Magnesium in PDB 5xlt: The Crystal Structure of Tubulin in Complex with 4'- Demethylepipodophyllotoxin

The structure of The Crystal Structure of Tubulin in Complex with 4'- Demethylepipodophyllotoxin, PDB code: 5xlt was solved by Y.Yu, Q.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.86 / 2.81
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.473, 156.926, 180.868, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 24.9

The structure of The Crystal Structure of Tubulin in Complex with 4'- Demethylepipodophyllotoxin also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the The Crystal Structure of Tubulin in Complex with 4'- Demethylepipodophyllotoxin (pdb code 5xlt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Crystal Structure of Tubulin in Complex with 4'- Demethylepipodophyllotoxin, PDB code: 5xlt:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the The Crystal Structure of Tubulin in Complex with 4'- Demethylepipodophyllotoxin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of Tubulin in Complex with 4'- Demethylepipodophyllotoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:22.4 occ:1.00 O2G A:GTP501 2.1 18.7 1.0 O A:HOH614 2.1 41.6 1.0 O A:HOH612 2.2 40.1 1.0 O A:HOH610 2.3 36.5 1.0 O A:HOH611 2.4 32.1 1.0 O2B A:GTP501 2.4 21.9 1.0 HZ1 B:LYS252 3.2 67.5 1.0 HB2 A:GLN11 3.3 38.0 1.0 PG A:GTP501 3.4 27.6 1.0 PB A:GTP501 3.6 19.3 1.0 OE1 A:GLU71 3.6 40.3 1.0 HB2 A:ASP98 3.9 44.5 1.0 O3A A:GTP501 3.9 28.0 1.0 O3B A:GTP501 3.9 35.8 1.0 HB3 A:ASP98 4.0 44.5 1.0 NZ B:LYS252 4.0 56.2 1.0 H A:GLN11 4.1 32.0 1.0 O3G A:GTP501 4.1 31.2 1.0 HB3 A:GLU71 4.1 46.9 1.0 CB A:GLN11 4.2 31.6 1.0 OE1 A:GLN11 4.2 36.9 1.0 HB3 A:GLN11 4.2 38.0 1.0 HZ2 B:LYS252 4.2 67.5 1.0 OD1 A:ASP69 4.3 30.1 1.0 CB A:ASP98 4.3 37.0 1.0 HZ3 B:LYS252 4.4 67.5 1.0 O1G A:GTP501 4.5 22.2 1.0 OD2 A:ASP69 4.5 34.9 1.0 OD2 A:ASP98 4.6 37.6 1.0 CD A:GLU71 4.6 41.1 1.0 N A:GLN11 4.7 26.6 1.0 HB2 A:GLU71 4.8 46.9 1.0 CG A:ASP98 4.8 39.5 1.0 CB A:GLU71 4.8 39.1 1.0 CG A:ASP69 4.9 38.3 1.0 O1B A:GTP501 4.9 31.8 1.0 HG21 A:VAL74 4.9 51.7 1.0 HG1 A:THR145 4.9 41.5 1.0 O2A A:GTP501 4.9 26.4 1.0 CA A:GLN11 5.0 29.5 1.0 PA A:GTP501 5.0 21.9 1.0 CD A:GLN11 5.0 24.8 1.0 HE3 B:LYS252 5.0 60.5 1.0

Magnesium binding site 2 out of 4 in the The Crystal Structure of Tubulin in Complex with 4'- Demethylepipodophyllotoxin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of Tubulin in Complex with 4'- Demethylepipodophyllotoxin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:30.0 occ:1.00 OE1 B:GLN11 2.0 48.8 1.0 O B:HOH610 2.0 48.9 1.0 O2A B:GDP501 2.1 29.9 1.0 O B:HOH616 2.6 27.1 1.0 CD B:GLN11 3.2 48.3 1.0 OD2 B:ASP177 3.3 36.9 1.0 HD21 B:ASN99 3.4 24.3 1.0 HB3 B:GLN11 3.6 47.8 1.0 PA B:GDP501 3.6 22.1 1.0 H8 B:GDP501 3.7 32.4 1.0 HE22 B:GLN11 4.0 58.0 1.0 HB2 B:GLN11 4.0 47.8 1.0 NE2 B:GLN11 4.0 48.3 1.0 OE1 C:GLU254 4.1 68.7 1.0 CB B:GLN11 4.1 39.9 1.0 CG B:GLN11 4.2 47.7 1.0 ND2 B:ASN99 4.2 20.2 1.0 C5' B:GDP501 4.3 25.9 1.0 O3A B:GDP501 4.4 34.7 1.0 O5' B:GDP501 4.4 14.5 1.0 O1A B:GDP501 4.5 17.2 1.0 HG2 B:GLN11 4.5 57.3 1.0 CG B:ASP177 4.5 39.2 1.0 O2B B:GDP501 4.5 36.6 1.0 HD22 B:ASN99 4.7 24.3 1.0 C8 B:GDP501 4.7 27.0 1.0 HE21 B:GLN11 4.9 58.0 1.0 HB3 B:ASP177 4.9 42.5 1.0 HG3 B:GLN11 5.0 57.3 1.0

Magnesium binding site 3 out of 4 in the The Crystal Structure of Tubulin in Complex with 4'- Demethylepipodophyllotoxin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of Tubulin in Complex with 4'- Demethylepipodophyllotoxin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:23.0 occ:1.00 O C:HOH604 2.0 39.4 1.0 O C:HOH610 2.0 28.2 1.0 O2B C:GTP501 2.1 20.5 1.0 O C:HOH627 2.1 34.0 1.0 O3G C:GTP501 2.1 18.0 1.0 O C:HOH608 2.1 23.8 1.0 HB2 C:GLN11 3.1 34.0 1.0 PB C:GTP501 3.2 13.6 1.0 PG C:GTP501 3.4 19.8 1.0 H C:GLN11 3.5 19.5 1.0 HZ1 D:LYS252 3.6 64.3 1.0 OE1 C:GLU71 3.6 43.8 1.0 O3A C:GTP501 3.6 24.7 1.0 O3B C:GTP501 3.7 26.5 1.0 HB3 C:GLN11 3.8 34.0 1.0 CB C:GLN11 3.9 28.4 1.0 OD1 C:ASP69 4.1 22.2 1.0 OD2 C:ASP69 4.1 24.9 1.0 OE1 C:GLN11 4.2 39.3 1.0 N C:GLN11 4.2 16.3 1.0 HB2 C:ASP98 4.2 31.7 1.0 O2G C:GTP501 4.2 18.9 1.0 HB3 C:GLU71 4.3 41.3 1.0 NZ D:LYS252 4.4 53.6 1.0 HB3 C:ASP98 4.4 31.7 1.0 HG21 C:VAL74 4.5 46.3 1.0 O1G C:GTP501 4.5 17.7 1.0 O1B C:GTP501 4.5 22.5 1.0 CG C:ASP69 4.5 24.8 1.0 HZ2 D:LYS252 4.6 64.3 1.0 HZ3 D:LYS252 4.6 64.3 1.0 CA C:GLN11 4.6 28.3 1.0 PA C:GTP501 4.6 21.5 1.0 O2A C:GTP501 4.7 25.3 1.0 HA2 C:GLY10 4.7 31.0 1.0 CB C:ASP98 4.8 26.4 1.0 CD C:GLU71 4.8 41.2 1.0 HB C:THR145 4.8 28.0 1.0 HA C:GLN11 4.9 33.9 1.0 HB2 C:GLU71 4.9 41.3 1.0 HG1 C:THR145 4.9 26.2 1.0 CD C:GLN11 5.0 30.1 1.0 OD2 C:ASP98 5.0 28.1 1.0 O1A C:GTP501 5.0 12.6 1.0 CG C:GLN11 5.0 27.3 1.0 HG23 C:VAL74 5.0 46.3 1.0 CB C:GLU71 5.0 34.4 1.0

Magnesium binding site 4 out of 4 in the The Crystal Structure of Tubulin in Complex with 4'- Demethylepipodophyllotoxin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Crystal Structure of Tubulin in Complex with 4'- Demethylepipodophyllotoxin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:53.6 occ:1.00 O2A D:GDP501 2.3 79.1 1.0 OE1 D:GLN11 2.6 69.0 1.0 O D:HOH602 2.7 53.7 1.0 O D:HOH605 3.4 56.7 1.0 PA D:GDP501 3.6 57.8 1.0 H8 D:GDP501 3.8 65.5 1.0 CD D:GLN11 3.8 72.8 1.0 O1A D:GDP501 4.0 42.4 1.0 HB3 D:GLN11 4.0 98.5 1.0 C5' D:GDP501 4.2 61.0 1.0 O5' D:GDP501 4.4 45.3 1.0 HB2 D:GLN11 4.5 98.5 1.0 HE22 D:GLN11 4.5 96.7 1.0 CB D:GLN11 4.6 82.1 1.0 NE2 D:GLN11 4.6 80.6 1.0 OD1 D:ASN99 4.6 67.7 1.0 C8 D:GDP501 4.8 54.5 1.0 O2B D:GDP501 4.8 72.5 1.0 HD21 D:ASN99 4.8 96.8 1.0 CG D:GLN11 4.8 79.2 1.0 O3A D:GDP501 4.9 64.2 1.0

L.Niu, Y.Wang, C.Wang, Y.Wang, X.Jiang, L.Ma, C.Wu, Y.Yu, Q.Chen. Structure of 4'-Demethylepipodophyllotoxin in Complex with Tubulin Provides A Rationale For Drug Design Biochem. Biophys. Res. V. 493 718 2017COMMUN..
ISSN: ESSN 1090-2104
PubMed: 28864414
DOI: 10.1016/J.BBRC.2017.08.125