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Calcium 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
Magnesium (Mg) 5 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Tubulin-MTD147 Complex (pdb code 5m7g). 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-MTD147 Complex, PDB code: 5m7g:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 5m7g

Go back to Calcium Binding Sites List in 5m7g
Calcium binding site 1 out of 5 in the Tubulin-MTD147 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-MTD147 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:81.3
occ:1.00
O A:GLY44 2.4 0.7 1.0
O A:HOH622 2.4 68.2 1.0
OD2 A:ASP39 2.4 78.2 1.0
OE1 A:GLU55 2.5 85.2 1.0
OD1 A:ASP39 2.5 83.2 1.0
O A:THR41 2.6 90.1 1.0
OG1 A:THR41 2.7 77.4 1.0
OE2 A:GLU55 2.8 73.8 1.0
CG A:ASP39 2.8 80.2 1.0
CD A:GLU55 2.9 81.4 1.0
C A:GLY44 3.3 95.3 1.0
CB A:THR41 3.6 84.0 1.0
C A:THR41 3.6 94.0 1.0
CA A:THR41 4.0 90.7 1.0
N A:GLY45 4.1 87.9 1.0
CA A:GLY45 4.1 87.0 1.0
N A:GLY44 4.3 93.0 1.0
CA A:GLY44 4.3 93.8 1.0
CB A:ASP39 4.3 71.7 1.0
N A:THR41 4.4 89.7 1.0
CG A:GLU55 4.4 82.3 1.0
OD1 A:ASN50 4.4 76.8 1.0
CZ A:PHE49 4.5 67.9 1.0
O A:HOH675 4.6 80.7 1.0
N A:ILE42 4.7 94.9 1.0
OD2 A:ASP47 4.8 79.2 1.0
NE2 A:HIS61 4.9 83.7 1.0
CG2 A:THR41 4.9 83.8 1.0
ND2 A:ASN50 4.9 76.7 1.0

Calcium binding site 2 out of 5 in 5m7g

Go back to Calcium Binding Sites List in 5m7g
Calcium binding site 2 out of 5 in the Tubulin-MTD147 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-MTD147 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:0.3
occ:1.00
O A:HOH643 2.7 77.2 1.0
O A:HOH662 2.9 73.8 1.0
O A:HOH651 3.1 69.7 1.0
OD2 E:ASP44 3.6 0.5 1.0
O A:HOH672 4.0 67.3 1.0
OG A:SER158 4.1 61.2 1.0
O A:GLU196 4.3 62.1 1.0
NZ A:LYS166 4.4 50.4 1.0
O A:GLY162 4.5 77.2 1.0
O A:HOH607 4.6 65.3 1.0
CB A:SER158 4.7 56.5 1.0
CG E:ASP44 4.7 0.8 1.0
CA A:HIS197 4.8 50.8 1.0
OD1 A:ASP199 4.9 66.6 1.0
O A:HIS197 4.9 58.1 1.0

Calcium binding site 3 out of 5 in 5m7g

Go back to Calcium Binding Sites List in 5m7g
Calcium binding site 3 out of 5 in the Tubulin-MTD147 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-MTD147 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:83.6
occ:1.00
O B:HOH652 2.4 76.3 1.0
OE2 B:GLU113 2.6 84.0 1.0
CD B:GLU113 3.4 82.2 1.0
OE1 B:GLU113 3.4 87.1 1.0
OE1 B:GLU110 4.6 52.4 1.0
CG B:GLU113 4.9 62.7 1.0

Calcium binding site 4 out of 5 in 5m7g

Go back to Calcium Binding Sites List in 5m7g
Calcium binding site 4 out of 5 in the Tubulin-MTD147 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-MTD147 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:68.0
occ:1.00
O C:HOH605 2.4 59.2 1.0
O C:GLY44 2.4 71.1 1.0
O C:THR41 2.5 74.2 1.0
OE1 C:GLU55 2.5 61.7 1.0
OE2 C:GLU55 2.5 63.2 1.0
OD2 C:ASP39 2.5 69.5 1.0
OD1 C:ASP39 2.6 68.5 1.0
OG1 C:THR41 2.6 73.0 1.0
CD C:GLU55 2.8 62.4 1.0
CG C:ASP39 2.9 70.4 1.0
C C:THR41 3.4 77.2 1.0
C C:GLY44 3.4 73.6 1.0
CB C:THR41 3.5 67.4 1.0
CA C:THR41 3.9 73.3 1.0
OD2 C:ASP47 4.2 75.6 1.0
N C:THR41 4.2 75.7 1.0
N C:GLY45 4.3 75.9 1.0
CG C:GLU55 4.3 59.5 1.0
CA C:GLY45 4.3 77.3 1.0
O C:HOH613 4.3 59.7 1.0
CA C:GLY44 4.4 76.1 1.0
N C:GLY44 4.4 75.5 1.0
CB C:ASP39 4.4 70.6 1.0
OD1 C:ASN50 4.4 50.4 1.0
CZ C:PHE49 4.5 63.4 1.0
N C:ILE42 4.6 77.9 1.0
NE2 C:HIS61 4.7 47.3 1.0
CE1 C:PHE49 4.8 59.3 1.0
CG2 C:THR41 4.9 53.0 1.0
ND2 C:ASN50 4.9 44.9 1.0

Calcium binding site 5 out of 5 in 5m7g

Go back to Calcium Binding Sites List in 5m7g
Calcium binding site 5 out of 5 in the Tubulin-MTD147 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Tubulin-MTD147 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca504

b:0.3
occ:1.00
O C:HOH767 2.4 96.0 1.0
O C:HOH763 2.8 81.2 1.0
OE2 C:GLU220 4.2 0.9 1.0
CG C:GLU220 4.6 92.5 1.0
CD C:GLU220 4.8 0.8 1.0
O C:ASP218 4.8 67.8 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: Sat Dec 12 05:37:00 2020

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