Magnesium in PDB 6kpp: BNC105 in Complex with Tubulin

The structure of BNC105 in Complex with Tubulin, PDB code: 6kpp was solved by T.Wang, C.Wu, D.Pu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.27 / 2.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.455, 157.664, 183.135, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 23.5

The structure of BNC105 in Complex with Tubulin also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the BNC105 in Complex with Tubulin (pdb code 6kpp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the BNC105 in Complex with Tubulin, PDB code: 6kpp:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the BNC105 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 BNC105 in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:31.8 occ:1.00 O1G A:GTP501 2.0 31.1 1.0 O1B A:GTP501 2.3 28.3 1.0 PG A:GTP501 3.2 37.6 1.0 OE2 A:GLU71 3.3 64.8 1.0 PB A:GTP501 3.5 31.9 1.0 O3B A:GTP501 3.6 41.3 1.0 O2G A:GTP501 3.6 34.2 1.0 OD2 A:ASP69 3.7 48.6 1.0 OD1 A:ASP69 3.8 50.5 1.0 O3A A:GTP501 4.2 34.7 1.0 CB A:ASP98 4.2 45.8 1.0 CG A:ASP69 4.2 46.7 1.0 OD2 A:ASP98 4.2 47.5 1.0 CD A:GLU71 4.4 61.8 1.0 CB A:GLN11 4.4 35.0 1.0 O3G A:GTP501 4.5 27.6 1.0 N A:GLN11 4.5 30.5 1.0 CG A:ASP98 4.6 46.9 1.0 O2B A:GTP501 4.7 39.7 1.0 CB A:GLU71 4.8 51.4 1.0 OG1 A:THR145 4.8 34.6 1.0

Magnesium binding site 2 out of 4 in the BNC105 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 BNC105 in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:27.6 occ:1.00 O1A B:GDP503 2.3 25.0 1.0 O C:HOH622 2.4 33.9 1.0 O B:HOH624 2.6 31.7 1.0 OE1 B:GLN11 2.7 50.1 1.0 OD2 B:ASP177 3.2 52.2 1.0 PA B:GDP503 3.7 18.0 1.0 CD B:GLN11 3.8 46.6 1.0 OD1 B:ASN99 4.1 36.6 1.0 C5' B:GDP503 4.1 23.2 1.0 CG B:ASP177 4.2 52.5 1.0 O3A B:GDP503 4.3 28.3 1.0 OE1 C:GLU254 4.3 52.0 1.0 O5' B:GDP503 4.3 12.8 1.0 O C:HOH613 4.5 37.1 1.0 CB B:GLN11 4.5 31.9 1.0 CG B:GLN11 4.6 36.5 1.0 ND2 B:ASN99 4.7 28.0 1.0 NE2 B:GLN11 4.7 49.3 1.0 O2A B:GDP503 4.7 28.4 1.0 O1B B:GDP503 4.7 21.9 1.0 CG B:ASN99 4.8 30.0 1.0 CB B:ASP177 4.8 45.5 1.0 C8 B:GDP503 4.9 35.3 1.0

Magnesium binding site 3 out of 4 in the BNC105 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 BNC105 in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:32.8 occ:1.00 O1G C:GTP501 2.1 29.4 1.0 O1B C:GTP501 2.5 28.9 1.0 OE2 C:GLU71 3.2 55.8 1.0 PG C:GTP501 3.4 32.9 1.0 PB C:GTP501 3.6 32.7 1.0 O2G C:GTP501 3.9 31.9 1.0 O3B C:GTP501 3.9 30.0 1.0 OD2 C:ASP69 3.9 42.3 1.0 OD2 C:ASP98 4.2 43.0 1.0 OD1 C:ASP69 4.2 42.6 1.0 CB C:GLN11 4.2 25.3 1.0 O3A C:GTP501 4.3 29.6 1.0 NE2 C:GLN11 4.3 34.6 1.0 O2A C:GTP501 4.3 33.8 1.0 CD C:GLU71 4.4 51.4 1.0 CB C:ASP98 4.4 35.5 1.0 CG C:ASP69 4.5 39.0 1.0 N C:GLN11 4.6 25.3 1.0 O3G C:GTP501 4.6 19.7 1.0 CG C:ASP98 4.7 38.5 1.0 O2B C:GTP501 4.9 38.4 1.0 CA C:GLN11 5.0 29.9 1.0

Magnesium binding site 4 out of 4 in the BNC105 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 BNC105 in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:68.2 occ:1.00 OE1 D:GLN11 2.3 99.1 1.0 O1A D:GDP503 2.7 78.8 1.0 OD1 D:ASN99 3.2 89.3 1.0 CD D:GLN11 3.5 99.4 1.0 OD2 D:ASP177 3.7 0.7 1.0 O3A D:GDP503 3.7 77.5 1.0 PA D:GDP503 3.7 74.6 1.0 ND2 D:ASN99 3.8 88.5 1.0 CG D:ASN99 3.9 89.6 1.0 O1B D:GDP503 4.0 79.9 1.0 NE2 D:GLN11 4.3 0.7 1.0 C5' D:GDP503 4.4 66.8 1.0 PB D:GDP503 4.4 77.3 1.0 CB D:GLN11 4.5 93.0 1.0 CG D:GLN11 4.6 96.7 1.0 O5' D:GDP503 4.6 71.0 1.0 CG D:ASP177 4.6 0.5 1.0 O2A D:GDP503 4.9 74.6 1.0 CB D:ASP177 4.9 0.6 1.0 O2B D:GDP503 5.0 71.1 1.0

T.Wang, C.Wu, C.Wang, G.Zhang, K.E.Arnst, Y.Yao, Z.Zhang, Y.Wang, D.Pu, W.Li. Unraveling the Molecular Mechanism of BNC105, A Phase II Clinical Trial Vascular Disrupting Agent, Provides Insights Into Drug Design. Biochem.Biophys.Res.Commun. 2020.
ISSN: ESSN 1090-2104
PubMed: 32085900
DOI: 10.1016/J.BBRC.2019.12.083