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Magnesium in PDB 5m8g: Tubulin-MTD265 Complex

Protein crystallography data

The structure of Tubulin-MTD265 Complex, PDB code: 5m8g was solved by T.Bohnacker, A.E.Prota, M.O.Steinmetz, M.P.Wymann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.29 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.768, 157.508, 179.235, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 20.8

Other elements in 5m8g:

The structure of Tubulin-MTD265 Complex also contains other interesting chemical elements:

Fluorine (F) 6 atoms
Calcium (Ca) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Tubulin-MTD265 Complex (pdb code 5m8g). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Tubulin-MTD265 Complex, PDB code: 5m8g:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5m8g

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Magnesium binding site 1 out of 5 in the Tubulin-MTD265 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-MTD265 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:38.0
occ:1.00
O1G A:GTP501 2.0 33.7 1.0
O A:HOH663 2.1 37.1 1.0
O A:HOH609 2.1 36.3 1.0
O A:HOH630 2.1 44.7 1.0
O A:HOH614 2.2 34.8 1.0
O1B A:GTP501 2.3 32.2 1.0
PG A:GTP501 3.1 42.4 1.0
PB A:GTP501 3.3 35.3 1.0
O3B A:GTP501 3.6 54.5 1.0
O2G A:GTP501 3.7 46.2 1.0
NZ B:LYS254 3.7 44.4 1.0
O3A A:GTP501 3.8 40.9 1.0
OE1 A:GLU71 4.0 65.8 1.0
CB A:GLN11 4.2 36.5 1.0
OD2 A:ASP98 4.2 59.7 1.0
OD1 A:ASP69 4.2 50.2 1.0
OD2 A:ASP69 4.3 46.2 1.0
O3G A:GTP501 4.4 34.8 1.0
CG A:GLU71 4.4 57.4 1.0
N A:GLN11 4.4 40.4 1.0
CB A:ASP98 4.4 45.8 1.0
O1A A:GTP501 4.6 39.3 1.0
OE1 A:GLN11 4.6 44.2 1.0
O2B A:GTP501 4.6 42.4 1.0
CG A:ASP69 4.7 53.3 1.0
CD A:GLU71 4.7 58.2 1.0
CG A:ASP98 4.7 55.3 1.0
ND2 B:ASN249 4.8 66.2 1.0
OD1 B:ASN249 4.8 80.3 1.0
CE B:LYS254 4.8 42.5 1.0
PA A:GTP501 4.8 39.0 1.0
CG B:ASN249 4.9 74.0 1.0
CA A:GLN11 4.9 40.8 1.0
OG1 A:THR145 5.0 42.6 1.0

Magnesium binding site 2 out of 5 in 5m8g

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Magnesium binding site 2 out of 5 in the Tubulin-MTD265 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-MTD265 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:30.1
occ:1.00
O B:HOH641 2.1 52.2 1.0
OE1 B:GLN11 2.3 46.4 1.0
O C:HOH657 2.3 48.6 1.0
O1A B:GDP502 2.3 36.9 1.0
O B:HOH671 2.5 42.6 1.0
O B:HOH607 2.6 48.6 1.0
CD B:GLN11 3.5 47.4 1.0
PA B:GDP502 3.6 34.7 1.0
OD2 B:ASP179 3.8 55.1 1.0
O3A B:GDP502 3.8 37.1 1.0
CB B:GLN11 4.1 39.6 1.0
CG B:GLN11 4.1 41.5 1.0
OD1 B:ASN101 4.3 41.6 1.0
C5' B:GDP502 4.3 36.6 1.0
O5' B:GDP502 4.4 37.1 1.0
OE1 C:GLU254 4.4 52.9 1.0
O C:HOH642 4.4 57.4 1.0
NE2 B:GLN11 4.5 55.0 1.0
O1B B:GDP502 4.6 31.2 1.0
O2A B:GDP502 4.7 33.9 1.0
C8 B:GDP502 4.7 43.1 1.0
CG B:ASP179 4.8 55.7 1.0
PB B:GDP502 4.9 37.1 1.0

Magnesium binding site 3 out of 5 in 5m8g

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Magnesium binding site 3 out of 5 in the Tubulin-MTD265 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-MTD265 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:39.1
occ:1.00
O1G C:GTP501 1.9 34.6 1.0
O C:HOH621 2.0 38.7 1.0
O C:HOH627 2.1 33.4 1.0
O C:HOH647 2.1 38.0 1.0
O C:HOH672 2.2 32.0 1.0
O1B C:GTP501 2.3 30.6 1.0
PG C:GTP501 3.1 39.9 1.0
PB C:GTP501 3.3 33.7 1.0
O2G C:GTP501 3.5 41.5 1.0
O3B C:GTP501 3.5 44.1 1.0
NZ D:LYS254 3.8 39.3 1.0
O3A C:GTP501 3.8 40.5 1.0
OD2 C:ASP98 4.0 54.0 1.0
OE1 C:GLU71 4.1 54.8 1.0
OD1 C:ASP69 4.1 38.7 1.0
CG C:GLU71 4.3 45.2 1.0
CB C:GLN11 4.3 29.6 1.0
OD2 C:ASP69 4.3 38.9 1.0
O3G C:GTP501 4.4 31.9 1.0
CB C:ASP98 4.4 42.1 1.0
N C:GLN11 4.5 34.0 1.0
O2B C:GTP501 4.6 39.1 1.0
CG C:ASP98 4.6 48.7 1.0
CG C:ASP69 4.6 41.9 1.0
CD C:GLU71 4.7 55.2 1.0
O1A C:GTP501 4.7 37.1 1.0
OE1 C:GLN11 4.8 41.4 1.0
ND2 D:ASN249 4.8 67.4 1.0
CG D:ASN249 4.8 72.2 1.0
CE D:LYS254 4.9 43.3 1.0
PA C:GTP501 4.9 35.3 1.0
OG1 C:THR145 4.9 33.9 1.0
CA C:GLN11 5.0 31.9 1.0

Magnesium binding site 4 out of 5 in 5m8g

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Magnesium binding site 4 out of 5 in the Tubulin-MTD265 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-MTD265 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:61.1
occ:1.00
O D:HOH626 2.0 57.5 1.0
OE1 D:GLN11 2.1 71.9 1.0
O1A D:GDP502 2.4 72.7 1.0
O D:HOH638 2.7 63.9 1.0
CD D:GLN11 3.3 72.9 1.0
PA D:GDP502 3.8 62.4 1.0
CB D:GLN11 4.1 67.0 1.0
CG D:GLN11 4.1 69.4 1.0
O3A D:GDP502 4.2 59.7 1.0
NE2 D:GLN11 4.2 72.5 1.0
C5' D:GDP502 4.5 59.5 1.0
O5' D:GDP502 4.6 66.0 1.0
ND2 D:ASN101 4.7 65.4 1.0
O2A D:GDP502 4.7 62.5 1.0
O1B D:GDP502 4.8 47.2 1.0
C8 D:GDP502 4.9 51.4 1.0

Magnesium binding site 5 out of 5 in 5m8g

Go back to Magnesium Binding Sites List in 5m8g
Magnesium binding site 5 out of 5 in the Tubulin-MTD265 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-MTD265 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg401

b:71.1
occ:1.00
O1B F:ACP402 2.1 0.1 1.0
OE2 F:GLU331 2.1 0.1 1.0
O1G F:ACP402 2.3 0.6 1.0
OD1 F:ASN333 2.8 0.9 1.0
CD F:GLU331 2.9 96.6 1.0
OE1 F:GLU331 3.0 97.8 1.0
PG F:ACP402 3.5 0.8 1.0
PB F:ACP402 3.5 0.5 1.0
CG F:ASN333 3.6 0.6 1.0
ND2 F:ASN333 3.7 0.9 1.0
NZ F:LYS74 3.9 93.6 1.0
O3G F:ACP402 4.0 0.8 1.0
O2B F:ACP402 4.1 0.9 1.0
C3B F:ACP402 4.2 1.0 1.0
CG F:GLU331 4.4 87.5 1.0
O3A F:ACP402 4.7 0.5 1.0
O1A F:ACP402 4.8 96.5 1.0
O2G F:ACP402 4.8 0.6 1.0
CE F:LYS74 4.9 91.5 1.0
CB F:ASN333 5.0 85.3 1.0

Reference:

T.Bohnacker, A.E.Prota, F.Beaufils, J.E.Burke, A.Melone, A.J.Inglis, D.Rageot, A.M.Sele, V.Cmiljanovic, N.Cmiljanovic, K.Bargsten, A.Aher, A.Akhmanova, J.F.Diaz, D.Fabbro, M.Zvelebil, R.L.Williams, M.O.Steinmetz, M.P.Wymann. Deconvolution of Buparlisib'S Mechanism of Action Defines Specific PI3K and Tubulin Inhibitors For Therapeutic Intervention. Nat Commun V. 8 14683 2017.
ISSN: ESSN 2041-1723
PubMed: 28276440
DOI: 10.1038/NCOMMS14683
Page generated: Sun Sep 29 21:17:38 2024

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