Magnesium in PDB 7yhn: Anti-Tumor Agent Y48 in Complex with Tubulin

The structure of Anti-Tumor Agent Y48 in Complex with Tubulin, PDB code: 7yhn was solved by T.Du, M.Ji, Z.Hou, S.Lin, J.Zhang, D.Wu, K.Zhang, D.Lu, H.Xu, X.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	78.33 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.87, 102.03, 131.13, 90, 106.91, 90
R / Rfree (%)	23 / 27.2

The binding sites of Magnesium atom in the Anti-Tumor Agent Y48 in Complex with Tubulin (pdb code 7yhn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Anti-Tumor Agent Y48 in Complex with Tubulin, PDB code: 7yhn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Anti-Tumor Agent Y48 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 Anti-Tumor Agent Y48 in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:85.2 occ:1.00 O1B A:GTP501 2.1 87.3 1.0 O A:HOH601 2.2 78.6 1.0 O1G A:GTP501 2.4 82.8 1.0 PB A:GTP501 3.4 76.3 1.0 PG A:GTP501 3.5 75.8 1.0 OD2 A:ASP69 3.5 90.9 1.0 OE2 A:GLU71 3.6 99.9 1.0 CG A:GLU71 3.6 97.8 1.0 O3B A:GTP501 3.7 87.1 1.0 OD1 A:ASP69 3.9 91.9 1.0 CD A:GLU71 3.9 97.5 1.0 O2G A:GTP501 4.0 74.6 1.0 CB A:GLN11 4.0 76.3 1.0 O3A A:GTP501 4.1 77.3 1.0 CG A:ASP69 4.1 90.2 1.0 OE1 A:GLN11 4.3 98.5 1.0 N A:GLN11 4.3 84.8 1.0 OD2 A:ASP98 4.4 93.7 1.0 CB A:ASP98 4.6 87.8 1.0 O2B A:GTP501 4.6 82.6 1.0 CA A:GLN11 4.7 83.5 1.0 O3G A:GTP501 4.8 78.5 1.0 CB A:GLU71 4.8 96.1 1.0 O1A A:GTP501 4.9 79.8 1.0 PA A:GTP501 4.9 86.1 1.0

Magnesium binding site 2 out of 6 in the Anti-Tumor Agent Y48 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 Anti-Tumor Agent Y48 in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:106.3 occ:1.00 OE2 A:GLU55 2.3 119.8 1.0 O A:GLY44 2.3 118.5 1.0 OE1 A:GLU55 2.4 116.8 1.0 OD2 A:ASP39 2.4 119.7 1.0 O A:THR41 2.5 120.5 1.0 OG1 A:THR41 2.5 123.2 1.0 OD1 A:ASP39 2.6 118.0 1.0 CD A:GLU55 2.7 118.2 1.0 CG A:ASP39 2.8 115.5 1.0 C A:GLY44 3.5 120.6 1.0 C A:THR41 3.6 120.2 1.0 CB A:THR41 3.7 119.5 1.0 CA A:THR41 4.1 120.0 1.0 CG A:GLU55 4.2 114.5 1.0 OD1 A:ASN50 4.2 115.5 1.0 OD2 A:ASP47 4.2 119.8 1.0 CA A:GLY45 4.3 123.3 1.0 N A:GLY45 4.3 123.8 1.0 N A:THR41 4.3 120.0 1.0 CB A:ASP39 4.3 114.1 1.0 N A:GLY44 4.4 118.5 1.0 CA A:GLY44 4.5 119.5 1.0 CZ A:PHE49 4.6 115.7 1.0 ND2 A:ASN50 4.7 110.9 1.0 N A:ILE42 4.7 120.2 1.0 CE2 A:PHE49 4.8 114.3 1.0 CG A:ASN50 4.9 112.1 1.0 CG2 A:THR41 4.9 124.2 1.0 CB A:GLU55 5.0 113.5 1.0

Magnesium binding site 3 out of 6 in the Anti-Tumor Agent Y48 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 Anti-Tumor Agent Y48 in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:73.7 occ:1.00 O B:HOH603 2.2 88.2 1.0 OD1 C:ASN249 2.3 78.3 1.0 OE2 C:GLU254 2.3 73.5 1.0 O C:ASN249 2.8 85.2 1.0 O B:HOH604 2.8 79.1 1.0 CD C:GLU254 3.2 79.1 1.0 OE1 C:GLU254 3.3 77.4 1.0 CG C:ASN249 3.5 80.4 1.0 C C:ASN249 3.6 83.8 1.0 NZ C:LYS352 4.1 72.7 1.0 N C:ASN249 4.1 88.0 1.0 CA C:ASN249 4.2 82.5 1.0 ND2 C:ASN249 4.4 79.0 1.0 CB C:ASN249 4.4 77.0 1.0 OD1 B:ASP177 4.4 87.7 1.0 NE2 B:GLN11 4.5 89.3 1.0 N C:VAL250 4.6 75.1 1.0 CG C:GLU254 4.6 75.8 1.0 OE1 B:GLU69 4.6 97.4 1.0 OE1 B:GLN11 4.7 83.6 1.0 ND2 B:ASN99 4.9 71.5 1.0 CD B:GLN11 4.9 92.0 1.0 CA C:VAL250 4.9 80.3 1.0 CE C:LYS352 4.9 74.2 1.0

Magnesium binding site 4 out of 6 in the Anti-Tumor Agent Y48 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 Anti-Tumor Agent Y48 in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:70.1 occ:1.00 O1B C:GTP502 2.0 79.6 1.0 O C:HOH602 2.0 80.4 1.0 O C:HOH603 2.2 66.5 1.0 O C:HOH606 2.4 70.7 1.0 O1G C:GTP502 2.4 67.6 1.0 OD2 C:ASP69 3.4 73.1 1.0 PB C:GTP502 3.4 69.8 1.0 OE1 C:GLU71 3.5 86.5 1.0 PG C:GTP502 3.6 70.2 1.0 OD1 C:ASP69 3.6 70.2 1.0 O3B C:GTP502 3.8 74.7 1.0 CG C:ASP69 3.9 72.0 1.0 CB C:GLN11 4.0 69.2 1.0 O3A C:GTP502 4.1 69.9 1.0 N C:GLN11 4.2 79.3 1.0 O2G C:GTP502 4.2 69.8 1.0 OE1 C:GLN11 4.4 79.5 1.0 OG1 C:THR145 4.5 73.4 1.0 CD C:GLU71 4.5 85.8 1.0 O2B C:GTP502 4.6 73.6 1.0 CA C:GLN11 4.6 77.0 1.0 CB C:ASP98 4.6 73.7 1.0 OD2 C:ASP98 4.7 84.6 1.0 NZ D:LYS252 4.9 79.2 1.0 O3G C:GTP502 4.9 67.6 1.0

Magnesium binding site 5 out of 6 in the Anti-Tumor Agent Y48 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 Anti-Tumor Agent Y48 in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg504 b:93.4 occ:1.00 OG1 C:THR41 1.9 116.1 1.0 OD1 C:ASP39 2.3 97.0 1.0 OE1 C:GLU55 2.4 108.1 1.0 OE2 C:GLU55 2.4 94.4 1.0 O C:THR41 2.5 107.1 1.0 CD C:GLU55 2.7 97.1 1.0 OD2 C:ASP39 2.9 102.7 1.0 CG C:ASP39 2.9 103.9 1.0 O C:GLY44 2.9 102.0 1.0 CB C:THR41 3.2 108.0 1.0 C C:THR41 3.4 109.5 1.0 CA C:THR41 3.7 107.4 1.0 OD2 C:ASP47 3.9 107.1 1.0 N C:THR41 4.0 111.1 1.0 C C:GLY44 4.0 108.1 1.0 ND2 C:ASN50 4.0 99.5 1.0 CG C:GLU55 4.2 98.1 1.0 CZ C:PHE49 4.3 99.1 1.0 CG2 C:THR41 4.3 107.9 1.0 CA C:GLY45 4.4 105.7 1.0 CB C:ASP39 4.4 103.8 1.0 OD1 C:ASN50 4.5 98.6 1.0 N C:GLY45 4.6 107.7 1.0 N C:ILE42 4.6 109.5 1.0 CE1 C:PHE49 4.7 93.1 1.0 CG C:ASP47 4.7 102.6 1.0 CG C:ASN50 4.7 95.6 1.0 N C:GLY44 4.9 101.8 1.0 C C:GLY45 4.9 106.9 1.0 O C:GLY45 5.0 107.8 1.0

Magnesium binding site 6 out of 6 in the Anti-Tumor Agent Y48 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 Anti-Tumor Agent Y48 in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:82.0 occ:1.00 O1B D:GTP501 2.2 86.0 1.0 O3G D:GTP501 2.5 80.4 1.0 PB D:GTP501 3.4 73.5 1.0 PG D:GTP501 3.5 85.5 1.0 O3B D:GTP501 3.8 76.8 1.0 O1G D:GTP501 3.8 75.4 1.0 OD2 D:ASP67 3.8 89.1 1.0 CB D:GLN11 3.8 82.3 1.0 O3A D:GTP501 3.9 75.3 1.0 N D:GLN11 4.0 83.7 1.0 OD1 D:ASP67 4.2 84.4 1.0 OE1 D:GLU69 4.2 108.0 1.0 CB D:GLU69 4.2 88.1 1.0 CD D:GLU69 4.4 102.4 1.0 NE2 D:GLN11 4.4 106.1 1.0 CG D:ASP67 4.4 87.1 1.0 CA D:GLN11 4.4 86.0 1.0 O1A D:GTP501 4.4 82.0 1.0 OG1 D:THR143 4.6 82.8 1.0 PA D:GTP501 4.7 79.8 1.0 CG D:GLN11 4.7 84.9 1.0 CG D:GLU69 4.7 94.5 1.0 O2B D:GTP501 4.7 80.6 1.0 OE2 D:GLU69 4.8 99.8 1.0 CG2 D:THR72 4.8 99.5 1.0 O2G D:GTP501 4.9 82.0 1.0 C D:GLY10 4.9 79.4 1.0 CD D:GLN11 5.0 104.5 1.0

T.Du, M.Ji, Z.Hou, S.Lin, J.Zhang, D.Wu, K.Zhang, D.Lu, H.Xu, X.Chen. Anti-Tumor Agent Y48 in Complex with Tubulin To Be Published.