Magnesium in PDB 6k9v: Crystal Structure of Tubulin in Complex with Inhibitor D64

The structure of Crystal Structure of Tubulin in Complex with Inhibitor D64, PDB code: 6k9v 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)	47.73 / 2.54
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.219, 157.435, 180.045, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 24.8

The structure of Crystal Structure of Tubulin in Complex with Inhibitor D64 also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Tubulin in Complex with Inhibitor D64 (pdb code 6k9v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Tubulin in Complex with Inhibitor D64, PDB code: 6k9v:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of Tubulin in Complex with Inhibitor D64


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Tubulin in Complex with Inhibitor D64 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:26.5 occ:1.00 O A:HOH613 2.1 43.4 1.0 O2G A:GTP501 2.1 36.2 1.0 O1B A:GTP501 2.1 32.2 1.0 O A:HOH653 2.1 29.9 1.0 O A:HOH681 2.2 36.7 1.0 O A:HOH666 2.3 24.9 1.0 PB A:GTP501 3.1 18.7 1.0 HB2 A:GLN11 3.3 36.1 1.0 PG A:GTP501 3.3 19.0 1.0 O3A A:GTP501 3.5 31.9 1.0 O3B A:GTP501 3.6 41.2 1.0 H A:GLN11 3.7 31.4 1.0 O1G A:GTP501 3.9 25.3 1.0 HB2 A:ASP98 3.9 54.6 1.0 HB3 A:GLN11 4.0 36.1 1.0 CB A:GLN11 4.0 30.1 1.0 HB3 A:ASP98 4.1 54.6 1.0 OD1 A:ASP69 4.1 35.6 1.0 OD2 A:ASP69 4.1 31.0 1.0 HZ1 B:LYS252 4.3 64.9 1.0 HD22 B:ASN247 4.4 65.1 1.0 HB3 A:GLU71 4.4 54.1 1.0 N A:GLN11 4.4 26.1 1.0 CB A:ASP98 4.4 45.5 1.0 OE1 A:GLN11 4.4 29.0 1.0 O2B A:GTP501 4.5 31.1 1.0 O3G A:GTP501 4.5 30.8 1.0 CG A:ASP69 4.6 30.4 1.0 O1A A:GTP501 4.6 28.5 1.0 PA A:GTP501 4.6 23.6 1.0 HG1 A:THR145 4.6 33.1 1.0 HG21 A:VAL74 4.8 52.9 1.0 OD2 A:ASP98 4.8 39.0 1.0 HB A:THR145 4.8 32.8 1.0 ND2 B:ASN247 4.8 54.2 1.0 CA A:GLN11 4.8 27.6 1.0 HA2 A:GLY10 4.8 40.8 1.0 HD21 B:ASN247 4.9 65.1 1.0 CG A:ASP98 4.9 36.1 1.0 OG1 A:THR145 5.0 27.6 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of Tubulin in Complex with Inhibitor D64


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Tubulin in Complex with Inhibitor D64 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:56.6 occ:1.00 HG1 A:THR41 1.7 86.3 1.0 OD2 A:ASP39 2.0 62.3 1.0 OD1 A:ASP39 2.2 59.6 1.0 O A:GLY44 2.3 59.9 1.0 OE2 A:GLU55 2.3 55.5 1.0 CG A:ASP39 2.4 61.7 1.0 O A:THR41 2.4 70.5 1.0 OG1 A:THR41 2.5 72.0 1.0 OE1 A:GLU55 2.5 69.0 1.0 CD A:GLU55 2.8 57.0 1.0 C A:THR41 3.4 62.1 1.0 C A:GLY44 3.4 60.5 1.0 HZ A:PHE49 3.5 79.7 1.0 CB A:THR41 3.5 60.7 1.0 HB A:THR41 3.6 72.8 1.0 H A:GLY44 3.6 69.3 1.0 HA3 A:GLY45 3.6 76.9 1.0 HD21 A:ASN50 3.8 70.7 1.0 H A:THR41 3.8 79.9 1.0 CB A:ASP39 3.9 60.4 1.0 CA A:THR41 3.9 62.2 1.0 N A:THR41 4.2 66.6 1.0 HB2 A:ASP39 4.2 72.5 1.0 NE2 A:HIS61 4.2 65.1 1.0 N A:GLY44 4.3 57.8 1.0 CG A:GLU55 4.3 65.6 1.0 O A:HOH662 4.3 59.7 1.0 HB3 A:ASP39 4.3 72.5 1.0 CZ A:PHE49 4.3 66.4 1.0 CA A:GLY44 4.3 60.4 1.0 N A:GLY45 4.3 58.8 1.0 CA A:GLY45 4.4 64.1 1.0 HE1 A:PHE49 4.4 67.8 1.0 N A:ILE42 4.6 71.9 1.0 HA2 A:GLY44 4.6 72.5 1.0 HA A:ILE42 4.6 74.6 1.0 HG2 A:GLU55 4.6 78.8 1.0 ND2 A:ASN50 4.6 58.9 1.0 HG3 A:GLU55 4.6 78.8 1.0 HA A:ASP39 4.7 72.0 1.0 CA A:ASP39 4.8 60.0 1.0 OD1 A:ASN50 4.8 63.7 1.0 CE1 A:PHE49 4.8 56.5 1.0 HA A:THR41 4.8 74.7 1.0 CG2 A:THR41 4.8 61.0 1.0 C A:ASP39 4.8 60.5 1.0 H A:GLY43 4.8 72.2 1.0 HG21 A:THR41 5.0 73.2 1.0 CA A:ILE42 5.0 62.2 1.0 HE1 A:HIS61 5.0 86.0 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of Tubulin in Complex with Inhibitor D64


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Tubulin in Complex with Inhibitor D64 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:29.0 occ:1.00 O B:HOH635 2.0 33.0 1.0 OE1 B:GLN11 2.0 49.9 1.0 O2A B:GDP501 2.0 32.3 1.0 O C:HOH633 2.2 34.5 1.0 O B:HOH678 2.6 43.0 1.0 CD B:GLN11 3.2 42.5 1.0 PA B:GDP501 3.5 17.3 1.0 HB3 B:GLN11 3.5 47.9 1.0 OD2 B:ASP177 3.6 34.5 1.0 H8 B:GDP501 3.6 42.3 1.0 HB2 B:GLN11 4.0 47.9 1.0 CB B:GLN11 4.1 39.9 1.0 HE22 B:GLN11 4.1 54.9 1.0 O3A B:GDP501 4.1 35.0 1.0 NE2 B:GLN11 4.2 45.8 1.0 C5' B:GDP501 4.2 32.6 1.0 CG B:GLN11 4.2 39.2 1.0 OD1 B:ASN99 4.2 23.6 1.0 OE1 C:GLU254 4.2 62.0 1.0 O5' B:GDP501 4.3 26.0 1.0 O1A B:GDP501 4.5 29.4 1.0 HG2 B:GLN11 4.5 47.0 1.0 CG B:ASP177 4.5 35.7 1.0 HD21 B:ASN99 4.5 33.7 1.0 C8 B:GDP501 4.6 35.2 1.0 O2B B:GDP501 4.7 22.4 1.0 HB3 B:ASP177 4.8 45.1 1.0 HE21 B:GLN11 5.0 54.9 1.0 PB B:GDP501 5.0 17.5 1.0 HG3 B:GLN11 5.0 47.0 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of Tubulin in Complex with Inhibitor D64


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Tubulin in Complex with Inhibitor D64 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:22.9 occ:1.00 O C:HOH611 2.0 35.7 1.0 O C:HOH634 2.1 29.2 1.0 O C:HOH720 2.1 20.9 1.0 O1B C:GTP501 2.3 17.5 1.0 O1G C:GTP501 2.6 27.7 1.0 HB2 C:GLN11 2.8 32.5 1.0 OE1 C:GLU71 3.3 70.9 1.0 H C:GLN11 3.4 26.4 1.0 OD2 C:ASP69 3.6 28.6 1.0 PB C:GTP501 3.6 12.7 1.0 HB3 C:GLU71 3.7 44.9 1.0 OD1 C:ASP69 3.7 28.8 1.0 CB C:GLN11 3.7 27.1 1.0 HB3 C:GLN11 3.8 32.5 1.0 PG C:GTP501 3.9 25.5 1.0 O3A C:GTP501 4.0 34.6 1.0 N C:GLN11 4.0 22.0 1.0 HG21 C:VAL74 4.0 37.3 1.0 CG C:ASP69 4.0 21.0 1.0 CD C:GLU71 4.1 48.9 1.0 O3B C:GTP501 4.1 30.0 1.0 HZ1 D:LYS252 4.1 59.6 1.0 OE1 C:GLN11 4.2 39.2 1.0 HB2 C:ASP98 4.3 43.7 1.0 HD22 D:ASN247 4.3 88.2 1.0 HB3 C:ASP98 4.3 43.7 1.0 CA C:GLN11 4.4 21.3 1.0 O2G C:GTP501 4.4 19.3 1.0 HG23 C:VAL74 4.5 37.3 1.0 HA C:GLN11 4.5 25.6 1.0 CB C:GLU71 4.5 37.4 1.0 HA2 C:GLY10 4.5 33.9 1.0 CB C:ASP98 4.7 36.4 1.0 CG2 C:VAL74 4.7 31.1 1.0 CG C:GLU71 4.8 42.1 1.0 CG C:GLN11 4.8 28.4 1.0 O2B C:GTP501 4.8 23.3 1.0 OE2 C:GLU71 4.8 80.9 1.0 HG2 C:GLU71 4.8 50.5 1.0 HG1 C:THR145 4.8 28.6 1.0 O1A C:GTP501 4.8 21.8 1.0 CD C:GLN11 4.8 26.9 1.0 HB2 C:GLU71 4.8 44.9 1.0 OD2 C:ASP98 4.9 30.3 1.0 PA C:GTP501 4.9 14.9 1.0 NZ D:LYS252 4.9 49.6 1.0 HG3 C:GLN11 5.0 34.1 1.0 C C:GLY10 5.0 20.1 1.0 ND2 D:ASN247 5.0 73.5 1.0 HZ2 D:LYS252 5.0 59.6 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of Tubulin in Complex with Inhibitor D64


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Tubulin in Complex with Inhibitor D64 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:76.9 occ:1.00 O3G D:GTP501 2.6 94.4 1.0 HB2 D:GLN11 2.7 87.3 1.0 OE1 D:GLN11 2.9 69.1 1.0 O1B D:GTP501 3.0 95.0 1.0 HB3 D:GLN11 3.1 87.3 1.0 O D:HOH610 3.1 63.1 1.0 O3A D:GTP501 3.2 87.4 1.0 CB D:GLN11 3.3 72.8 1.0 PB D:GTP501 3.6 68.9 1.0 O1A D:GTP501 3.7 77.8 1.0 H D:GLN11 3.7 73.8 1.0 PG D:GTP501 3.8 0.6 1.0 CD D:GLN11 3.9 70.4 1.0 PA D:GTP501 4.0 58.9 1.0 OE1 D:GLU69 4.0 0.6 1.0 CG D:GLN11 4.1 72.2 1.0 O1G D:GTP501 4.1 94.4 1.0 O3B D:GTP501 4.3 82.4 1.0 N D:GLN11 4.4 61.5 1.0 HG3 D:GLN11 4.4 86.7 1.0 CA D:GLN11 4.5 74.8 1.0 CD D:GLU69 4.6 0.9 1.0 O2A D:GTP501 4.7 61.8 1.0 OE2 D:GLU69 4.7 0.7 1.0 HA D:GLN11 4.9 89.8 1.0 HG2 D:GLN11 4.9 86.7 1.0 O2B D:GTP501 5.0 67.7 1.0

Y.Li, J.Yang, L.Niu, D.Hu, H.Li, L.Chen, Y.Yu, Q.Chen. Structural Insights Into the Design of Indole Derivatives As Tubulin Polymerization Inhibitors. Febs Lett. 2019.
ISSN: ISSN 0014-5793
PubMed: 31369682
DOI: 10.1002/1873-3468.13566