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Calcium in PDB 4zol: Crystal Structure of Tubulin-Stathmin-Ttl-Tubulysin M Complex

Protein crystallography data

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-Tubulysin M Complex, PDB code: 4zol was solved by Y.Wang, R.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.63 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.127, 154.824, 186.524, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 23.2

Other elements in 4zol:

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-Tubulysin M Complex also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Tubulin-Stathmin-Ttl-Tubulysin M Complex (pdb code 4zol). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Tubulin-Stathmin-Ttl-Tubulysin M Complex, PDB code: 4zol:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 4zol

Go back to Calcium Binding Sites List in 4zol
Calcium binding site 1 out of 2 in the Crystal Structure of Tubulin-Stathmin-Ttl-Tubulysin M Complex


Mono view


Stereo pair view

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

b:50.0
occ:1.00
O A:GLY44 2.2 52.0 1.0
O A:THR41 2.4 72.0 1.0
OE2 A:GLU55 2.4 47.0 1.0
OD2 A:ASP39 2.5 50.4 1.0
OD1 A:ASP39 2.5 45.2 1.0
OG1 A:THR41 2.7 55.2 1.0
O A:HOH603 2.7 32.9 1.0
OE1 A:GLU55 2.8 62.5 1.0
CG A:ASP39 2.9 50.4 1.0
CD A:GLU55 2.9 55.0 1.0
C A:GLY44 3.4 60.5 1.0
C A:THR41 3.4 67.5 1.0
CB A:THR41 3.8 58.2 1.0
CA A:THR41 3.9 59.8 1.0
N A:THR41 4.0 62.9 1.0
CA A:GLY45 4.1 60.2 1.0
N A:GLY45 4.1 59.4 1.0
CG A:GLU55 4.4 57.1 1.0
CB A:ASP39 4.5 50.6 1.0
N A:GLY44 4.5 64.5 1.0
CA A:GLY44 4.5 60.4 1.0
CZ A:PHE49 4.5 55.2 1.0
N A:ILE42 4.6 70.5 1.0
OD2 A:ASP47 4.7 61.7 1.0
OD1 A:ASN50 4.7 42.7 1.0
NE2 A:HIS61 4.8 63.6 1.0
ND2 A:ASN50 4.9 44.7 1.0
CG2 A:THR41 5.0 55.3 1.0
CE1 A:PHE49 5.0 53.1 1.0

Calcium binding site 2 out of 2 in 4zol

Go back to Calcium Binding Sites List in 4zol
Calcium binding site 2 out of 2 in the Crystal Structure of Tubulin-Stathmin-Ttl-Tubulysin M Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Tubulin-Stathmin-Ttl-Tubulysin M Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:38.5
occ:1.00
O C:THR41 2.4 53.7 1.0
O C:GLY44 2.4 54.8 1.0
OD2 C:ASP39 2.4 38.1 1.0
OE2 C:GLU55 2.5 39.5 1.0
OG1 C:THR41 2.5 38.8 1.0
OE1 C:GLU55 2.6 42.7 1.0
O C:HOH602 2.6 31.9 1.0
OD1 C:ASP39 2.7 43.2 1.0
CD C:GLU55 2.8 41.4 1.0
CG C:ASP39 2.9 42.8 1.0
C C:THR41 3.3 48.0 1.0
CB C:THR41 3.5 41.2 1.0
C C:GLY44 3.5 53.1 1.0
CA C:THR41 3.8 45.0 1.0
N C:THR41 4.1 46.8 1.0
CA C:GLY45 4.2 56.0 1.0
N C:GLY45 4.3 53.8 1.0
CG C:GLU55 4.3 35.0 1.0
CB C:ASP39 4.4 41.9 1.0
OD2 C:ASP47 4.5 53.7 1.0
N C:ILE42 4.5 50.3 1.0
CA C:GLY44 4.5 49.3 1.0
N C:GLY44 4.5 48.2 1.0
NE2 C:HIS61 4.6 35.3 1.0
O C:HOH616 4.6 44.0 1.0
OD1 C:ASN50 4.6 32.2 1.0
CZ C:PHE49 4.6 33.1 1.0
CG2 C:THR41 4.8 35.1 1.0
CE1 C:PHE49 4.9 36.0 1.0
ND2 C:ASN50 5.0 31.2 1.0
CA C:ILE42 5.0 44.9 1.0

Reference:

Y.Wang, F.W.Benz, Y.Wu, Q.Wang, Y.Chen, X.Chen, H.Li, Y.Zhang, R.Zhang, J.Yang. Structural Insights Into the Pharmacophore of Vinca Domain Inhibitors of Microtubules Mol.Pharmacol. V. 89 233 2016.
ISSN: ESSN 1521-0111
PubMed: 26660762
DOI: 10.1124/MOL.115.100149
Page generated: Wed Jul 9 03:48:47 2025

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