Atomistry » Calcium » PDB 5c02-5ck1 » 5ca1
Atomistry »
  Calcium »
    PDB 5c02-5ck1 »
      5ca1 »

Calcium in PDB 5ca1: Crystal Structure of T2R-Ttl-Nocodazole Complex

Protein crystallography data

The structure of Crystal Structure of T2R-Ttl-Nocodazole Complex, PDB code: 5ca1 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) 41.52 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.440, 158.362, 180.692, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 22.5

Other elements in 5ca1:

The structure of Crystal Structure of T2R-Ttl-Nocodazole 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-Nocodazole Complex (pdb code 5ca1). 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-Nocodazole Complex, PDB code: 5ca1:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5ca1

Go back to Calcium Binding Sites List in 5ca1
Calcium binding site 1 out of 2 in the Crystal Structure of T2R-Ttl-Nocodazole 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-Nocodazole Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:54.4
occ:1.00
O A:GLY44 2.3 48.1 1.0
OD2 A:ASP39 2.4 52.0 1.0
OE2 A:GLU55 2.5 52.2 1.0
OD1 A:ASP39 2.5 49.2 1.0
OG1 A:THR41 2.5 71.3 1.0
O A:THR41 2.5 63.0 1.0
OE1 A:GLU55 2.6 57.7 1.0
CG A:ASP39 2.8 55.9 1.0
CD A:GLU55 2.9 56.5 1.0
CB A:THR41 3.5 64.8 1.0
C A:GLY44 3.5 59.3 1.0
C A:THR41 3.5 66.8 1.0
CA A:THR41 3.9 61.5 1.0
N A:THR41 4.2 62.8 1.0
CA A:GLY45 4.3 63.0 1.0
N A:GLY45 4.3 55.3 1.0
CB A:ASP39 4.3 49.4 1.0
CZ A:PHE49 4.3 53.4 1.0
CG A:GLU55 4.4 57.2 1.0
N A:GLY44 4.4 55.3 1.0
CA A:GLY44 4.4 50.2 1.0
OD1 A:ASN50 4.5 65.7 1.0
OD2 A:ASP47 4.5 63.8 1.0
NE2 A:HIS61 4.6 58.2 1.0
N A:ILE42 4.7 66.3 1.0
CG2 A:THR41 4.8 57.1 1.0
CE1 A:PHE49 4.8 58.5 1.0
ND2 A:ASN50 4.9 53.7 1.0

Calcium binding site 2 out of 2 in 5ca1

Go back to Calcium Binding Sites List in 5ca1
Calcium binding site 2 out of 2 in the Crystal Structure of T2R-Ttl-Nocodazole 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-Nocodazole Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:45.7
occ:1.00
OG1 C:THR41 2.4 46.8 1.0
O C:GLY44 2.4 41.1 1.0
O C:THR41 2.4 54.0 1.0
OE2 C:GLU55 2.5 44.2 1.0
OD2 C:ASP39 2.5 42.4 1.0
OD1 C:ASP39 2.6 41.3 1.0
OE1 C:GLU55 2.6 43.7 1.0
CG C:ASP39 2.9 41.6 1.0
CD C:GLU55 2.9 40.9 1.0
C C:THR41 3.5 45.8 1.0
C C:GLY44 3.5 46.5 1.0
CB C:THR41 3.5 48.6 1.0
CA C:THR41 3.9 45.5 1.0
OD2 C:ASP47 4.1 58.9 1.0
CA C:GLY45 4.1 44.0 1.0
N C:THR41 4.2 46.7 1.0
N C:GLY45 4.2 47.3 1.0
O C:HOH611 4.4 41.9 1.0
CB C:ASP39 4.4 46.3 1.0
CG C:GLU55 4.4 35.4 1.0
OD1 C:ASN50 4.5 42.7 1.0
N C:GLY44 4.5 42.2 1.0
CA C:GLY44 4.6 46.6 1.0
CZ C:PHE49 4.6 32.8 1.0
NE2 C:HIS61 4.6 40.4 1.0
N C:ILE42 4.7 46.1 1.0
CG2 C:THR41 4.8 38.7 1.0
CE1 C:PHE49 4.8 39.4 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 04:31:45 2025

Last articles

Ca in 7F8L
Ca in 7F7R
Ca in 7F5F
Ca in 7F5B
Ca in 7F58
Ca in 7F55
Ca in 7F54
Ca in 7F4Y
Ca in 7F53
Ca in 7F4I
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy