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Calcium in PDB 4i4t: Crystal Structure of Tubulin-RB3-Ttl-Zampanolide Complex

Protein crystallography data

The structure of Crystal Structure of Tubulin-RB3-Ttl-Zampanolide Complex, PDB code: 4i4t was solved by A.E.Prota, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 79.32 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.770, 158.640, 179.240, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 20.4

Other elements in 4i4t:

The structure of Crystal Structure of Tubulin-RB3-Ttl-Zampanolide Complex also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms
Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Tubulin-RB3-Ttl-Zampanolide Complex (pdb code 4i4t). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Tubulin-RB3-Ttl-Zampanolide Complex, PDB code: 4i4t:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4i4t

Go back to Calcium Binding Sites List in 4i4t
Calcium binding site 1 out of 4 in the Crystal Structure of Tubulin-RB3-Ttl-Zampanolide 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 Tubulin-RB3-Ttl-Zampanolide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:45.0
occ:1.00
O A:GLY44 2.4 49.1 1.0
O A:THR41 2.5 50.7 1.0
OG1 A:THR41 2.5 41.7 1.0
OE1 A:GLU55 2.5 41.9 1.0
OD2 A:ASP39 2.6 48.0 1.0
OE2 A:GLU55 2.6 38.7 1.0
O A:HOH702 2.6 38.3 1.0
OD1 A:ASP39 2.7 54.6 1.0
CD A:GLU55 2.9 42.3 1.0
CG A:ASP39 3.0 56.2 1.0
CB A:THR41 3.4 55.4 1.0
HB A:THR41 3.4 66.4 1.0
C A:THR41 3.5 66.7 1.0
C A:GLY44 3.5 70.1 1.0
H A:GLY44 3.6 72.8 1.0
HA3 A:GLY45 3.6 68.9 1.0
H A:THR41 3.7 67.9 1.0
HZ A:PHE49 3.7 54.9 1.0
CA A:THR41 3.9 56.8 1.0
HE2 A:HIS61 4.1 57.6 1.0
N A:THR41 4.2 56.6 1.0
HD21 A:ASN50 4.2 45.8 1.0
O A:HOH716 4.3 48.0 1.0
N A:GLY44 4.3 60.7 1.0
HE1 A:PHE49 4.3 53.4 1.0
N A:GLY45 4.3 56.3 1.0
CG A:GLU55 4.4 42.2 1.0
CA A:GLY45 4.4 57.4 1.0
CA A:GLY44 4.4 68.6 1.0
CB A:ASP39 4.5 44.5 1.0
CZ A:PHE49 4.5 45.7 1.0
OD1 A:ASN50 4.6 45.3 1.0
OD1 A:ASP47 4.6 46.0 1.0
HA2 A:GLY44 4.7 82.3 1.0
N A:ILE42 4.7 57.2 1.0
HG2 A:GLU55 4.7 50.7 1.0
CG2 A:THR41 4.8 57.6 1.0
HA A:ILE42 4.8 65.1 1.0
H A:GLY43 4.8 58.6 1.0
HA A:THR41 4.8 68.1 1.0
HG3 A:GLU55 4.8 50.7 1.0
CE1 A:PHE49 4.8 44.5 1.0
NE2 A:HIS61 4.8 48.0 1.0
HB3 A:ASP39 4.9 53.4 1.0
HB2 A:ASP39 4.9 53.4 1.0
HG21 A:THR41 4.9 69.1 1.0
HA2 A:GLY45 4.9 68.9 1.0
ND2 A:ASN50 5.0 38.1 1.0

Calcium binding site 2 out of 4 in 4i4t

Go back to Calcium Binding Sites List in 4i4t
Calcium binding site 2 out of 4 in the Crystal Structure of Tubulin-RB3-Ttl-Zampanolide 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 Tubulin-RB3-Ttl-Zampanolide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:80.9
occ:1.00
O E:HOH258 2.6 55.2 1.0
O A:HOH916 2.7 71.1 1.0
HO2 A:GOL507 2.8 64.8 1.0
O A:HOH712 2.9 44.4 1.0
O A:HOH900 2.9 63.1 1.0
O A:HOH901 3.1 39.0 1.0
HO3 A:GOL507 3.2 0.2 1.0
O2 A:GOL507 3.2 54.0 1.0
O3 A:GOL507 3.5 91.9 1.0
H31 A:GOL507 3.6 0.3 1.0
O A:HOH902 3.7 69.8 1.0
C3 A:GOL507 3.9 94.4 1.0
HZ3 A:LYS166 4.0 33.5 1.0
HZ1 A:LYS166 4.0 33.5 1.0
C2 A:GOL507 4.2 89.7 1.0
HA A:HIS197 4.2 36.3 1.0
OD2 E:ASP44 4.3 62.7 1.0
OD2 A:ASP199 4.3 35.0 1.0
NZ A:LYS166 4.4 27.9 1.0
HG A:SER158 4.4 41.7 1.0
O A:GLU196 4.5 36.8 1.0
O A:GLY162 4.5 49.2 1.0
OG A:SER158 4.5 34.7 1.0
HZ2 A:LYS166 4.6 33.5 1.0
HB3 A:SER158 4.7 41.1 1.0
O A:HIS197 4.7 37.9 1.0
H2 A:GOL507 4.9 0.7 1.0
OD1 A:ASP199 4.9 31.7 1.0
H32 A:GOL507 5.0 0.3 1.0

Calcium binding site 3 out of 4 in 4i4t

Go back to Calcium Binding Sites List in 4i4t
Calcium binding site 3 out of 4 in the Crystal Structure of Tubulin-RB3-Ttl-Zampanolide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Tubulin-RB3-Ttl-Zampanolide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:76.3
occ:1.00
OE2 B:GLU113 2.4 57.2 1.0
O B:HOH833 2.4 48.2 1.0
O B:HOH729 2.5 61.3 1.0
O B:HOH741 2.5 44.6 1.0
O B:HOH677 2.6 37.8 1.0
CD B:GLU113 3.4 47.8 1.0
OE1 B:GLU113 3.7 53.2 1.0
OE1 B:GLU110 3.8 38.1 1.0
OE2 B:GLU110 4.5 46.2 1.0
CD B:GLU110 4.5 43.5 1.0
HB2 B:GLU113 4.6 34.4 1.0
HA B:GLU110 4.6 34.2 1.0
HG B:SER97 4.7 0.9 1.0
HB3 B:GLU113 4.7 34.4 1.0
CG B:GLU113 4.7 38.4 1.0
O B:HOH655 4.7 44.1 1.0
CB B:GLU113 4.9 28.6 1.0

Calcium binding site 4 out of 4 in 4i4t

Go back to Calcium Binding Sites List in 4i4t
Calcium binding site 4 out of 4 in the Crystal Structure of Tubulin-RB3-Ttl-Zampanolide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Tubulin-RB3-Ttl-Zampanolide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:39.9
occ:1.00
O C:THR41 2.4 38.5 1.0
O C:HOH792 2.5 32.6 1.0
OG1 C:THR41 2.5 39.1 1.0
OE2 C:GLU55 2.6 36.3 1.0
OE1 C:GLU55 2.6 39.7 1.0
O C:GLY44 2.6 48.3 1.0
OD2 C:ASP39 2.6 45.9 1.0
OD1 C:ASP39 2.6 45.8 1.0
CD C:GLU55 2.9 42.2 1.0
CG C:ASP39 2.9 47.6 1.0
C C:THR41 3.4 51.1 1.0
CB C:THR41 3.5 56.4 1.0
C C:GLY44 3.5 53.3 1.0
HA3 C:GLY45 3.6 63.3 1.0
H C:THR41 3.6 47.2 1.0
HB C:THR41 3.6 67.7 1.0
H C:GLY44 3.7 56.5 1.0
HZ C:PHE49 3.8 43.2 1.0
CA C:THR41 3.8 43.7 1.0
HE2 C:HIS61 3.9 42.5 1.0
N C:THR41 4.1 39.4 1.0
HD21 C:ASN50 4.1 40.7 1.0
HE1 C:PHE49 4.2 44.5 1.0
N C:GLY45 4.3 49.9 1.0
O C:HOH613 4.3 38.5 1.0
CA C:GLY45 4.3 52.8 1.0
N C:GLY44 4.4 47.1 1.0
CG C:GLU55 4.4 38.6 1.0
CB C:ASP39 4.4 41.4 1.0
CA C:GLY44 4.4 47.5 1.0
OD1 C:ASP47 4.5 47.0 1.0
CZ C:PHE49 4.6 36.0 1.0
HA C:ILE42 4.6 49.0 1.0
OD1 C:ASN50 4.6 36.4 1.0
N C:ILE42 4.6 45.4 1.0
NE2 C:HIS61 4.6 35.5 1.0
HA2 C:GLY44 4.7 57.0 1.0
HG2 C:GLU55 4.8 46.3 1.0
HB3 C:ASP39 4.8 49.7 1.0
HG3 C:GLU55 4.8 46.3 1.0
CE1 C:PHE49 4.8 37.1 1.0
HA C:THR41 4.8 52.4 1.0
HA2 C:GLY45 4.8 63.3 1.0
H C:GLY43 4.8 46.3 1.0
CG2 C:THR41 4.9 51.0 1.0
ND2 C:ASN50 4.9 33.9 1.0
HB2 C:ASP39 4.9 49.7 1.0
O C:HOH735 4.9 40.9 1.0

Reference:

A.E.Prota, K.Bargsten, D.Zurwerra, J.J.Field, J.F.Diaz, K.H.Altmann, M.O.Steinmetz. Molecular Mechanism of Action of Microtubule-Stabilizing Anticancer Agents. Science V. 339 587 2013.
ISSN: ISSN 0036-8075
PubMed: 23287720
DOI: 10.1126/SCIENCE.1230582
Page generated: Sat Dec 12 04:51:04 2020

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