Calcium in PDB 6brf: Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4B

Protein crystallography data

The structure of Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4B, PDB code: 6brf was solved by G.Kumar, Y.Wang, W.Li, S.W.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.78 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.129, 157.747, 181.596, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 23.7

Other elements in 6brf:

The structure of Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4B also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4B (pdb code 6brf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4B, PDB code: 6brf:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6brf

Go back to Calcium Binding Sites List in 6brf
Calcium binding site 1 out of 2 in the Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:66.7
occ:1.00
O A:THR41 2.3 74.0 1.0
O A:GLY44 2.4 69.9 1.0
OD2 A:ASP39 2.4 54.6 1.0
OE2 A:GLU55 2.4 54.8 1.0
OD1 A:ASP39 2.6 54.9 1.0
CG2 A:THR41 2.6 71.3 1.0
OE1 A:GLU55 2.7 64.4 1.0
CG A:ASP39 2.8 55.5 1.0
CD A:GLU55 2.9 59.9 1.0
C A:THR41 3.4 73.9 1.0
C A:GLY44 3.4 70.8 1.0
CB A:THR41 3.6 76.2 1.0
OG1 A:THR41 3.9 82.0 1.0
CA A:THR41 3.9 76.1 1.0
N A:GLY45 4.1 69.2 1.0
CA A:GLY45 4.2 68.7 1.0
N A:GLY44 4.3 72.0 1.0
N A:THR41 4.3 73.3 1.0
CA A:GLY44 4.3 71.3 1.0
CZ A:PHE49 4.3 57.1 1.0
CB A:ASP39 4.3 57.0 1.0
CG A:GLU55 4.4 58.0 1.0
OD1 A:ASP47 4.4 60.2 1.0
N A:ILE42 4.5 72.5 1.0
OD1 A:ASN50 4.6 55.4 1.0
NE2 A:HIS61 4.7 61.8 1.0
ND2 A:ASN50 4.8 50.4 1.0
CE1 A:PHE49 4.8 57.6 1.0
CA A:ILE42 4.9 70.3 1.0

Calcium binding site 2 out of 2 in 6brf

Go back to Calcium Binding Sites List in 6brf
Calcium binding site 2 out of 2 in the Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:41.6
occ:1.00
OE2 C:GLU55 2.3 39.3 1.0
O C:THR41 2.3 50.6 1.0
O C:HOH614 2.4 31.7 1.0
OE1 C:GLU55 2.5 37.5 1.0
O C:GLY44 2.5 45.7 1.0
OG1 C:THR41 2.5 48.3 1.0
OD1 C:ASP39 2.6 50.7 1.0
OD2 C:ASP39 2.6 53.5 1.0
CD C:GLU55 2.7 37.1 1.0
CG C:ASP39 2.9 53.3 1.0
C C:THR41 3.4 48.5 1.0
CB C:THR41 3.4 45.9 1.0
C C:GLY44 3.5 45.3 1.0
CA C:THR41 3.8 46.8 1.0
CA C:GLY45 4.1 43.6 1.0
N C:THR41 4.1 47.4 1.0
N C:GLY45 4.2 43.7 1.0
CG C:GLU55 4.2 33.1 1.0
OD2 C:ASP47 4.4 41.7 1.0
N C:GLY44 4.4 47.1 1.0
O C:HOH631 4.4 49.2 1.0
CB C:ASP39 4.4 54.6 1.0
CA C:GLY44 4.5 46.3 1.0
N C:ILE42 4.5 52.9 1.0
OD1 C:ASN50 4.6 34.1 1.0
CZ C:PHE49 4.7 31.9 1.0
NE2 C:HIS61 4.8 37.2 1.0
CG2 C:THR41 4.8 41.5 1.0
ND2 C:ASN50 4.8 27.7 1.0
CE1 C:PHE49 4.9 33.1 1.0

Reference:

S.Banerjee, K.E.Arnst, Y.Wang, G.Kumar, S.Deng, L.Yang, G.B.Li, J.Yang, S.W.White, W.Li, D.D.Miller. Heterocyclic-Fused Pyrimidines As Novel Tubulin Polymerization Inhibitors Targeting the Colchicine Binding Site: Structural Basis and Antitumor Efficacy. J. Med. Chem. V. 61 1704 2018.
ISSN: ISSN 1520-4804
PubMed: 29406710
DOI: 10.1021/ACS.JMEDCHEM.7B01858
Page generated: Sat Dec 12 05:59:48 2020

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