the A Novel Anti-Tumor Agent S-40 in Complex with Tubulin (pdb code 6ls4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the A Novel Anti-Tumor Agent S-40 in Complex with Tubulin, PDB code: 6ls4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the A Novel Anti-Tumor Agent S-40 in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A Novel Anti-Tumor Agent S-40 in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:78.9 occ:1.00 O A:HOH602 2.0 83.3 1.0 O A:HOH601 2.1 72.9 1.0 O1B A:GTP501 2.1 72.8 1.0 O1G A:GTP501 2.1 70.3 1.0 O A:HOH603 2.1 80.1 1.0 OE1 A:GLU71 3.2 103.5 1.0 PB A:GTP501 3.2 65.9 1.0 PG A:GTP501 3.4 67.7 1.0 O3A A:GTP501 3.6 75.0 1.0 OE1 A:GLN11 3.7 91.7 1.0 O3B A:GTP501 3.7 77.0 1.0 CB A:GLN11 4.1 72.0 1.0 O2G A:GTP501 4.1 64.6 1.0 OD2 A:ASP69 4.1 78.5 1.0 OD1 A:ASP69 4.3 77.2 1.0 N A:GLN11 4.4 71.6 1.0 CD A:GLU71 4.4 102.8 1.0 O3G A:GTP501 4.5 70.0 1.0 O2B A:GTP501 4.5 72.0 1.0 NZ B:LYS252 4.5 86.8 1.0 OD2 A:ASP98 4.5 82.6 1.0 CB A:ASP98 4.6 74.3 1.0 CG A:ASP69 4.6 83.0 1.0 CD A:GLN11 4.7 79.6 1.0 PA A:GTP501 4.8 67.4 1.0 CA A:GLN11 4.9 77.5 1.0 O1A A:GTP501 4.9 67.9 1.0 CB A:GLU71 5.0 88.7 1.0 OG1 A:THR145 5.0 77.9 1.0

Magnesium binding site 2 out of 6 in the A Novel Anti-Tumor Agent S-40 in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A Novel Anti-Tumor Agent S-40 in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:92.6 occ:1.00 OG1 A:THR41 2.3 110.5 1.0 O A:GLY44 2.5 106.5 1.0 O A:THR41 2.6 113.3 1.0 OE2 A:GLU55 2.6 101.9 1.0 OD1 A:ASP39 2.7 101.7 1.0 OE1 A:GLU55 2.7 111.8 1.0 CD A:GLU55 3.0 105.9 1.0 CG A:ASP39 3.3 108.6 1.0 OD2 A:ASP39 3.3 108.1 1.0 C A:THR41 3.6 113.0 1.0 C A:GLY44 3.7 111.0 1.0 CB A:THR41 3.7 112.5 1.0 OD1 A:ASN50 4.0 106.4 1.0 ND2 A:ASN50 4.0 102.0 1.0 CA A:THR41 4.1 108.7 1.0 OD1 A:ASP47 4.4 95.4 1.0 CZ A:PHE49 4.4 103.2 1.0 CG A:ASN50 4.4 101.8 1.0 CA A:GLY45 4.4 115.4 1.0 CG2 A:THR41 4.5 115.7 1.0 CG A:GLU55 4.5 104.1 1.0 N A:THR41 4.5 113.5 1.0 N A:GLY45 4.5 116.9 1.0 N A:GLY44 4.5 114.0 1.0 CG A:ASP47 4.6 104.5 1.0 CA A:GLY44 4.7 112.8 1.0 OD2 A:ASP47 4.7 108.3 1.0 CB A:ASP39 4.8 107.9 1.0 N A:ILE42 4.8 110.7 1.0

Magnesium binding site 3 out of 6 in the A Novel Anti-Tumor Agent S-40 in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of A Novel Anti-Tumor Agent S-40 in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:68.2 occ:1.00 O C:HOH601 2.2 65.0 1.0 O C:HOH604 2.2 76.8 1.0 O C:HOH605 2.2 65.9 1.0 O1B C:GTP501 2.3 75.3 1.0 O1G C:GTP501 2.8 66.9 1.0 PB C:GTP501 3.6 64.8 1.0 OD2 C:ASP69 3.8 73.4 1.0 PG C:GTP501 3.8 61.2 1.0 CB C:GLN11 3.9 63.5 1.0 O2G C:GTP501 4.0 56.2 1.0 OE1 C:GLU71 4.0 72.7 1.0 O3B C:GTP501 4.1 75.8 1.0 OD1 C:ASP69 4.1 75.4 1.0 OE1 C:GLN11 4.1 91.3 1.0 O3A C:GTP501 4.2 71.3 1.0 CG C:ASP69 4.4 72.8 1.0 N C:GLN11 4.4 67.8 1.0 OD2 C:ASP98 4.5 75.9 1.0 NZ D:LYS252 4.6 83.9 1.0 O2B C:GTP501 4.6 69.2 1.0 CB C:ASP98 4.7 68.9 1.0 CA C:GLN11 4.7 68.9 1.0 CB C:GLU71 4.8 74.5 1.0 O1A C:GTP501 4.8 73.8 1.0 OG1 C:THR145 5.0 69.1 1.0 CD C:GLN11 5.0 76.1 1.0

Magnesium binding site 4 out of 6 in the A Novel Anti-Tumor Agent S-40 in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of A Novel Anti-Tumor Agent S-40 in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:83.2 occ:1.00 OG1 C:THR41 2.0 109.0 1.0 OD2 C:ASP39 2.0 94.3 1.0 OE2 C:GLU55 2.2 100.9 1.0 OD1 C:ASP39 2.5 97.8 1.0 O C:THR41 2.5 103.3 1.0 CG C:ASP39 2.6 95.3 1.0 O C:GLY44 2.6 94.6 1.0 CD C:GLU55 2.9 95.5 1.0 OE1 C:GLU55 3.0 97.7 1.0 CB C:THR41 3.3 98.6 1.0 C C:THR41 3.5 104.5 1.0 C C:GLY44 3.8 99.0 1.0 CA C:THR41 3.8 104.5 1.0 CB C:ASP39 4.0 99.3 1.0 CG2 C:THR41 4.1 103.8 1.0 N C:THR41 4.1 106.4 1.0 CZ C:PHE49 4.2 92.2 1.0 CG C:GLU55 4.2 97.6 1.0 ND2 C:ASN50 4.2 94.1 1.0 CA C:GLY45 4.5 99.4 1.0 CE1 C:PHE49 4.5 91.7 1.0 N C:GLY44 4.6 93.8 1.0 N C:GLY45 4.6 97.1 1.0 N C:ILE42 4.7 103.6 1.0 O C:GLY45 4.7 100.9 1.0 OD1 C:ASN50 4.8 94.8 1.0 CA C:GLY44 4.8 100.6 1.0 C C:GLY45 4.8 98.5 1.0 C C:ASP39 4.9 100.7 1.0 CA C:ASP39 4.9 100.4 1.0 O C:ASP39 5.0 103.5 1.0 CG C:ASN50 5.0 90.8 1.0

Magnesium binding site 5 out of 6 in the A Novel Anti-Tumor Agent S-40 in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of A Novel Anti-Tumor Agent S-40 in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg504 b:63.6 occ:1.00 OE2 C:GLU254 2.1 58.8 1.0 OD1 C:ASN249 2.2 63.2 1.0 O B:HOH601 2.3 62.7 1.0 O B:HOH605 2.6 75.2 1.0 O B:HOH602 2.6 62.7 1.0 O C:ASN249 2.7 75.7 1.0 CD C:GLU254 3.1 70.5 1.0 OE1 C:GLU254 3.4 74.3 1.0 CG C:ASN249 3.4 64.8 1.0 C C:ASN249 3.6 71.5 1.0 N C:ASN249 4.0 78.0 1.0 NZ C:LYS352 4.0 63.4 1.0 CA C:ASN249 4.2 70.9 1.0 OD1 B:ASP177 4.2 78.1 1.0 ND2 C:ASN249 4.3 69.9 1.0 CB C:ASN249 4.4 64.6 1.0 OE2 B:GLU69 4.5 82.3 1.0 CG C:GLU254 4.5 69.9 1.0 OE1 B:GLN11 4.6 76.7 1.0 N C:VAL250 4.6 68.3 1.0 ND2 B:ASN99 4.7 71.8 1.0 OD2 B:ASP177 4.7 76.7 1.0 CE C:LYS352 4.8 69.6 1.0 NE2 B:GLN11 4.9 72.0 1.0 CA C:VAL250 4.9 67.6 1.0 CG B:ASP177 4.9 72.3 1.0 C C:LEU248 5.0 79.2 1.0

Magnesium binding site 6 out of 6 in the A Novel Anti-Tumor Agent S-40 in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of A Novel Anti-Tumor Agent S-40 in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:77.4 occ:1.00 O D:HOH603 2.0 76.4 1.0 O D:HOH602 2.1 72.2 1.0 O1B D:GTP501 2.4 74.7 1.0 O3G D:GTP501 2.6 61.2 1.0 OE1 D:GLU69 3.4 95.2 1.0 CB D:GLN11 3.5 67.5 1.0 PB D:GTP501 3.6 62.4 1.0 PG D:GTP501 3.7 67.6 1.0 O3A D:GTP501 3.9 65.9 1.0 N D:GLN11 4.0 71.7 1.0 OD2 D:ASP67 4.1 76.2 1.0 O1G D:GTP501 4.1 64.3 1.0 O3B D:GTP501 4.1 70.2 1.0 CG D:GLN11 4.3 74.6 1.0 CA D:GLN11 4.3 73.5 1.0 NE2 D:GLN11 4.4 86.9 1.0 O1A D:GTP501 4.4 72.9 1.0 CB D:GLU69 4.5 83.9 1.0 OD1 D:ASP67 4.5 67.4 1.0 CD D:GLU69 4.6 96.9 1.0 PA D:GTP501 4.7 70.3 1.0 CG D:ASP67 4.7 68.8 1.0 O2B D:GTP501 4.8 73.7 1.0 CD D:GLN11 4.9 89.0 1.0 CG2 D:THR72 5.0 83.7 1.0

T.Du, S.Lin, M.Ji, N.Xue, Y.Liu, Z.Zhang, K.Zhang, J.Zhang, Y.Zhang, X.Zou, L.Sheng, Y.Li, D.Lu, X.Chen, H.Xu. Discovery of A Novel Anti-Tumor Agent S-40 That Simultaneously Inhibits Tubulin Polymerization and STAT3 Signaling To Be Published.