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Calcium 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
Magnesium (Mg) 5 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Tubulin MTD265-R1 Complex (pdb code 5m8d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Tubulin MTD265-R1 Complex, PDB code: 5m8d:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 5m8d

Go back to Calcium Binding Sites List in 5m8d
Calcium binding site 1 out of 5 in the Tubulin MTD265-R1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin MTD265-R1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:71.2
occ:1.00
O A:GLY44 2.3 92.1 1.0
OD1 A:ASP39 2.4 73.8 1.0
O A:THR41 2.5 90.7 1.0
OD2 A:ASP39 2.5 75.4 1.0
OE1 A:GLU55 2.6 71.4 1.0
OE2 A:GLU55 2.6 64.9 1.0
O A:HOH607 2.6 64.2 1.0
OG1 A:THR41 2.7 74.0 1.0
CG A:ASP39 2.8 75.5 1.0
CD A:GLU55 2.9 75.9 1.0
C A:GLY44 3.3 90.2 1.0
CB A:THR41 3.4 79.7 1.0
C A:THR41 3.5 92.6 1.0
CA A:THR41 3.9 89.1 1.0
CA A:GLY45 4.0 92.7 1.0
N A:GLY45 4.0 90.9 1.0
N A:GLY44 4.2 84.5 1.0
N A:THR41 4.3 88.3 1.0
CB A:ASP39 4.3 76.5 1.0
CA A:GLY44 4.3 86.8 1.0
CG A:GLU55 4.4 73.1 1.0
CZ A:PHE49 4.5 65.0 1.0
OD1 A:ASN50 4.5 73.4 1.0
OD2 A:ASP47 4.6 75.0 1.0
N A:ILE42 4.7 97.3 1.0
CG2 A:THR41 4.8 80.2 1.0
NE2 A:HIS61 4.8 84.7 1.0
ND2 A:ASN50 4.9 69.0 1.0

Calcium binding site 2 out of 5 in 5m8d

Go back to Calcium Binding Sites List in 5m8d
Calcium binding site 2 out of 5 in the Tubulin MTD265-R1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin MTD265-R1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:1.0
occ:1.00
O A:HOH704 2.8 90.6 1.0
O A:HOH690 2.9 67.1 1.0
O A:HOH669 3.3 57.1 1.0
OD2 E:ASP44 3.5 0.3 1.0
OG A:SER158 3.9 61.4 1.0
NZ A:LYS166 4.2 47.3 1.0
O A:GLU196 4.3 69.6 1.0
CB A:SER158 4.4 53.0 1.0
O A:GLY162 4.5 74.3 1.0
O A:HOH636 4.7 55.2 1.0
CG E:ASP44 4.7 0.0 1.0
CA A:HIS197 4.8 50.3 1.0
O A:HIS197 4.8 50.7 1.0
OD1 A:ASP199 4.9 57.6 1.0

Calcium binding site 3 out of 5 in 5m8d

Go back to Calcium Binding Sites List in 5m8d
Calcium binding site 3 out of 5 in the Tubulin MTD265-R1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin MTD265-R1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:0.9
occ:1.00
O B:HOH637 2.4 80.7 1.0
O B:HOH679 3.4 69.5 1.0
OD1 B:ASP120 3.8 66.0 1.0
OD2 B:ASP120 4.1 65.2 1.0
CG B:ASP120 4.4 65.1 1.0
CB B:ASP116 4.4 47.0 1.0
OD2 B:ASP116 4.5 79.4 1.0
CG B:ASP116 4.6 62.0 1.0
O B:ASP116 4.9 55.0 1.0

Calcium binding site 4 out of 5 in 5m8d

Go back to Calcium Binding Sites List in 5m8d
Calcium binding site 4 out of 5 in the Tubulin MTD265-R1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin MTD265-R1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca505

b:92.4
occ:1.00
OE1 B:GLU113 2.6 89.7 1.0
CD B:GLU113 3.6 80.9 1.0
OE2 B:GLU113 3.8 88.9 1.0
OE1 B:GLU110 4.5 51.3 1.0
CG B:GLU113 4.9 59.5 1.0

Calcium binding site 5 out of 5 in 5m8d

Go back to Calcium Binding Sites List in 5m8d
Calcium binding site 5 out of 5 in the Tubulin MTD265-R1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Tubulin MTD265-R1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:63.6
occ:1.00
O C:HOH601 2.4 56.3 1.0
O C:THR41 2.4 70.7 1.0
O C:GLY44 2.4 61.8 1.0
OE1 C:GLU55 2.5 48.1 1.0
OD1 C:ASP39 2.5 50.3 1.0
OE2 C:GLU55 2.5 54.7 1.0
OD2 C:ASP39 2.5 59.4 1.0
OG1 C:THR41 2.6 52.3 1.0
CD C:GLU55 2.8 56.2 1.0
CG C:ASP39 2.9 57.4 1.0
C C:THR41 3.4 74.5 1.0
CB C:THR41 3.5 63.8 1.0
C C:GLY44 3.6 71.2 1.0
CA C:THR41 3.9 70.7 1.0
N C:THR41 4.2 70.7 1.0
OD2 C:ASP47 4.2 58.6 1.0
O C:HOH604 4.2 54.7 1.0
CG C:GLU55 4.3 57.1 1.0
CA C:GLY45 4.4 76.9 1.0
CB C:ASP39 4.4 60.2 1.0
N C:GLY45 4.4 76.1 1.0
CZ C:PHE49 4.5 52.9 1.0
N C:GLY44 4.5 75.5 1.0
N C:ILE42 4.5 76.7 1.0
CA C:GLY44 4.6 75.0 1.0
OD1 C:ASN50 4.7 46.0 1.0
NE2 C:HIS61 4.7 45.4 1.0
CE1 C:PHE49 4.9 51.5 1.0
ND2 C:ASN50 4.9 42.1 1.0
CG2 C:THR41 4.9 53.1 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: Wed Jul 9 08:06:40 2025

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