Magnesium in PDB 5xlz: The Crystal Structure of Tubulin Complexed with A Benzylidene Derivative of 9(10H)-Anthracenone

The structure of The Crystal Structure of Tubulin Complexed with A Benzylidene Derivative of 9(10H)-Anthracenone, PDB code: 5xlz 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)	42.67 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.465, 158.439, 181.600, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 24.7

The structure of The Crystal Structure of Tubulin Complexed with A Benzylidene Derivative of 9(10H)-Anthracenone also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the The Crystal Structure of Tubulin Complexed with A Benzylidene Derivative of 9(10H)-Anthracenone (pdb code 5xlz). 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 Complexed with A Benzylidene Derivative of 9(10H)-Anthracenone, PDB code: 5xlz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the The Crystal Structure of Tubulin Complexed with A Benzylidene Derivative of 9(10H)-Anthracenone


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 Complexed with A Benzylidene Derivative of 9(10H)-Anthracenone within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:24.8 occ:1.00 O A:HOH688 2.0 30.0 1.0 O2G A:GTP501 2.1 20.3 1.0 O A:HOH713 2.1 26.5 1.0 O A:HOH630 2.1 27.6 1.0 O2B A:GTP501 2.1 19.7 1.0 O A:HOH695 2.2 27.1 1.0 HZ1 B:LYS252 3.2 44.3 1.0 PB A:GTP501 3.2 14.5 1.0 PG A:GTP501 3.3 23.5 1.0 HB2 A:GLN11 3.3 32.9 1.0 O3A A:GTP501 3.6 24.2 1.0 O3B A:GTP501 3.7 27.5 1.0 H A:GLN11 3.7 30.8 1.0 OE1 A:GLU71 3.8 43.7 1.0 O3G A:GTP501 3.8 23.1 1.0 HB2 A:ASP98 4.0 35.0 1.0 NZ B:LYS252 4.0 36.9 1.0 HB3 A:GLN11 4.0 32.9 1.0 HZ2 B:LYS252 4.1 44.3 1.0 CB A:GLN11 4.1 27.4 1.0 OD1 A:ASP69 4.1 26.0 1.0 OD2 A:ASP69 4.3 29.5 1.0 HB3 A:ASP98 4.3 35.0 1.0 HZ3 B:LYS252 4.3 44.3 1.0 HB3 A:GLU71 4.3 47.0 1.0 OE1 A:GLN11 4.4 36.4 1.0 N A:GLN11 4.4 25.6 1.0 O1G A:GTP501 4.5 23.7 1.0 CB A:ASP98 4.5 29.1 1.0 O1B A:GTP501 4.6 26.2 1.0 CG A:ASP69 4.6 31.7 1.0 HG1 A:THR145 4.6 28.8 1.0 OD2 A:ASP98 4.7 30.9 1.0 PA A:GTP501 4.7 16.8 1.0 O2A A:GTP501 4.7 21.4 1.0 HB A:THR145 4.8 28.8 1.0 CA A:GLN11 4.8 27.6 1.0 HG21 A:VAL74 4.8 48.7 1.0 HA2 A:GLY10 4.9 31.2 1.0 CD A:GLU71 4.9 44.6 1.0 O A:HOH620 4.9 36.4 1.0 CG A:ASP98 4.9 28.6 1.0 OG1 A:THR145 5.0 24.0 1.0

Magnesium binding site 2 out of 4 in the The Crystal Structure of Tubulin Complexed with A Benzylidene Derivative of 9(10H)-Anthracenone


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 Complexed with A Benzylidene Derivative of 9(10H)-Anthracenone within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:16.2 occ:1.00 OE1 B:GLN11 2.1 24.3 1.0 O B:HOH679 2.1 23.7 1.0 O2A B:GDP501 2.1 22.8 1.0 O B:HOH621 2.2 31.1 1.0 O C:HOH641 2.2 26.4 1.0 O B:HOH706 2.5 23.4 1.0 CD B:GLN11 3.3 30.3 1.0 HB3 B:GLN11 3.5 29.6 1.0 PA B:GDP501 3.5 17.4 1.0 H8 B:GDP501 3.7 34.1 1.0 OD2 B:ASP177 3.8 26.4 1.0 HB2 B:GLN11 3.9 29.6 1.0 O3A B:GDP501 4.0 17.4 1.0 CB B:GLN11 4.0 24.6 1.0 HE22 B:GLN11 4.2 41.7 1.0 CG B:GLN11 4.2 29.2 1.0 OE1 C:GLU254 4.2 37.0 1.0 NE2 B:GLN11 4.2 34.8 1.0 OD1 B:ASN99 4.3 21.3 1.0 C5' B:GDP501 4.4 20.0 1.0 HD21 B:ASN99 4.4 22.1 1.0 O5' B:GDP501 4.4 20.3 1.0 O C:HOH808 4.5 39.6 1.0 O1A B:GDP501 4.5 16.5 1.0 O2B B:GDP501 4.5 19.6 1.0 HG2 B:GLN11 4.5 35.0 1.0 C8 B:GDP501 4.7 28.4 1.0 CG B:ASP177 4.8 29.2 1.0 PB B:GDP501 4.9 13.4 1.0 HB3 B:ASP177 5.0 31.9 1.0

Magnesium binding site 3 out of 4 in the The Crystal Structure of Tubulin Complexed with A Benzylidene Derivative of 9(10H)-Anthracenone


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 Complexed with A Benzylidene Derivative of 9(10H)-Anthracenone within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:19.3 occ:1.00 O C:HOH628 2.0 16.9 1.0 O3G C:GTP501 2.0 16.2 1.0 O C:HOH802 2.1 19.4 1.0 O C:HOH723 2.1 21.0 1.0 O C:HOH673 2.1 20.9 1.0 O2B C:GTP501 2.1 14.3 1.0 PB C:GTP501 3.3 9.3 1.0 HZ1 D:LYS252 3.3 35.8 1.0 HB2 C:GLN11 3.3 20.5 1.0 PG C:GTP501 3.3 16.8 1.0 H C:GLN11 3.6 20.5 1.0 O3B C:GTP501 3.7 19.8 1.0 O3A C:GTP501 3.7 18.1 1.0 OE1 C:GLU71 3.7 34.5 1.0 OD1 C:ASP69 4.0 17.9 1.0 O2G C:GTP501 4.0 20.7 1.0 HB2 C:ASP98 4.0 28.6 1.0 OD2 C:ASP69 4.0 20.3 1.0 HB3 C:GLN11 4.1 20.5 1.0 NZ D:LYS252 4.1 29.8 1.0 CB C:GLN11 4.1 17.1 1.0 HZ2 D:LYS252 4.2 35.8 1.0 HB3 C:GLU71 4.3 37.4 1.0 HB3 C:ASP98 4.3 28.6 1.0 N C:GLN11 4.4 17.1 1.0 HZ3 D:LYS252 4.4 35.8 1.0 CG C:ASP69 4.5 18.6 1.0 O1G C:GTP501 4.5 18.6 1.0 OE1 C:GLN11 4.5 26.6 1.0 O1B C:GTP501 4.6 16.2 1.0 CB C:ASP98 4.6 23.8 1.0 O2A C:GTP501 4.7 19.3 1.0 HG21 C:VAL74 4.7 31.9 1.0 OD2 C:ASP98 4.7 26.4 1.0 PA C:GTP501 4.7 14.6 1.0 HA2 C:GLY10 4.8 20.0 1.0 HG1 C:THR145 4.8 22.9 1.0 CA C:GLN11 4.8 19.0 1.0 CD C:GLU71 4.8 33.4 1.0 HB C:THR145 4.9 19.3 1.0 O C:HOH640 5.0 37.9 1.0

Magnesium binding site 4 out of 4 in the The Crystal Structure of Tubulin Complexed with A Benzylidene Derivative of 9(10H)-Anthracenone


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 Complexed with A Benzylidene Derivative of 9(10H)-Anthracenone within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:69.3 occ:1.00 O D:HOH616 2.1 69.1 1.0 O D:HOH618 2.1 64.6 1.0 O3G D:GTP501 2.4 78.3 1.0 O D:HOH624 2.6 60.3 1.0 O D:HOH657 2.7 72.4 1.0 O3A D:GTP501 2.8 60.2 1.0 O2A D:GTP501 2.9 60.6 1.0 OE1 D:GLN11 3.5 64.4 1.0 PA D:GTP501 3.5 48.3 1.0 O2B D:GTP501 3.7 65.2 1.0 OD1 D:ASN99 3.7 63.6 1.0 PG D:GTP501 3.8 0.4 1.0 PB D:GTP501 3.8 51.5 1.0 HB3 D:GLN11 3.9 72.1 1.0 HB2 D:GLN11 4.0 72.1 1.0 O3B D:GTP501 4.2 57.3 1.0 CB D:GLN11 4.4 60.1 1.0 O1G D:GTP501 4.5 80.1 1.0 O5' D:GTP501 4.5 49.7 1.0 CD D:GLN11 4.5 71.0 1.0 OE2 D:GLU69 4.6 95.0 1.0 O1A D:GTP501 4.6 59.2 1.0 HD21 D:ASN99 4.7 68.7 1.0 C5' D:GTP501 4.7 54.3 1.0 H D:GLN11 4.7 64.5 1.0 CG D:ASN99 4.8 54.9 1.0 O2G D:GTP501 4.8 97.2 1.0 H8 D:GTP501 4.9 60.9 1.0

J.Cheng, Y.Wu, Y.Wang, C.Wang, Y.Wang, C.Wu, S.Zeng, Y.Yu, Q.Chen. Structure of A Benzylidene Derivative of 9(10H)-Anthracenone in Complex with Tubulin Provides A Rationale For Drug Design. Biochem. Biophys. Res. V. 495 185 2018COMMUN..
ISSN: ESSN 1090-2104
PubMed: 29102632
DOI: 10.1016/J.BBRC.2017.10.104