Calcium in PDB 6n47: The Structure of Sb-2-204-Tubulin Complex

Protein crystallography data

The structure of The Structure of Sb-2-204-Tubulin Complex, PDB code: 6n47 was solved by K.Arnst, S.Banerjee, Y.Wang, W.Li, D.Miller, W.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.295, 157.835, 182.068, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 24.6

Other elements in 6n47:

The structure of The Structure of Sb-2-204-Tubulin Complex also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Chlorine (Cl) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the The Structure of Sb-2-204-Tubulin Complex (pdb code 6n47). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the The Structure of Sb-2-204-Tubulin Complex, PDB code: 6n47:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6n47

Go back to Calcium Binding Sites List in 6n47
Calcium binding site 1 out of 4 in the The Structure of Sb-2-204-Tubulin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Structure of Sb-2-204-Tubulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:55.0
occ:1.00
OD2 A:ASP39 2.3 49.5 1.0
OD1 A:ASP39 2.4 46.5 1.0
O A:THR41 2.5 72.4 1.0
O A:GLY44 2.5 53.8 1.0
OE1 A:GLU55 2.6 53.0 1.0
OE2 A:GLU55 2.6 49.3 1.0
CG A:ASP39 2.7 51.9 1.0
CD A:GLU55 2.9 54.8 1.0
OG1 A:THR41 3.1 71.8 1.0
C A:THR41 3.5 66.4 1.0
C A:GLY44 3.6 60.7 1.0
CB A:THR41 3.7 64.4 1.0
OD1 A:ASP47 3.9 61.9 1.0
CA A:THR41 4.0 63.0 1.0
CB A:ASP39 4.1 53.5 1.0
CZ A:PHE49 4.3 64.7 1.0
N A:THR41 4.3 57.3 1.0
CA A:GLY45 4.4 60.1 1.0
N A:GLY45 4.4 57.3 1.0
CG A:GLU55 4.4 53.4 1.0
CE1 A:HIS61 4.6 63.1 1.0
CA A:GLY44 4.6 60.5 1.0
N A:GLY44 4.6 58.6 1.0
OD1 A:ASN50 4.6 49.4 1.0
N A:ILE42 4.7 64.3 1.0
ND2 A:ASN50 4.7 46.3 1.0
CE1 A:PHE49 5.0 63.9 1.0

Calcium binding site 2 out of 4 in 6n47

Go back to Calcium Binding Sites List in 6n47
Calcium binding site 2 out of 4 in the The Structure of Sb-2-204-Tubulin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Structure of Sb-2-204-Tubulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:73.2
occ:1.00
OE2 B:GLU111 2.5 60.6 1.0
CD B:GLU111 3.4 58.6 1.0
OE1 B:GLU111 3.5 64.6 1.0
OE1 B:GLU108 4.6 32.5 1.0
CG B:GLU111 4.8 54.2 1.0

Calcium binding site 3 out of 4 in 6n47

Go back to Calcium Binding Sites List in 6n47
Calcium binding site 3 out of 4 in the The Structure of Sb-2-204-Tubulin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Structure of Sb-2-204-Tubulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:43.1
occ:1.00
OG1 C:THR41 2.3 48.6 1.0
OD1 C:ASP39 2.4 37.6 1.0
OE2 C:GLU55 2.4 41.2 1.0
O C:THR41 2.4 50.6 1.0
OD2 C:ASP39 2.6 37.8 1.0
OE1 C:GLU55 2.6 35.5 1.0
O C:GLY44 2.7 47.3 1.0
CG C:ASP39 2.8 40.2 1.0
CD C:GLU55 2.9 35.8 1.0
C C:THR41 3.5 46.7 1.0
CB C:THR41 3.5 46.5 1.0
C C:GLY44 3.6 46.3 1.0
CA C:THR41 3.9 47.4 1.0
OD2 C:ASP47 4.0 47.9 1.0
CA C:GLY45 4.1 41.4 1.0
N C:GLY45 4.2 41.0 1.0
N C:THR41 4.2 46.3 1.0
CB C:ASP39 4.3 41.5 1.0
CG C:GLU55 4.4 34.4 1.0
OD1 C:ASN50 4.4 30.6 1.0
CZ C:PHE49 4.5 33.1 1.0
CA C:GLY44 4.7 49.3 1.0
N C:ILE42 4.7 48.6 1.0
O C:HOH617 4.7 42.0 1.0
N C:GLY44 4.7 48.0 1.0
CG2 C:THR41 4.7 43.0 1.0
CE1 C:PHE49 4.7 32.9 1.0
NE2 C:HIS61 4.8 27.3 1.0
ND2 C:ASN50 4.8 29.5 1.0

Calcium binding site 4 out of 4 in 6n47

Go back to Calcium Binding Sites List in 6n47
Calcium binding site 4 out of 4 in the The Structure of Sb-2-204-Tubulin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Structure of Sb-2-204-Tubulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca201

b:73.1
occ:1.00
OD2 E:ASP44 3.1 74.8 1.0
OG A:SER158 3.9 39.5 1.0
O A:GLU196 3.9 49.0 1.0
CG E:ASP44 4.3 80.5 1.0
NZ A:LYS166 4.6 41.4 1.0
O A:GLY162 4.7 50.3 1.0
OD1 A:ASP199 4.8 27.6 1.0
CA A:HIS197 4.8 37.9 1.0
OD1 E:ASP44 4.8 66.9 1.0

Reference:

K.E.Arnst, S.Banerjee, Y.Wang, H.Chen, Y.Li, L.Yang, W.Li, D.D.Miller, W.Li. X-Ray Crystal Structure Guided Discovery and Antitumor Efficacy of Dihydroquinoxalinone As Potent Tubulin Polymerization Inhibitors. Acs Chem.Biol. 2019.
ISSN: ESSN 1554-8937
PubMed: 31714738
DOI: 10.1021/ACSCHEMBIO.9B00696
Page generated: Sat Dec 12 07:22:21 2020

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