Calcium 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:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium 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 Calcium atom.
In total 3 binding sites of Calcium where determined in the Structures of A Beta-Lactam Bridged Analogue in Complex with Tubulin, PDB code: 5gon:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structures of A Beta-Lactam Bridged Analogue in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca505 b:60.0 occ:1.00 OD2 A:ASP39 2.2 54.4 1.0 OG1 A:THR41 2.4 64.7 1.0 OE2 A:GLU55 2.4 51.2 1.0 O A:GLY44 2.4 47.2 1.0 OD1 A:ASP39 2.4 52.5 1.0 O A:THR41 2.6 60.9 1.0 CG A:ASP39 2.7 54.8 1.0 OE1 A:GLU55 3.0 53.2 1.0 CD A:GLU55 3.1 55.3 1.0 C A:GLY44 3.4 50.5 1.0 CB A:THR41 3.6 53.7 1.0 C A:THR41 3.6 65.8 1.0 CA A:GLY45 3.9 58.4 1.0 CA A:THR41 4.0 61.9 1.0 N A:GLY45 4.0 54.7 1.0 OD1 A:ASN50 4.1 53.8 1.0 CB A:ASP39 4.2 52.9 1.0 N A:THR41 4.3 56.2 1.0 N A:GLY44 4.4 57.0 1.0 CZ A:PHE49 4.4 58.0 1.0 CA A:GLY44 4.5 55.3 1.0 CG A:GLU55 4.5 53.3 1.0 OD2 A:ASP47 4.6 57.2 1.0 ND2 A:ASN50 4.7 49.9 1.0 NE2 A:HIS61 4.7 52.0 1.0 CG2 A:THR41 4.7 47.6 1.0 CG A:ASN50 4.8 46.4 1.0 N A:ILE42 4.9 62.6 1.0 CA A:ASP39 5.0 55.0 1.0

Calcium binding site 2 out of 3 in the Structures of A Beta-Lactam Bridged Analogue in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca506 b:81.7 occ:1.00 OE1 B:GLU113 2.9 46.9 1.0 OE1 B:GLU110 3.7 25.4 1.0 CD B:GLU113 3.9 41.5 1.0 OE2 B:GLU113 4.2 44.0 1.0 OE2 B:GLU110 4.2 34.4 1.0 CD B:GLU110 4.3 29.4 1.0

Calcium binding site 3 out of 3 in the Structures of A Beta-Lactam Bridged Analogue in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca501 b:82.8 occ:1.00 O C:TYR282 3.8 34.1 1.0 O C:GLU279 3.9 33.4 1.0 O C:LYS280 4.6 32.3 1.0 CA C:LYS280 4.8 28.5 1.0 C C:LYS280 4.8 27.7 1.0 C C:TYR282 5.0 28.7 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