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Calcium in PDB 6kpp: BNC105 in Complex with Tubulin

Protein crystallography data

The structure of BNC105 in Complex with Tubulin, PDB code: 6kpp was solved by T.Wang, C.Wu, D.Pu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.27 / 2.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.455, 157.664, 183.135, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 23.5

Other elements in 6kpp:

The structure of BNC105 in Complex with Tubulin also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the BNC105 in Complex with Tubulin (pdb code 6kpp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the BNC105 in Complex with Tubulin, PDB code: 6kpp:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6kpp

Go back to Calcium Binding Sites List in 6kpp
Calcium binding site 1 out of 2 in the BNC105 in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of BNC105 in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:82.3
occ:1.00
OE2 A:GLU55 2.4 71.3 1.0
O A:THR41 2.4 73.4 1.0
O A:GLY44 2.5 71.0 1.0
OE1 A:GLU55 2.8 72.7 1.0
OD2 A:ASP39 2.8 58.1 1.0
OD1 A:ASP39 2.8 55.5 1.0
CG2 A:THR41 2.9 74.7 1.0
CD A:GLU55 2.9 69.3 1.0
CG A:ASP39 3.2 60.6 1.0
C A:THR41 3.5 77.0 1.0
C A:GLY44 3.5 72.3 1.0
OG1 A:THR41 3.5 80.7 1.0
CB A:THR41 3.6 77.6 1.0
CA A:GLY45 4.0 74.9 1.0
CA A:THR41 4.0 76.2 1.0
OD2 A:ASP47 4.1 67.0 1.0
N A:GLY45 4.1 72.9 1.0
CZ A:PHE49 4.3 58.1 1.0
N A:THR41 4.4 74.0 1.0
CG A:GLU55 4.4 64.7 1.0
OD1 A:ASN50 4.4 51.4 1.0
N A:GLY44 4.5 77.0 1.0
CA A:GLY44 4.5 74.5 1.0
N A:ILE42 4.6 78.8 1.0
CB A:ASP39 4.7 60.9 1.0
CE1 A:PHE49 4.8 53.3 1.0
NE2 A:HIS61 4.9 63.0 1.0
ND2 A:ASN50 4.9 51.4 1.0

Calcium binding site 2 out of 2 in 6kpp

Go back to Calcium Binding Sites List in 6kpp
Calcium binding site 2 out of 2 in the BNC105 in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of BNC105 in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:55.2
occ:1.00
OE2 C:GLU55 2.3 53.0 1.0
OG1 C:THR41 2.4 63.5 1.0
O C:THR41 2.4 60.8 1.0
OD2 C:ASP39 2.4 58.6 1.0
O C:GLY44 2.6 62.3 1.0
OD1 C:ASP39 2.7 63.4 1.0
OE1 C:GLU55 2.8 52.5 1.0
CD C:GLU55 2.9 51.8 1.0
CG C:ASP39 2.9 60.8 1.0
C C:THR41 3.4 58.9 1.0
CB C:THR41 3.4 62.4 1.0
C C:GLY44 3.5 60.2 1.0
CA C:THR41 3.9 60.1 1.0
OD2 C:ASP47 4.0 61.0 1.0
CA C:GLY45 4.2 61.7 1.0
N C:GLY45 4.2 61.1 1.0
N C:THR41 4.2 58.0 1.0
OD1 C:ASN50 4.4 47.5 1.0
CG C:GLU55 4.4 45.6 1.0
CB C:ASP39 4.4 59.3 1.0
N C:GLY44 4.5 58.2 1.0
CA C:GLY44 4.5 56.7 1.0
CZ C:PHE49 4.6 40.5 1.0
N C:ILE42 4.6 61.4 1.0
CG2 C:THR41 4.7 65.1 1.0
NE2 C:HIS61 4.8 39.9 1.0
O C:HOH645 4.9 29.4 1.0
CE1 C:PHE49 4.9 42.2 1.0
ND2 C:ASN50 4.9 46.4 1.0

Reference:

T.Wang, C.Wu, C.Wang, G.Zhang, K.E.Arnst, Y.Yao, Z.Zhang, Y.Wang, D.Pu, W.Li. Unraveling the Molecular Mechanism of BNC105, A Phase II Clinical Trial Vascular Disrupting Agent, Provides Insights Into Drug Design. Biochem.Biophys.Res.Commun. 2020.
ISSN: ESSN 1090-2104
PubMed: 32085900
DOI: 10.1016/J.BBRC.2019.12.083
Page generated: Tue Jul 16 10:35:33 2024

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