Magnesium in PDB 5gon: Structures of A Beta-Lactam Bridged Analogue in Complex with Tubulin

The structure of Structures of A Beta-Lactam Bridged Analogue in Complex with Tubulin, PDB code: 5gon was solved by L.Zhou, Y.Liu, L.Cheng, Y.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	118.60 / 2.48
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.507, 156.463, 181.838, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 25.7

The structure of Structures of A Beta-Lactam Bridged Analogue in Complex with Tubulin also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Magnesium atom in the Structures of A Beta-Lactam Bridged Analogue in Complex with Tubulin (pdb code 5gon). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Structures of A Beta-Lactam Bridged Analogue in Complex with Tubulin, PDB code: 5gon:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Structures of A Beta-Lactam Bridged Analogue 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 Structures of A Beta-Lactam Bridged Analogue in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:37.6 occ:1.00 O2G A:GTP501 1.7 24.5 1.0 O A:HOH635 1.9 31.4 1.0 O A:HOH611 2.1 24.9 1.0 O1B A:GTP501 2.5 20.7 1.0 PG A:GTP501 3.0 31.7 1.0 PB A:GTP501 3.5 23.4 1.0 O1G A:GTP501 3.6 26.9 1.0 O3B A:GTP501 3.6 33.4 1.0 OD2 A:ASP98 3.9 35.7 1.0 CG A:GLU71 4.1 43.1 1.0 O3A A:GTP501 4.2 30.4 1.0 CB A:ASP98 4.2 30.9 1.0 OD1 A:ASP69 4.2 28.8 1.0 O3G A:GTP501 4.2 19.1 1.0 CG A:ASP98 4.3 31.7 1.0 OD2 A:ASP69 4.3 28.4 1.0 NZ B:LYS254 4.3 50.4 1.0 OE1 A:GLU71 4.4 51.6 1.0 CB A:GLN11 4.6 23.3 1.0 N A:GLN11 4.7 27.9 1.0 CG A:ASP69 4.7 31.5 1.0 O2B A:GTP501 4.8 26.3 1.0 CD A:GLU71 4.8 45.5 1.0 O1A A:GTP501 4.8 23.1 1.0 OG1 A:THR145 4.9 33.6 1.0

Magnesium binding site 2 out of 5 in the Structures of A Beta-Lactam Bridged Analogue 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 Structures of A Beta-Lactam Bridged Analogue in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:16.9 occ:1.00 O1A B:GDP501 2.1 24.5 1.0 OE1 B:GLN11 2.1 26.7 1.0 O B:HOH648 2.7 23.2 1.0 OD2 B:ASP179 3.0 47.1 1.0 CD B:GLN11 3.4 23.6 1.0 PA B:GDP501 3.4 17.4 1.0 O3A B:GDP501 3.8 20.7 1.0 C5' B:GDP501 4.2 15.4 1.0 CB B:GLN11 4.2 21.3 1.0 CG B:ASP179 4.2 34.9 1.0 O5' B:GDP501 4.2 13.3 1.0 OD1 B:ASN101 4.2 24.1 1.0 CG B:GLN11 4.2 24.5 1.0 NE2 B:GLN11 4.3 26.6 1.0 O2A B:GDP501 4.5 16.5 1.0 OE1 C:GLU254 4.7 32.4 1.0 C8 B:GDP501 4.7 18.0 1.0 O1B B:GDP501 4.8 13.4 1.0 PB B:GDP501 4.9 14.7 1.0

Magnesium binding site 3 out of 5 in the Structures of A Beta-Lactam Bridged Analogue 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 Structures of A Beta-Lactam Bridged Analogue in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg504 b:38.6 occ:1.00 O1G C:GTP503 1.8 22.6 1.0 O C:HOH628 1.9 17.7 1.0 O1B C:GTP503 2.3 19.8 1.0 PG C:GTP503 3.1 20.3 1.0 PB C:GTP503 3.4 14.7 1.0 O2G C:GTP503 3.6 20.5 1.0 O3B C:GTP503 3.6 20.1 1.0 OE1 C:GLU71 3.9 38.2 1.0 OD2 C:ASP98 4.0 25.2 1.0 O3A C:GTP503 4.0 18.5 1.0 NZ D:LYS254 4.1 30.3 1.0 OD2 C:ASP69 4.2 15.0 1.0 OD1 C:ASP69 4.2 19.5 1.0 CB C:ASP98 4.2 21.7 1.0 CG C:GLU71 4.3 29.6 1.0 O3G C:GTP503 4.3 13.6 1.0 CG C:ASP98 4.4 21.6 1.0 CB C:GLN11 4.6 13.9 1.0 O2B C:GTP503 4.6 18.1 1.0 CD C:GLU71 4.6 34.0 1.0 CG C:ASP69 4.6 18.2 1.0 N C:GLN11 4.7 14.3 1.0 OE1 C:GLN11 4.8 22.8 1.0 OG1 C:THR145 4.9 16.4 1.0 O1A C:GTP503 5.0 17.9 1.0

Magnesium binding site 4 out of 5 in the Structures of A Beta-Lactam Bridged Analogue 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 Structures of A Beta-Lactam Bridged Analogue in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:40.8 occ:1.00 OE1 D:GLN11 1.9 49.2 1.0 O1A D:GDP501 2.3 60.9 1.0 OD2 D:ASP179 3.0 71.0 1.0 CD D:GLN11 3.1 50.2 1.0 PA D:GDP501 3.6 44.9 1.0 NE2 D:GLN11 3.7 50.0 1.0 CG D:ASP179 3.8 85.5 1.0 O3A D:GDP501 3.8 46.5 1.0 OD1 D:ASP179 3.9 80.2 1.0 CG D:GLN11 4.3 54.3 1.0 OD1 D:ASN101 4.3 72.8 1.0 CB D:GLN11 4.3 52.9 1.0 C5' D:GDP501 4.4 45.2 1.0 O5' D:GDP501 4.4 49.0 1.0 ND2 D:ASN101 4.5 66.9 1.0 O2A D:GDP501 4.6 46.5 1.0 CG D:ASN101 4.8 62.0 1.0 O1B D:GDP501 5.0 43.0 1.0

Magnesium binding site 5 out of 5 in the Structures of A Beta-Lactam Bridged Analogue 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 Structures of A Beta-Lactam Bridged Analogue in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:86.2 occ:1.00 OE2 F:GLU331 2.6 87.8 1.0 CD F:GLU331 3.4 81.8 1.0 CG F:GLU331 3.9 68.7 1.0 CG2 F:ILE330 4.2 51.3 1.0 OE1 F:GLU331 4.3 78.9 1.0 OD2 F:ASP318 4.7 60.5 1.0

P.Zhou, Y.Liu, L.Zhou, K.Zhu, K.Feng, H.Zhang, Y.Liang, H.Jiang, C.Luo, M.Liu, Y.Wang. Potent Antitumor Activities and Structure Basis of the Chiral Beta-Lactam Bridged Analogue of Combretastatin A-4 Binding to Tubulin. J. Med. Chem. V. 59 10329 2016.
ISSN: ISSN 1520-4804
PubMed: 27805821
DOI: 10.1021/ACS.JMEDCHEM.6B01268