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Calcium in PDB 5bmv: Crystal Structure of Tubulin-Stathmin-Ttl-Vinblastine Complex

Protein crystallography data

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-Vinblastine Complex, PDB code: 5bmv was solved by Y.Wang, Q.Chen, R.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.470, 157.420, 183.180, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 23.5

Other elements in 5bmv:

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-Vinblastine 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-Vinblastine Complex (pdb code 5bmv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Tubulin-Stathmin-Ttl-Vinblastine Complex, PDB code: 5bmv:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 5bmv

Go back to Calcium Binding Sites List in 5bmv
Calcium binding site 1 out of 3 in the Crystal Structure of Tubulin-Stathmin-Ttl-Vinblastine 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-Vinblastine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:62.1
occ:1.00
OD2 A:ASP39 2.1 59.4 1.0
O A:HOH624 2.4 54.4 1.0
OD1 A:ASP39 2.4 58.7 1.0
O A:THR41 2.4 79.0 1.0
O A:GLY44 2.4 59.8 1.0
OE2 A:GLU55 2.5 68.1 1.0
CG A:ASP39 2.6 62.2 1.0
OE1 A:GLU55 2.7 73.6 1.0
OG1 A:THR41 2.7 67.9 1.0
CD A:GLU55 2.9 74.3 1.0
C A:THR41 3.5 71.9 1.0
C A:GLY44 3.5 69.8 1.0
CB A:THR41 3.5 64.1 1.0
CA A:THR41 3.9 69.4 1.0
CB A:ASP39 4.1 60.3 1.0
N A:THR41 4.2 63.1 1.0
N A:GLY45 4.3 74.4 1.0
CA A:GLY45 4.3 77.0 1.0
CZ A:PHE49 4.3 72.7 1.0
N A:GLY44 4.4 70.7 1.0
CG A:GLU55 4.4 73.8 1.0
OD2 A:ASP47 4.4 59.7 1.0
CA A:GLY44 4.5 68.8 1.0
NE2 A:HIS61 4.6 64.4 1.0
N A:ILE42 4.6 72.7 1.0
OD1 A:ASN50 4.8 67.4 1.0
CE1 A:PHE49 4.8 71.3 1.0
ND2 A:ASN50 4.9 75.3 1.0
CG2 A:THR41 4.9 62.1 1.0
CA A:ASP39 4.9 62.6 1.0
C A:ASP39 5.0 64.7 1.0

Calcium binding site 2 out of 3 in 5bmv

Go back to Calcium Binding Sites List in 5bmv
Calcium binding site 2 out of 3 in the Crystal Structure of Tubulin-Stathmin-Ttl-Vinblastine 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-Vinblastine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:76.6
occ:1.00
OE2 B:GLU113 2.5 79.4 1.0
O B:HOH651 2.7 58.4 1.0
CD B:GLU113 3.5 74.9 1.0
OE1 B:GLU113 3.8 81.8 1.0
OE1 B:GLU110 4.5 43.1 1.0
O B:HOH639 4.6 43.2 1.0
CG B:GLU113 4.8 66.2 1.0

Calcium binding site 3 out of 3 in 5bmv

Go back to Calcium Binding Sites List in 5bmv
Calcium binding site 3 out of 3 in the Crystal Structure of Tubulin-Stathmin-Ttl-Vinblastine Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Tubulin-Stathmin-Ttl-Vinblastine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:49.4
occ:1.00
OE2 C:GLU55 2.2 54.9 1.0
OG1 C:THR41 2.2 74.0 1.0
OD2 C:ASP39 2.3 43.4 1.0
O C:GLY44 2.4 56.7 1.0
O C:HOH645 2.5 46.8 1.0
OD1 C:ASP39 2.5 41.8 1.0
O C:THR41 2.5 72.2 1.0
OE1 C:GLU55 2.6 50.2 1.0
CD C:GLU55 2.7 48.7 1.0
CG C:ASP39 2.8 46.4 1.0
C C:THR41 3.3 68.9 1.0
CB C:THR41 3.4 75.2 1.0
C C:GLY44 3.5 63.3 1.0
CA C:THR41 3.8 69.7 1.0
N C:THR41 4.2 67.3 1.0
CG C:GLU55 4.2 46.7 1.0
CB C:ASP39 4.3 48.7 1.0
N C:GLY45 4.3 63.1 1.0
CA C:GLY45 4.4 65.3 1.0
N C:ILE42 4.4 67.7 1.0
CA C:GLY44 4.5 58.7 1.0
NE2 C:HIS61 4.5 43.6 1.0
OD2 C:ASP47 4.5 54.7 1.0
N C:GLY44 4.6 54.9 1.0
CZ C:PHE49 4.6 46.7 1.0
CG2 C:THR41 4.6 73.8 1.0
OD1 C:ASN50 4.8 46.5 1.0
ND2 C:ASN50 4.8 39.5 1.0
CE1 C:PHE49 4.8 50.3 1.0
O C:HOH632 4.9 41.3 1.0
CA C:ILE42 4.9 64.9 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: Sat Dec 12 05:18:39 2020

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