Calcium in PDB 5ylj: Crystal Structure of T2R-Ttl-Millepachine Complex

Protein crystallography data

The structure of Crystal Structure of T2R-Ttl-Millepachine Complex, PDB code: 5ylj was solved by J.H.Yang, L.J.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.90 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.231, 157.367, 182.684, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 25.5

Other elements in 5ylj:

The structure of Crystal Structure of T2R-Ttl-Millepachine 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 T2R-Ttl-Millepachine Complex (pdb code 5ylj). 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 T2R-Ttl-Millepachine Complex, PDB code: 5ylj:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5ylj

Go back to Calcium Binding Sites List in 5ylj
Calcium binding site 1 out of 2 in the Crystal Structure of T2R-Ttl-Millepachine 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 T2R-Ttl-Millepachine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:70.8
occ:1.00
O A:GLY44 2.4 70.7 1.0
OD1 A:ASP39 2.5 75.0 1.0
O A:THR41 2.6 82.3 1.0
OD2 A:ASP39 2.8 77.0 1.0
OE2 A:GLU55 2.8 74.3 1.0
OG1 A:THR41 3.0 83.8 1.0
OE1 A:GLU55 3.0 77.4 1.0
CG A:ASP39 3.1 76.3 1.0
CD A:GLU55 3.3 75.3 1.0
C A:GLY44 3.6 73.4 1.0
C A:THR41 3.7 82.7 1.0
CB A:THR41 3.8 83.6 1.0
CA A:THR41 4.1 83.0 1.0
CZ A:PHE49 4.2 78.7 1.0
N A:THR41 4.3 81.3 1.0
CA A:GLY45 4.3 75.7 1.0
OD2 A:ASP47 4.3 74.0 1.0
N A:GLY45 4.4 73.7 1.0
OD1 A:ASN50 4.5 65.2 1.0
N A:GLY44 4.5 75.7 1.0
CB A:ASP39 4.6 77.1 1.0
NE2 A:HIS61 4.6 74.3 1.0
CA A:GLY44 4.6 75.2 1.0
ND2 A:ASN50 4.8 64.7 1.0
CG A:GLU55 4.8 75.3 1.0
CE1 A:PHE49 4.8 76.8 1.0
N A:ILE42 4.9 81.1 1.0

Calcium binding site 2 out of 2 in 5ylj

Go back to Calcium Binding Sites List in 5ylj
Calcium binding site 2 out of 2 in the Crystal Structure of T2R-Ttl-Millepachine 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 T2R-Ttl-Millepachine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:64.3
occ:1.00
O C:GLY44 2.4 70.0 1.0
OG1 C:THR41 2.6 72.3 1.0
O C:THR41 2.6 70.6 1.0
OE2 C:GLU55 2.7 57.7 1.0
OD2 C:ASP39 2.7 57.6 1.0
OD1 C:ASP39 2.7 57.7 1.0
OE1 C:GLU55 2.9 57.4 1.0
CG C:ASP39 3.1 59.3 1.0
CD C:GLU55 3.2 57.0 1.0
C C:GLY44 3.5 70.5 1.0
C C:THR41 3.7 69.9 1.0
CB C:THR41 3.7 70.6 1.0
OD2 C:ASP47 3.9 64.1 1.0
CA C:GLY45 3.9 69.9 1.0
CA C:THR41 4.1 70.0 1.0
N C:GLY45 4.1 70.2 1.0
OD1 C:ASN50 4.2 51.7 1.0
N C:THR41 4.4 68.4 1.0
CZ C:PHE49 4.6 49.0 1.0
CB C:ASP39 4.6 62.1 1.0
CA C:GLY44 4.7 70.3 1.0
CG C:GLU55 4.7 55.4 1.0
CE1 C:PHE49 4.7 48.8 1.0
N C:GLY44 4.8 70.4 1.0
N C:ILE42 4.9 70.5 1.0
NE2 C:HIS61 4.9 48.6 1.0
ND2 C:ASN50 5.0 48.8 1.0
CG2 C:THR41 5.0 70.2 1.0

Reference:

J.H.Yang, W.Yan, Y.M.Yu, Y.X.Wang, T.Yang, L.L.Xue, X.Yuan, C.F.Long, Z.W.Liu, X.X.Chen, M.S.Hu, L.Zheng, Q.Qiu, H.Y.Pei, D.Li, F.Wang, P.Bai, J.L.Wen, H.Y.Ye, L.J.Chen. The Compound Millepachine and Its Derivatives Inhibit Tubulin Polymerization By Irreversibly Binding to the Colchicine-Binding Site in Beta-Tubulin. J. Biol. Chem. V. 293 9461 2018.
ISSN: ESSN 1083-351X
PubMed: 29691282
DOI: 10.1074/JBC.RA117.001658
Page generated: Sat Dec 12 05:54:37 2020

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