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Magnesium in PDB 5m7g: Tubulin-MTD147 Complex

Protein crystallography data

The structure of Tubulin-MTD147 Complex, PDB code: 5m7g 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) 46.72 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.083, 156.864, 179.684, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 21.7

Other elements in 5m7g:

The structure of Tubulin-MTD147 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-MTD147 Complex (pdb code 5m7g). 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-MTD147 Complex, PDB code: 5m7g:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5m7g

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Magnesium binding site 1 out of 5 in the Tubulin-MTD147 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-MTD147 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:74.2
occ:1.00
O1G A:GTP501 2.0 44.3 1.0
O A:HOH627 2.0 50.9 1.0
O1B A:GTP501 2.1 44.0 1.0
O A:HOH660 2.2 63.3 1.0
O A:HOH618 2.2 47.3 1.0
O A:HOH606 2.4 39.6 1.0
PG A:GTP501 3.1 41.8 1.0
PB A:GTP501 3.3 35.7 1.0
O3G A:GTP501 3.6 39.5 1.0
O3B A:GTP501 3.6 49.8 1.0
O3A A:GTP501 3.8 48.2 1.0
NZ B:LYS254 3.9 47.0 1.0
OE1 A:GLU71 4.0 56.7 1.0
ND2 B:ASN249 4.0 85.3 1.0
CB A:GLN11 4.0 38.5 1.0
OD1 A:ASP69 4.1 52.4 1.0
OD2 A:ASP69 4.2 46.1 1.0
N A:GLN11 4.3 38.2 1.0
CG A:GLU71 4.4 58.5 1.0
OD2 A:ASP98 4.4 58.1 1.0
CB A:ASP98 4.4 49.4 1.0
O2G A:GTP501 4.4 38.7 1.0
O1A A:GTP501 4.5 45.2 1.0
O2B A:GTP501 4.6 44.4 1.0
OE1 A:GLN11 4.6 48.9 1.0
CG A:ASP69 4.6 52.7 1.0
CD A:GLU71 4.7 57.8 1.0
CG A:ASP98 4.7 56.8 1.0
PA A:GTP501 4.8 41.5 1.0
CA A:GLN11 4.8 41.2 1.0
CG B:ASN249 5.0 90.0 1.0
CE B:LYS254 5.0 45.1 1.0

Magnesium binding site 2 out of 5 in 5m7g

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Magnesium binding site 2 out of 5 in the Tubulin-MTD147 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-MTD147 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:34.1
occ:1.00
O B:HOH635 2.0 43.0 1.0
OE1 B:GLN11 2.2 54.1 1.0
O1A B:GDP502 2.3 37.9 1.0
O C:HOH607 2.4 51.6 1.0
O B:HOH669 2.5 51.6 1.0
O B:HOH605 2.7 50.1 1.0
CD B:GLN11 3.4 47.4 1.0
PA B:GDP502 3.6 37.3 1.0
O3A B:GDP502 3.8 43.5 1.0
OD2 B:ASP179 3.9 48.9 1.0
CB B:GLN11 3.9 40.6 1.0
CG B:GLN11 4.1 42.9 1.0
OD1 B:ASN101 4.2 41.4 1.0
C5' B:GDP502 4.3 36.2 1.0
O5' B:GDP502 4.4 36.5 1.0
NE2 B:GLN11 4.4 58.5 1.0
OE1 C:GLU254 4.5 62.3 1.0
O1B B:GDP502 4.6 29.1 1.0
O2A B:GDP502 4.7 44.1 1.0
C8 B:GDP502 4.8 48.4 1.0
PB B:GDP502 4.8 36.5 1.0
CG B:ASP179 4.8 49.4 1.0

Magnesium binding site 3 out of 5 in 5m7g

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Magnesium binding site 3 out of 5 in the Tubulin-MTD147 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-MTD147 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:40.3
occ:1.00
O1G C:GTP501 1.9 37.8 1.0
O C:HOH646 2.0 35.7 1.0
O1B C:GTP501 2.1 36.4 1.0
O C:HOH637 2.1 41.6 1.0
O C:HOH638 2.1 39.6 1.0
O C:HOH700 2.2 38.6 1.0
PG C:GTP501 3.1 39.0 1.0
PB C:GTP501 3.2 35.7 1.0
O3B C:GTP501 3.5 51.9 1.0
O2G C:GTP501 3.6 38.5 1.0
NZ D:LYS254 3.7 52.4 1.0
O3A C:GTP501 3.8 43.5 1.0
O C:HOH640 3.9 0.9 1.0
OD1 C:ASP69 4.1 41.0 1.0
OE1 C:GLU71 4.2 58.0 1.0
CB C:GLN11 4.2 31.1 1.0
OD2 C:ASP98 4.2 56.7 1.0
CG C:GLU71 4.3 50.7 1.0
OD2 C:ASP69 4.3 41.3 1.0
O3G C:GTP501 4.4 34.3 1.0
CB C:ASP98 4.4 49.8 1.0
N C:GLN11 4.4 32.8 1.0
O2B C:GTP501 4.4 39.1 1.0
O C:HOH760 4.5 76.5 1.0
O1A C:GTP501 4.6 39.8 1.0
CG C:ASP69 4.6 42.5 1.0
PA C:GTP501 4.8 40.0 1.0
CD C:GLU71 4.8 54.3 1.0
CG C:ASP98 4.8 52.5 1.0
OE1 C:GLN11 4.8 49.4 1.0
CA C:GLN11 4.9 28.4 1.0
CE D:LYS254 4.9 46.1 1.0
OG1 C:THR145 5.0 35.6 1.0

Magnesium binding site 4 out of 5 in 5m7g

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Magnesium binding site 4 out of 5 in the Tubulin-MTD147 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-MTD147 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:58.5
occ:1.00
OE1 D:GLN11 1.9 98.5 1.0
O D:HOH616 2.1 54.0 1.0
O D:HOH601 2.2 73.7 1.0
O1A D:GDP501 2.3 74.4 1.0
O D:HOH642 2.6 76.0 1.0
CD D:GLN11 3.1 80.7 1.0
PA D:GDP501 3.6 68.2 1.0
OD2 D:ASP179 3.6 0.6 1.0
CB D:GLN11 3.7 62.1 1.0
O3A D:GDP501 4.0 63.0 1.0
CG D:GLN11 4.0 78.4 1.0
NE2 D:GLN11 4.1 82.6 1.0
O1B D:GDP501 4.5 49.6 1.0
O2A D:GDP501 4.5 68.2 1.0
OD1 D:ASN101 4.7 84.9 1.0
O5' D:GDP501 4.7 65.9 1.0
C5' D:GDP501 4.7 60.6 1.0
C8 D:GDP501 4.8 54.4 1.0
CG D:ASP179 4.8 0.9 1.0
PB D:GDP501 4.9 54.7 1.0

Magnesium binding site 5 out of 5 in 5m7g

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Magnesium binding site 5 out of 5 in the Tubulin-MTD147 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-MTD147 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg402

b:82.2
occ:1.00
OE2 F:GLU331 2.1 0.7 1.0
O1B F:ACP403 2.3 0.3 1.0
O2G F:ACP403 2.4 0.6 1.0
CD F:GLU331 2.9 0.9 1.0
OE1 F:GLU331 3.1 0.6 1.0
NZ F:LYS74 3.3 95.6 1.0
ND2 F:ASN333 3.5 1.0 1.0
O F:HOH501 3.7 76.3 1.0
PB F:ACP403 3.7 0.3 1.0
PG F:ACP403 3.8 0.1 1.0
O2B F:ACP403 4.1 0.7 1.0
CG F:ASN333 4.3 0.6 1.0
CG F:GLU331 4.3 90.8 1.0
C3B F:ACP403 4.5 0.9 1.0
CE F:LYS74 4.5 89.8 1.0
OD1 F:ASN333 4.8 0.7 1.0
O3G F:ACP403 4.8 0.0 1.0
O1G F:ACP403 4.8 0.6 1.0
O3A F:ACP403 4.9 0.8 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: Mon Dec 14 20:50:43 2020

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