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Magnesium in PDB 5m8d: Tubulin MTD265-R1 Complex

Protein crystallography data

The structure of Tubulin MTD265-R1 Complex, PDB code: 5m8d 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) 68.10 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.180, 157.020, 179.980, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 21

Other elements in 5m8d:

The structure of Tubulin MTD265-R1 Complex also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Calcium (Ca) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Tubulin MTD265-R1 Complex (pdb code 5m8d). 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-R1 Complex, PDB code: 5m8d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5m8d

Go back to Magnesium Binding Sites List in 5m8d
Magnesium binding site 1 out of 5 in the Tubulin MTD265-R1 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-R1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:37.6
occ:1.00
O A:HOH613 2.0 32.8 1.0
O A:HOH631 2.1 41.5 1.0
O2G A:GTP501 2.1 31.4 1.0
O A:HOH697 2.2 36.0 1.0
O1B A:GTP501 2.2 29.4 1.0
O A:HOH619 2.2 40.4 1.0
PG A:GTP501 3.3 41.6 1.0
PB A:GTP501 3.4 38.1 1.0
O3B A:GTP501 3.6 55.9 1.0
O1G A:GTP501 3.7 43.3 1.0
OE1 A:GLU71 3.8 60.0 1.0
NZ B:LYS254 3.9 50.7 1.0
O3A A:GTP501 3.9 41.0 1.0
OD1 A:ASP69 3.9 49.6 1.0
CB A:GLN11 4.0 37.0 1.0
OD2 A:ASP69 4.0 46.0 1.0
N A:GLN11 4.2 37.5 1.0
OD2 A:ASP98 4.3 48.7 1.0
CG A:GLU71 4.3 57.3 1.0
CG A:ASP69 4.4 47.0 1.0
CB A:ASP98 4.5 41.7 1.0
CD A:GLU71 4.5 60.8 1.0
O3G A:GTP501 4.6 35.3 1.0
ND2 B:ASN249 4.6 0.6 1.0
O1A A:GTP501 4.6 38.5 1.0
O2B A:GTP501 4.6 43.8 1.0
OE1 A:GLN11 4.7 48.8 1.0
CA A:GLN11 4.7 36.7 1.0
CG A:ASP98 4.8 48.4 1.0
PA A:GTP501 4.8 43.4 1.0

Magnesium binding site 2 out of 5 in 5m8d

Go back to Magnesium Binding Sites List in 5m8d
Magnesium binding site 2 out of 5 in the Tubulin MTD265-R1 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-R1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:33.0
occ:1.00
O B:HOH625 2.0 47.0 1.0
OE1 B:GLN11 2.2 45.3 1.0
O C:HOH632 2.3 54.9 1.0
O1A B:GDP502 2.3 42.0 1.0
O B:HOH665 2.4 39.1 1.0
O B:HOH605 2.6 45.1 1.0
O B:HOH693 3.3 66.2 1.0
CD B:GLN11 3.4 47.4 1.0
PA B:GDP502 3.6 33.6 1.0
O3A B:GDP502 3.9 40.5 1.0
OD2 B:ASP179 3.9 57.5 1.0
CB B:GLN11 4.0 37.7 1.0
CG B:GLN11 4.1 40.1 1.0
ND2 B:ASN101 4.4 41.7 1.0
C5' B:GDP502 4.4 37.6 1.0
NE2 B:GLN11 4.4 50.9 1.0
O5' B:GDP502 4.4 36.3 1.0
OE1 C:GLU254 4.5 55.0 1.0
O C:HOH678 4.6 57.4 1.0
O1B B:GDP502 4.6 27.0 1.0
O2A B:GDP502 4.7 41.3 1.0
CG B:ASP179 4.9 55.0 1.0
C8 B:GDP502 4.9 44.0 1.0
PB B:GDP502 4.9 35.1 1.0
OD1 B:ASN101 5.0 51.1 1.0

Magnesium binding site 3 out of 5 in 5m8d

Go back to Magnesium Binding Sites List in 5m8d
Magnesium binding site 3 out of 5 in the Tubulin MTD265-R1 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-R1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:36.7
occ:1.00
O1G C:GTP501 2.0 31.5 1.0
O C:HOH643 2.0 37.7 1.0
O1B C:GTP501 2.1 28.8 1.0
O C:HOH713 2.1 32.0 1.0
O C:HOH610 2.1 34.4 1.0
O C:HOH646 2.2 34.2 1.0
PG C:GTP501 3.1 35.9 1.0
PB C:GTP501 3.1 30.6 1.0
O3B C:GTP501 3.5 46.3 1.0
O2G C:GTP501 3.5 34.2 1.0
O3A C:GTP501 3.7 38.9 1.0
NZ D:LYS254 3.8 38.6 1.0
OD1 C:ASP69 4.0 39.3 1.0
CB C:GLN11 4.2 27.7 1.0
OE1 C:GLU71 4.2 51.2 1.0
OD2 C:ASP98 4.2 50.8 1.0
OD2 C:ASP69 4.3 35.0 1.0
N C:GLN11 4.3 31.5 1.0
CG C:GLU71 4.3 41.5 1.0
O3G C:GTP501 4.4 29.9 1.0
O2B C:GTP501 4.4 37.7 1.0
O1A C:GTP501 4.5 36.4 1.0
CB C:ASP98 4.5 38.7 1.0
CG C:ASP69 4.6 39.0 1.0
NE2 C:GLN11 4.7 39.8 1.0
PA C:GTP501 4.7 32.6 1.0
CG C:ASP98 4.8 43.5 1.0
CD C:GLU71 4.8 45.9 1.0
CA C:GLN11 4.8 31.4 1.0
CE D:LYS254 5.0 41.3 1.0

Magnesium binding site 4 out of 5 in 5m8d

Go back to Magnesium Binding Sites List in 5m8d
Magnesium binding site 4 out of 5 in the Tubulin MTD265-R1 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-R1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:55.3
occ:1.00
O D:HOH635 2.0 47.5 1.0
OE1 D:GLN11 2.1 70.8 1.0
O D:HOH634 2.4 66.8 1.0
O1A D:GDP501 2.5 65.3 1.0
CD D:GLN11 3.3 69.6 1.0
O D:HOH665 3.4 74.4 1.0
PA D:GDP501 3.8 63.2 1.0
CG D:GLN11 4.0 67.8 1.0
CB D:GLN11 4.1 66.1 1.0
O3A D:GDP501 4.1 55.4 1.0
NE2 D:GLN11 4.3 74.9 1.0
C5' D:GDP501 4.4 56.7 1.0
O5' D:GDP501 4.6 58.7 1.0
C8 D:GDP501 4.6 55.9 1.0
ND2 D:ASN101 4.7 63.1 1.0
O1B D:GDP501 4.8 46.0 1.0
O2A D:GDP501 4.8 65.2 1.0

Magnesium binding site 5 out of 5 in 5m8d

Go back to Magnesium Binding Sites List in 5m8d
Magnesium binding site 5 out of 5 in the Tubulin MTD265-R1 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-R1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg401

b:78.3
occ:1.00
O1B F:ACP402 2.1 0.6 1.0
OE2 F:GLU331 2.1 82.8 1.0
O1G F:ACP402 2.6 0.1 1.0
OD1 F:ASN333 2.8 94.9 1.0
CD F:GLU331 2.9 84.0 1.0
OE1 F:GLU331 3.0 92.7 1.0
PB F:ACP402 3.5 0.7 1.0
NZ F:LYS74 3.6 96.6 1.0
CG F:ASN333 3.6 84.1 1.0
PG F:ACP402 3.6 0.8 1.0
ND2 F:ASN333 3.6 85.6 1.0
O3G F:ACP402 3.9 0.9 1.0
C3B F:ACP402 4.1 0.8 1.0
O2B F:ACP402 4.2 0.6 1.0
CG F:GLU331 4.4 74.0 1.0
CE F:LYS74 4.6 86.2 1.0
O3A F:ACP402 4.7 0.2 1.0
O1A F:ACP402 4.9 0.4 1.0
CB F:ASN333 5.0 66.8 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 20:50:57 2020

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