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Calcium in PDB 5c8y: Crystal Structure of T2R-Ttl-Plinabulin Complex

Protein crystallography data

The structure of Crystal Structure of T2R-Ttl-Plinabulin Complex, PDB code: 5c8y was solved by Y.Wang, Y.Yu, Q.Chen, J.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.70 / 2.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.060, 158.444, 181.825, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 27.1

Other elements in 5c8y:

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

Magnesium (Mg) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of T2R-Ttl-Plinabulin Complex (pdb code 5c8y). 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-Plinabulin Complex, PDB code: 5c8y:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5c8y

Go back to Calcium Binding Sites List in 5c8y
Calcium binding site 1 out of 2 in the Crystal Structure of T2R-Ttl-Plinabulin 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-Plinabulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:76.7
occ:1.00
OG1 A:THR41 2.4 0.8 1.0
OE2 A:GLU55 2.4 91.2 1.0
O A:THR41 2.5 83.5 1.0
OD1 A:ASP39 2.5 67.5 1.0
OE1 A:GLU55 2.5 48.5 1.0
O A:GLY44 2.5 50.4 1.0
OD2 A:ASP39 2.6 82.4 1.0
CD A:GLU55 2.8 75.0 1.0
CG A:ASP39 2.9 77.4 1.0
HB A:THR41 3.4 0.2 1.0
CB A:THR41 3.4 0.2 1.0
C A:GLY44 3.4 68.7 1.0
HA3 A:GLY45 3.5 74.6 1.0
C A:THR41 3.5 85.2 1.0
HZ A:PHE49 3.7 78.5 1.0
H A:GLY44 3.8 84.2 1.0
CA A:THR41 3.9 82.9 1.0
HD21 A:ASN50 3.9 69.0 1.0
H A:THR41 3.9 0.1 1.0
N A:GLY45 4.2 69.5 1.0
CA A:GLY45 4.3 62.1 1.0
CA A:GLY44 4.3 84.5 1.0
CG A:GLU55 4.3 94.7 1.0
N A:THR41 4.3 91.8 1.0
N A:GLY44 4.4 70.2 1.0
HA2 A:GLY44 4.4 0.3 1.0
CB A:ASP39 4.4 77.5 1.0
CZ A:PHE49 4.5 65.4 1.0
OD1 A:ASN50 4.6 60.5 1.0
NE2 A:HIS61 4.6 77.4 1.0
OD2 A:ASP47 4.6 59.5 1.0
N A:ILE42 4.7 56.4 1.0
HA A:ILE42 4.7 98.2 1.0
CG2 A:THR41 4.7 62.9 1.0
HG2 A:GLU55 4.7 0.6 1.0
HG3 A:GLU55 4.7 0.6 1.0
ND2 A:ASN50 4.7 57.5 1.0
HG21 A:THR41 4.8 75.5 1.0
HB3 A:ASP39 4.8 93.0 1.0
HA A:THR41 4.8 99.4 1.0
HA2 A:GLY45 4.8 74.6 1.0
HE2 A:PHE49 4.8 84.5 1.0
HB2 A:ASP39 4.8 93.0 1.0
H A:GLY45 5.0 83.4 1.0
HA A:ASP39 5.0 90.5 1.0

Calcium binding site 2 out of 2 in 5c8y

Go back to Calcium Binding Sites List in 5c8y
Calcium binding site 2 out of 2 in the Crystal Structure of T2R-Ttl-Plinabulin 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-Plinabulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:55.6
occ:1.00
OG1 C:THR41 2.4 72.7 1.0
OE2 C:GLU55 2.5 68.6 1.0
OD1 C:ASP39 2.5 40.7 1.0
OD2 C:ASP39 2.5 49.2 1.0
O C:THR41 2.5 69.9 1.0
OE1 C:GLU55 2.6 38.8 1.0
O C:GLY44 2.7 67.0 1.0
CG C:ASP39 2.8 53.4 1.0
CD C:GLU55 2.9 62.3 1.0
HA3 C:GLY45 3.1 62.7 1.0
C C:GLY44 3.5 60.3 1.0
CB C:THR41 3.5 58.5 1.0
C C:THR41 3.6 50.7 1.0
HB C:THR41 3.6 70.2 1.0
HZ C:PHE49 3.7 54.7 1.0
OD2 C:ASP47 3.9 76.4 1.0
HD21 C:ASN50 3.9 41.1 1.0
CA C:GLY45 4.0 52.2 1.0
H C:THR41 4.0 57.8 1.0
CA C:THR41 4.0 54.8 1.0
N C:GLY45 4.0 62.7 1.0
H C:GLY44 4.1 63.4 1.0
N C:THR41 4.3 48.1 1.0
CB C:ASP39 4.3 60.1 1.0
HE1 C:PHE49 4.4 58.3 1.0
CG C:GLU55 4.4 55.6 1.0
HA2 C:GLY45 4.4 62.7 1.0
OD1 C:ASN50 4.4 36.7 1.0
CZ C:PHE49 4.5 45.6 1.0
CA C:GLY44 4.5 51.0 1.0
HA2 C:GLY44 4.6 61.3 1.0
HB2 C:ASP39 4.6 72.1 1.0
N C:GLY44 4.6 52.9 1.0
O C:HOH656 4.7 40.2 1.0
ND2 C:ASN50 4.7 34.3 1.0
HA C:ILE42 4.7 75.8 1.0
HG3 C:GLU55 4.7 66.7 1.0
N C:ILE42 4.7 45.7 1.0
NE2 C:HIS61 4.8 37.8 1.0
H C:GLY45 4.8 75.3 1.0
CG2 C:THR41 4.8 32.6 1.0
HB3 C:ASP39 4.8 72.1 1.0
CE1 C:PHE49 4.8 48.6 1.0
HG2 C:GLU55 4.8 66.7 1.0
HG21 C:THR41 4.9 39.2 1.0
HA C:THR41 4.9 65.7 1.0
HG23 C:THR41 5.0 39.2 1.0

Reference:

Y.Wang, H.Zhang, B.Gigant, Y.Yu, Y.Wu, X.Chen, Q.Lai, Z.Yang, Q.Chen, J.Yang. Structures of A Diverse Set of Colchicine Binding Site Inhibitors in Complex with Tubulin Provide A Rationale For Drug Discovery. Febs J. V. 283 102 2016.
ISSN: ISSN 1742-464X
PubMed: 26462166
DOI: 10.1111/FEBS.13555
Page generated: Wed Jul 9 04:30:59 2025

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