Magnesium in PDB 6nng: Tubulin-RB3_SLD-Ttl in Complex with Compound DJ95

Protein crystallography data

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound DJ95, PDB code: 6nng was solved by G.Kumar, Y.Wang, W.Li, S.W.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.25 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.418, 157.979, 182.840, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 22.7

Other elements in 6nng:

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound DJ95 also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Tubulin-RB3_SLD-Ttl in Complex with Compound DJ95 (pdb code 6nng). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Tubulin-RB3_SLD-Ttl in Complex with Compound DJ95, PDB code: 6nng:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6nng

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Magnesium binding site 1 out of 4 in the Tubulin-RB3_SLD-Ttl in Complex with Compound DJ95


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-RB3_SLD-Ttl in Complex with Compound DJ95 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:26.8
occ:1.00
O2G A:GTP501 2.1 26.1 1.0
O A:HOH633 2.1 27.8 1.0
O A:HOH668 2.1 30.5 1.0
O A:HOH605 2.2 31.7 1.0
O A:HOH701 2.2 26.0 1.0
O1B A:GTP501 2.4 27.2 1.0
PG A:GTP501 3.3 29.8 1.0
PB A:GTP501 3.5 31.0 1.0
O3G A:GTP501 3.7 33.5 1.0
OE2 A:GLU71 3.8 58.1 1.0
O3B A:GTP501 3.8 42.0 1.0
NZ B:LYS252 3.9 43.0 1.0
O3A A:GTP501 3.9 32.9 1.0
OD2 A:ASP98 4.1 37.6 1.0
OD1 A:ASP69 4.1 40.4 1.0
CB A:GLN11 4.2 30.4 1.0
OD2 A:ASP69 4.2 39.6 1.0
CB A:ASP98 4.4 32.6 1.0
O2A A:GTP501 4.5 34.5 1.0
O1G A:GTP501 4.5 25.7 1.0
N A:GLN11 4.6 29.2 1.0
OE1 A:GLN11 4.6 38.2 1.0
CG A:ASP98 4.6 33.8 1.0
CG A:ASP69 4.6 39.7 1.0
O2B A:GTP501 4.8 40.9 1.0
CD A:GLU71 4.8 56.3 1.0
PA A:GTP501 4.9 30.6 1.0
CA A:GLN11 5.0 33.9 1.0

Magnesium binding site 2 out of 4 in 6nng

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Magnesium binding site 2 out of 4 in the Tubulin-RB3_SLD-Ttl in Complex with Compound DJ95


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-RB3_SLD-Ttl in Complex with Compound DJ95 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:33.8
occ:1.00
O2A B:GDP501 2.2 30.4 1.0
O B:HOH650 2.2 49.4 1.0
O B:HOH627 2.3 41.0 1.0
NE2 B:GLN11 2.5 56.5 1.0
O C:HOH708 2.6 34.9 1.0
O B:HOH649 2.6 37.4 1.0
O B:HOH624 2.6 32.1 1.0
CD B:GLN11 3.5 54.0 1.0
PA B:GDP501 3.6 24.6 1.0
OD2 B:ASP177 3.8 45.8 1.0
O3A B:GDP501 4.1 22.2 1.0
CB B:GLN11 4.2 31.0 1.0
OE1 B:GLN11 4.2 56.1 1.0
CG B:GLN11 4.3 41.3 1.0
C5' B:GDP501 4.3 21.1 1.0
OD1 B:ASN99 4.4 36.9 1.0
O5' B:GDP501 4.5 22.2 1.0
O1A B:GDP501 4.6 24.4 1.0
O3B B:GDP501 4.7 23.3 1.0
CG B:ASP177 4.9 49.8 1.0
OE1 C:GLU254 4.9 46.9 1.0
C8 B:GDP501 4.9 32.3 1.0
PB B:GDP501 5.0 25.3 1.0

Magnesium binding site 3 out of 4 in 6nng

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Magnesium binding site 3 out of 4 in the Tubulin-RB3_SLD-Ttl in Complex with Compound DJ95


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-RB3_SLD-Ttl in Complex with Compound DJ95 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:26.9
occ:1.00
O C:HOH646 2.1 29.4 1.0
O2B C:GTP501 2.1 26.1 1.0
O C:HOH676 2.1 26.9 1.0
O C:HOH748 2.1 26.9 1.0
O C:HOH614 2.2 27.3 1.0
O3G C:GTP501 2.2 26.8 1.0
PB C:GTP501 3.2 25.7 1.0
PG C:GTP501 3.3 27.9 1.0
O3B C:GTP501 3.6 28.7 1.0
O2G C:GTP501 3.7 31.5 1.0
OE1 C:GLU71 3.8 47.9 1.0
O3A C:GTP501 3.8 30.4 1.0
NZ D:LYS252 4.0 27.6 1.0
OD1 C:ASP69 4.0 26.8 1.0
OD2 C:ASP69 4.1 27.1 1.0
CB C:GLN11 4.2 26.5 1.0
N C:GLN11 4.4 25.8 1.0
OD2 C:ASP98 4.5 40.3 1.0
CG C:ASP69 4.5 30.4 1.0
CB C:ASP98 4.5 30.4 1.0
O C:HOH675 4.5 48.0 1.0
O1B C:GTP501 4.5 25.9 1.0
O1G C:GTP501 4.6 26.6 1.0
O2A C:GTP501 4.6 28.2 1.0
OE1 C:GLN11 4.7 37.8 1.0
PA C:GTP501 4.8 25.6 1.0
CG C:ASP98 4.8 35.3 1.0
CA C:GLN11 4.9 31.5 1.0
CD C:GLU71 4.9 47.7 1.0

Magnesium binding site 4 out of 4 in 6nng

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Magnesium binding site 4 out of 4 in the Tubulin-RB3_SLD-Ttl in Complex with Compound DJ95


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-RB3_SLD-Ttl in Complex with Compound DJ95 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg401

b:68.5
occ:1.00
O1B F:ACP402 2.3 0.8 1.0
OE1 F:GLU331 2.5 84.2 1.0
O2G F:ACP402 3.3 0.9 1.0
CD F:GLU331 3.3 78.8 1.0
OE2 F:GLU331 3.3 83.1 1.0
PB F:ACP402 3.6 0.2 1.0
NZ F:LYS74 3.7 73.8 1.0
ND2 F:ASN333 3.9 77.1 1.0
O1G F:ACP402 3.9 0.3 1.0
PG F:ACP402 4.0 0.1 1.0
O2B F:ACP402 4.2 0.6 1.0
C3B F:ACP402 4.2 0.5 1.0
CG F:GLU331 4.7 69.2 1.0
O3A F:ACP402 4.9 0.1 1.0
CG F:ASN333 4.9 70.9 1.0
O1A F:ACP402 5.0 0.9 1.0

Reference:

K.E.Arnst, Y.Wang, Z.N.Lei, D.J.Hwang, G.Kumar, D.Ma, D.N.Parke, Q.Chen, J.Yang, S.W.White, T.N.Seagroves, Z.S.Chen, D.D.Miller, W.Li. Colchicine Binding Site Agent DJ95 Overcomes Drug Resistance and Exhibits Antitumor Efficacy. Mol.Pharmacol. V. 96 73 2019.
ISSN: ESSN 1521-0111
PubMed: 31043459
DOI: 10.1124/MOL.118.114801
Page generated: Mon Dec 14 23:40:59 2020

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