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Calcium in PDB 4zi7: Crystal Structure of Tubulin-Stathmin-Ttl-HTI286 Complex

Protein crystallography data

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-HTI286 Complex, PDB code: 4zi7 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) 50.00 / 2.51
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.367, 157.343, 181.963, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 23.9

Other elements in 4zi7:

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-HTI286 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-HTI286 Complex (pdb code 4zi7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Tubulin-Stathmin-Ttl-HTI286 Complex, PDB code: 4zi7:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4zi7

Go back to Calcium Binding Sites List in 4zi7
Calcium binding site 1 out of 4 in the Crystal Structure of Tubulin-Stathmin-Ttl-HTI286 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-HTI286 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:62.6
occ:1.00
O A:THR41 2.3 72.2 1.0
OE2 A:GLU55 2.4 70.7 1.0
OD2 A:ASP39 2.4 51.5 1.0
OD1 A:ASP39 2.5 59.4 1.0
O A:GLY44 2.6 69.9 1.0
OG1 A:THR41 2.8 74.7 1.0
CG A:ASP39 2.8 62.0 1.0
OE1 A:GLU55 2.9 71.4 1.0
CD A:GLU55 3.0 72.0 1.0
C A:THR41 3.3 78.7 1.0
CB A:THR41 3.4 77.4 1.0
C A:GLY44 3.6 81.7 1.0
CA A:THR41 3.8 73.6 1.0
N A:THR41 4.1 70.2 1.0
N A:GLY44 4.3 80.5 1.0
CB A:ASP39 4.3 65.1 1.0
CA A:GLY44 4.4 80.4 1.0
CZ A:PHE49 4.4 75.9 1.0
N A:GLY45 4.5 81.5 1.0
CG A:GLU55 4.5 74.5 1.0
N A:ILE42 4.5 79.4 1.0
CA A:GLY45 4.6 77.7 1.0
NE2 A:HIS61 4.7 77.8 1.0
OD2 A:ASP47 4.8 69.2 1.0
ND2 A:ASN50 4.9 55.1 1.0
CG2 A:THR41 4.9 73.9 1.0
OD1 A:ASN50 4.9 54.5 1.0
CA A:ILE42 5.0 77.3 1.0

Calcium binding site 2 out of 4 in 4zi7

Go back to Calcium Binding Sites List in 4zi7
Calcium binding site 2 out of 4 in the Crystal Structure of Tubulin-Stathmin-Ttl-HTI286 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-HTI286 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:89.8
occ:1.00
OE2 B:GLU113 3.1 100.0 1.0
CD B:GLU113 4.1 96.3 1.0
OE1 B:GLU113 4.4 98.6 1.0
OE1 B:GLU110 4.7 61.1 1.0

Calcium binding site 3 out of 4 in 4zi7

Go back to Calcium Binding Sites List in 4zi7
Calcium binding site 3 out of 4 in the Crystal Structure of Tubulin-Stathmin-Ttl-HTI286 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-HTI286 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:96.0
occ:1.00
OD2 B:ASP120 3.6 59.8 1.0
OD1 B:ASP120 4.0 52.1 1.0
CG B:ASP120 4.2 58.3 1.0
O B:HOH638 4.3 51.8 1.0
CB B:ASP116 4.4 48.3 1.0

Calcium binding site 4 out of 4 in 4zi7

Go back to Calcium Binding Sites List in 4zi7
Calcium binding site 4 out of 4 in the Crystal Structure of Tubulin-Stathmin-Ttl-HTI286 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Tubulin-Stathmin-Ttl-HTI286 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca504

b:48.2
occ:1.00
OG1 C:THR41 2.2 57.1 1.0
O C:THR41 2.3 68.0 1.0
OD2 C:ASP39 2.3 44.2 1.0
OE2 C:GLU55 2.4 50.3 1.0
O C:GLY44 2.4 64.2 1.0
OD1 C:ASP39 2.4 50.4 1.0
O C:HOH604 2.5 50.6 1.0
OE1 C:GLU55 2.5 52.8 1.0
CG C:ASP39 2.7 49.9 1.0
CD C:GLU55 2.8 47.9 1.0
C C:THR41 3.2 56.8 1.0
CB C:THR41 3.3 56.1 1.0
C C:GLY44 3.5 60.8 1.0
CA C:THR41 3.6 54.6 1.0
N C:THR41 4.0 57.0 1.0
N C:GLY45 4.2 59.2 1.0
CB C:ASP39 4.2 52.8 1.0
CG C:GLU55 4.3 44.2 1.0
CA C:GLY45 4.3 59.9 1.0
OD2 C:ASP47 4.3 66.5 1.0
N C:ILE42 4.4 54.2 1.0
O C:HOH631 4.5 57.1 1.0
CA C:GLY44 4.5 60.2 1.0
OD1 C:ASN50 4.5 46.1 1.0
N C:GLY44 4.6 57.2 1.0
CZ C:PHE49 4.6 41.9 1.0
CG2 C:THR41 4.6 50.8 1.0
NE2 C:HIS61 4.7 45.6 1.0
CA C:ILE42 4.9 54.6 1.0
O C:HOH652 4.9 44.9 1.0
CE1 C:PHE49 5.0 43.7 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: Sun Jul 14 15:44:46 2024

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