Magnesium in PDB 8jjc: Tubulin-Y62

The structure of Tubulin-Y62, PDB code: 8jjc was solved by J.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.74 / 2.76
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.493, 157.005, 180.398, 90, 90, 90
R / Rfree (%)	23.5 / 26.4

The structure of Tubulin-Y62 also contains other interesting chemical elements:

Calcium	(Ca)	6 atoms
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Tubulin-Y62 (pdb code 8jjc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Tubulin-Y62, PDB code: 8jjc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Y62


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Y62 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:57.9 occ:0.00 O2G A:GTP501 2.4 55.7 0.0 O1G A:GTP501 2.7 54.8 0.0 O1B A:GTP501 2.9 54.9 0.0 PG A:GTP501 3.0 54.2 0.0 HZ1 B:LYS252 3.1 80.3 1.0 HB2 A:GLN11 3.4 61.7 1.0 HG2 A:GLU71 3.4 80.2 1.0 HG3 A:GLU71 3.5 80.2 1.0 O3A A:GTP501 3.5 54.1 0.0 PB A:GTP501 3.6 53.8 0.0 OE2 A:GLU71 3.7 73.9 1.0 HB2 A:ASP98 3.7 69.5 1.0 O3B A:GTP501 3.8 53.7 0.0 H A:GLN11 3.8 64.3 1.0 OD1 A:ASP69 3.8 62.0 1.0 NZ B:LYS252 3.9 66.9 1.0 CG A:GLU71 3.9 66.8 1.0 OD2 A:ASP69 3.9 62.8 1.0 HZ3 B:LYS252 3.9 80.3 1.0 HB3 A:ASP98 4.0 69.5 1.0 HZ2 B:LYS252 4.1 80.3 1.0 CB A:GLN11 4.2 51.4 1.0 HB3 A:GLN11 4.2 61.7 1.0 CD A:GLU71 4.2 69.8 1.0 CB A:ASP98 4.3 57.9 1.0 CG A:ASP69 4.3 63.1 1.0 O3G A:GTP501 4.4 53.6 0.0 HG1 A:THR145 4.4 69.7 1.0 OE1 A:GLN11 4.4 59.7 1.0 OD2 A:ASP98 4.4 58.1 1.0 N A:GLN11 4.5 53.6 1.0 HB A:THR145 4.7 65.4 1.0 O1A A:GTP501 4.7 53.6 0.0 CG A:ASP98 4.7 56.0 1.0 HG21 A:VAL74 4.7 82.5 1.0 OG1 A:THR145 4.7 58.1 1.0 PA A:GTP501 4.8 53.5 0.0 HA2 A:GLY10 4.8 67.0 1.0 CA A:GLN11 4.9 53.3 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Y62


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Y62 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:56.1 occ:0.00 O1A B:GDP506 2.0 54.0 0.0 OE1 B:GLN11 2.0 64.1 1.0 CD B:GLN11 3.2 62.2 1.0 PA B:GDP506 3.4 53.4 0.0 HB3 B:GLN11 3.8 65.4 1.0 HE22 B:GLN11 3.8 76.2 1.0 HB2 B:GLN11 3.8 65.4 1.0 O2A B:GDP506 3.9 54.0 0.0 NE2 B:GLN11 3.9 63.4 1.0 OD2 B:ASP177 4.1 58.0 1.0 CB B:GLN11 4.1 54.5 1.0 HD21 B:ASN99 4.2 61.1 1.0 O3B B:GDP506 4.2 53.4 0.0 CG B:GLN11 4.3 58.1 1.0 O1B B:GDP506 4.3 50.2 0.0 OE1 C:GLU254 4.3 60.3 1.0 OD1 B:ASN99 4.3 49.5 1.0 H8 B:GDP506 4.4 64.6 0.0 O5' B:GDP506 4.5 52.6 0.0 O3A B:GDP506 4.5 51.8 0.0 PB B:GDP506 4.6 51.0 0.0 C5' B:GDP506 4.7 53.5 0.0 HE21 B:GLN11 4.7 76.2 1.0 HG2 B:GLN11 4.8 69.8 1.0 ND2 B:ASN99 4.8 50.9 1.0 HG3 B:GLN11 4.9 69.8 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Y62


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Y62 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:50.9 occ:0.00 O1G C:GTP501 2.1 50.5 0.0 O1B C:GTP501 2.5 48.0 0.0 PG C:GTP501 3.2 49.6 0.0 HZ1 D:LYS252 3.4 68.4 1.0 PB C:GTP501 3.5 47.9 0.0 O2G C:GTP501 3.5 50.2 0.0 HB2 C:GLN11 3.5 58.0 1.0 HG2 C:GLU71 3.6 65.8 1.0 O3A C:GTP501 3.6 48.7 0.0 HG3 C:GLU71 3.7 65.8 1.0 O3B C:GTP501 3.7 48.3 0.0 HB2 C:ASP98 3.8 60.8 1.0 H C:GLN11 3.9 50.4 1.0 OE2 C:GLU71 4.0 63.5 1.0 CG C:GLU71 4.0 54.8 1.0 NZ D:LYS252 4.1 57.0 1.0 HZ3 D:LYS252 4.1 68.4 1.0 OD1 C:ASP69 4.1 50.9 1.0 OD2 C:ASP69 4.1 51.4 1.0 HZ2 D:LYS252 4.2 68.4 1.0 HB3 C:ASP98 4.3 60.8 1.0 HB3 C:GLN11 4.3 58.0 1.0 CB C:GLN11 4.3 48.3 1.0 OE1 C:GLN11 4.4 51.0 1.0 O3G C:GTP501 4.5 50.4 0.0 CB C:ASP98 4.5 50.6 1.0 CD C:GLU71 4.5 58.5 1.0 HG1 C:THR145 4.5 55.5 1.0 CG C:ASP69 4.6 50.9 1.0 N C:GLN11 4.6 42.0 1.0 HG21 C:VAL74 4.8 66.9 1.0 O1A C:GTP501 4.8 48.5 0.0 O2B C:GTP501 4.8 47.2 0.0 HA2 C:GLY10 4.9 56.6 1.0 PA C:GTP501 4.9 48.2 0.0 HB C:THR145 4.9 53.2 1.0 OG1 C:THR145 4.9 46.2 1.0 OD2 C:ASP98 5.0 60.6 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Y62


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Y62 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:85.6 occ:0.00 O3G D:GTP503 1.9 83.7 0.0 OE2 D:GLU69 2.0 90.4 1.0 CD D:GLU69 2.5 97.6 1.0 PG D:GTP503 2.6 82.4 0.0 OE1 D:GLU69 2.6 96.2 1.0 O2G D:GTP503 2.7 82.6 0.0 O2B D:GTP503 3.0 81.3 0.0 O3B D:GTP503 3.1 81.0 0.0 PB D:GTP503 3.6 80.3 0.0 O2A D:GTP503 3.7 80.7 0.0 HB2 D:GLN11 3.8 103.2 1.0 CG D:GLU69 3.8 93.9 1.0 HG2 D:GLU69 3.9 112.7 1.0 O1G D:GTP503 4.0 82.0 0.0 H D:GLN11 4.1 96.7 1.0 HG1 D:THR143 4.1 103.4 1.0 HB3 D:GLU69 4.3 108.8 1.0 O3A D:GTP503 4.3 79.7 0.0 HG3 D:GLU69 4.4 112.7 1.0 OD1 D:ASP67 4.5 85.3 1.0 HB3 D:GLN11 4.5 103.2 1.0 CB D:GLN11 4.6 86.0 1.0 OG1 D:THR143 4.6 86.1 1.0 PA D:GTP503 4.6 79.5 0.0 CB D:GLU69 4.6 90.6 1.0 OD2 D:ASP67 4.7 86.5 1.0 OE1 D:GLN11 4.7 89.0 1.0 N D:GLN11 4.8 80.5 1.0 HB D:THR143 4.8 96.3 1.0 H D:ALA97 4.9 105.7 1.0 O1B D:GTP503 4.9 79.4 0.0

Magnesium binding site 5 out of 5 in the Tubulin-Y62


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Y62 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:93.1 occ:0.00 O2B F:ACP402 2.7 92.8 0.0 HZ1 F:LYS74 3.0 118.2 1.0 O1G F:ACP402 3.2 91.1 0.0 HZ3 F:LYS74 3.3 118.2 1.0 OE1 F:GLU331 3.4 91.5 1.0 NZ F:LYS74 3.5 98.5 1.0 OE2 F:GLU331 3.6 90.2 1.0 O1B F:ACP402 3.7 96.0 0.0 HZ2 F:LYS74 3.8 118.2 1.0 PB F:ACP402 3.8 94.0 0.0 CD F:GLU331 3.9 89.0 1.0 HA F:SER152 4.3 139.0 1.0 PG F:ACP402 4.3 90.9 0.0 OD1 F:ASN333 4.3 88.0 1.0 O3G F:ACP402 4.5 89.2 0.0 CG F:ASN333 4.6 87.6 1.0 HB2 F:ASN333 4.7 99.7 1.0 C3B F:ACP402 4.8 94.7 0.0 O F:SER152 4.8 117.3 1.0 CE F:LYS74 4.9 101.3 1.0 ND2 F:ASN333 4.9 89.9 1.0 HD22 F:ASN333 4.9 108.0 1.0 HA F:ASN333 4.9 96.4 1.0 HE2 F:LYS74 4.9 121.6 1.0

C.Zhang, W.Yan, Y.Liu, M.Tang, Y.Teng, F.Wang, X.Hu, M.Zhao, J.Yang, Y.Li. Structure-Based Design and Synthesis of BML284 Derivatives: A Novel Class of Colchicine-Site Noncovalent Tubulin Degradation Agents. Eur.J.Med.Chem. V. 268 16265 2024.
ISSN: ISSN 0223-5234
PubMed: 38430854
DOI: 10.1016/J.EJMECH.2024.116265