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Calcium in PDB 5xp3: Crystal Structure of Apo T2R-Ttl

Protein crystallography data

The structure of Crystal Structure of Apo T2R-Ttl, PDB code: 5xp3 was solved by Y.Wang, J.Yang, T.Wang, L.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.168, 157.964, 181.408, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 24

Other elements in 5xp3:

The structure of Crystal Structure of Apo T2R-Ttl also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Apo T2R-Ttl (pdb code 5xp3). 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 Apo T2R-Ttl, PDB code: 5xp3:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5xp3

Go back to Calcium Binding Sites List in 5xp3
Calcium binding site 1 out of 2 in the Crystal Structure of Apo T2R-Ttl


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 Apo T2R-Ttl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:66.7
occ:1.00
OD2 A:ASP39 2.3 67.8 1.0
O A:GLY44 2.3 60.5 1.0
OD1 A:ASP39 2.5 61.9 1.0
O A:THR41 2.5 81.7 1.0
OE2 A:GLU55 2.7 63.1 1.0
OE1 A:GLU55 2.7 72.1 1.0
CG A:ASP39 2.7 67.4 1.0
OG1 A:THR41 2.8 67.3 1.0
CD A:GLU55 3.1 72.6 1.0
C A:THR41 3.5 79.3 1.0
C A:GLY44 3.5 69.3 1.0
CB A:THR41 3.7 75.5 1.0
CA A:THR41 4.0 77.9 1.0
N A:THR41 4.2 77.8 1.0
CA A:GLY45 4.2 76.8 1.0
CB A:ASP39 4.3 68.3 1.0
CZ A:PHE49 4.3 63.4 1.0
N A:GLY45 4.3 69.1 1.0
NE2 A:HIS61 4.5 74.7 1.0
O A:HOH643 4.5 61.9 1.0
N A:GLY44 4.5 67.8 1.0
CG A:GLU55 4.6 71.2 1.0
CA A:GLY44 4.6 72.4 1.0
OD2 A:ASP47 4.6 76.4 1.0
OD1 A:ASN50 4.7 73.2 1.0
N A:ILE42 4.7 82.3 1.0
ND2 A:ASN50 4.8 65.9 1.0
CE1 A:PHE49 4.8 64.2 1.0

Calcium binding site 2 out of 2 in 5xp3

Go back to Calcium Binding Sites List in 5xp3
Calcium binding site 2 out of 2 in the Crystal Structure of Apo T2R-Ttl


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 Apo T2R-Ttl within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:49.9
occ:1.00
O C:HOH623 2.4 49.8 1.0
O C:THR41 2.4 61.3 1.0
OE1 C:GLU55 2.4 48.2 1.0
O C:GLY44 2.4 53.4 1.0
OD2 C:ASP39 2.4 51.1 1.0
OG1 C:THR41 2.4 56.2 1.0
OE2 C:GLU55 2.5 51.5 1.0
OD1 C:ASP39 2.6 51.2 1.0
CD C:GLU55 2.8 49.6 1.0
CG C:ASP39 2.9 53.8 1.0
C C:THR41 3.4 58.1 1.0
C C:GLY44 3.5 57.8 1.0
CB C:THR41 3.5 62.0 1.0
CA C:THR41 3.9 56.2 1.0
CA C:GLY45 4.2 58.0 1.0
N C:THR41 4.2 60.8 1.0
N C:GLY45 4.2 59.0 1.0
CG C:GLU55 4.3 44.5 1.0
O C:HOH602 4.4 46.0 1.0
CB C:ASP39 4.4 52.9 1.0
N C:GLY44 4.5 56.8 1.0
OD1 C:ASN50 4.6 42.8 1.0
CA C:GLY44 4.6 56.1 1.0
OD2 C:ASP47 4.6 59.6 1.0
N C:ILE42 4.6 58.0 1.0
NE2 C:HIS61 4.6 45.0 1.0
CZ C:PHE49 4.7 48.4 1.0
CE1 C:PHE49 4.8 47.5 1.0
CG2 C:THR41 4.9 54.2 1.0

Reference:

Y.Jianhong, Y.Wei, Y.Yamei, W.Yuxi, Y.Tao, X.Linlin, Y.Xue, L.Caofeng, L.Zuowei, C.Xiaoxin, H.Mengshi, Z.Li, Q.Qiang, P.Heying, L.Dan, W.Fang, B.Peng, W.Jiaolin, Y.Haoyu, C.Lijuan. The Compound Millepachine and Its Derivatives Inhibit Tubulin Polymerization By Irreversibly Binding to the Colchicine-Binding Site in Beta-Tubulin. J. Biol. Chem. 2018.
ISSN: ESSN 1083-351X
PubMed: 29691282
DOI: 10.1074/JBC.RA117.001658
Page generated: Wed Jul 9 11:43:29 2025

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