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Calcium in PDB 5kx5: Crystal Structure of Tubulin-Stathmin-Ttl-Compound 11 Complex

Protein crystallography data

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-Compound 11 Complex, PDB code: 5kx5 was solved by K.Parris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.47 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.790, 153.900, 185.200, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 25.1

Other elements in 5kx5:

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-Compound 11 Complex also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound 11 Complex (pdb code 5kx5). 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-Stathmin-Ttl-Compound 11 Complex, PDB code: 5kx5:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5kx5

Go back to Calcium Binding Sites List in 5kx5
Calcium binding site 1 out of 4 in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound 11 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-Stathmin-Ttl-Compound 11 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:94.5
occ:1.00
OD1 A:ASP39 2.1 87.1 1.0
O A:GLY44 2.2 82.5 1.0
O A:THR41 2.6 89.4 1.0
OE1 A:GLU55 2.6 93.3 1.0
OE2 A:GLU55 2.8 63.6 1.0
OG1 A:THR41 2.9 95.0 1.0
CG A:ASP39 2.9 89.7 1.0
OD2 A:ASP39 3.1 0.8 1.0
CD A:GLU55 3.1 89.9 1.0
C A:GLY44 3.3 84.1 1.0
C A:THR41 3.7 88.6 1.0
CB A:THR41 3.8 92.8 1.0
OD1 A:ASP47 3.9 92.8 1.0
CA A:GLY45 4.0 81.4 1.0
N A:GLY45 4.1 81.2 1.0
CZ A:PHE49 4.1 75.4 1.0
CA A:THR41 4.1 84.3 1.0
OD1 A:ASN50 4.3 75.7 1.0
CB A:ASP39 4.3 83.8 1.0
N A:THR41 4.4 84.5 1.0
N A:GLY44 4.4 82.1 1.0
CA A:GLY44 4.4 81.5 1.0
NE2 A:HIS61 4.5 81.1 1.0
ND2 A:ASN50 4.6 73.2 1.0
CE1 A:PHE49 4.6 76.4 1.0
CG A:GLU55 4.6 82.4 1.0
N A:ILE42 4.9 83.5 1.0
CG A:ASN50 4.9 81.5 1.0
CG A:ASP47 4.9 90.3 1.0

Calcium binding site 2 out of 4 in 5kx5

Go back to Calcium Binding Sites List in 5kx5
Calcium binding site 2 out of 4 in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound 11 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-Stathmin-Ttl-Compound 11 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:0.6
occ:1.00
OE2 B:GLU113 3.2 97.5 1.0
OE1 B:GLU110 4.1 53.7 1.0
CD B:GLU113 4.3 0.1 1.0
OE2 B:GLU110 4.7 56.8 1.0
OE1 B:GLU113 4.7 0.5 1.0
CD B:GLU110 4.8 64.5 1.0

Calcium binding site 3 out of 4 in 5kx5

Go back to Calcium Binding Sites List in 5kx5
Calcium binding site 3 out of 4 in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound 11 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-Stathmin-Ttl-Compound 11 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:71.5
occ:1.00
OE2 C:GLU55 2.2 73.8 1.0
O C:THR41 2.4 80.0 1.0
OD2 C:ASP39 2.4 72.2 1.0
OD1 C:ASP39 2.6 72.6 1.0
CG C:ASP39 2.9 71.8 1.0
CD C:GLU55 3.0 76.9 1.0
CB C:THR41 3.1 82.8 1.0
OE1 C:GLU55 3.1 91.0 1.0
OG1 C:THR41 3.2 82.7 1.0
OD2 C:ASP47 3.3 96.7 1.0
C C:THR41 3.3 79.5 1.0
C C:GLY44 3.5 83.8 1.0
N C:GLY45 3.5 80.5 1.0
CA C:THR41 3.6 72.5 1.0
O C:GLY44 3.6 82.4 1.0
CA C:GLY45 3.7 80.1 1.0
N C:THR41 4.1 71.7 1.0
CA C:GLY44 4.2 79.6 1.0
OD1 C:ASN50 4.3 54.8 1.0
CG2 C:THR41 4.3 82.3 1.0
CB C:ASP39 4.4 67.6 1.0
CG C:GLU55 4.4 54.1 1.0
CZ C:PHE49 4.5 53.4 1.0
CG C:ASP47 4.5 89.8 1.0
N C:GLY44 4.5 79.5 1.0
N C:ILE42 4.6 77.2 1.0
CE1 C:PHE49 4.7 55.2 1.0
C C:GLY45 4.8 83.2 1.0
NE2 C:HIS61 4.8 57.3 1.0

Calcium binding site 4 out of 4 in 5kx5

Go back to Calcium Binding Sites List in 5kx5
Calcium binding site 4 out of 4 in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound 11 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-Stathmin-Ttl-Compound 11 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca201

b:0.2
occ:1.00
O A:HOH601 2.8 52.2 1.0
OD2 E:ASP44 3.5 0.5 1.0
OG A:SER158 3.6 55.3 1.0
O A:GLU196 3.7 63.5 1.0
NZ A:LYS166 4.0 89.9 1.0
CA A:HIS197 4.1 59.5 1.0
CE A:LYS166 4.2 76.1 1.0
O A:HIS197 4.4 62.9 1.0
C A:HIS197 4.4 63.1 1.0
OD1 A:ASP199 4.5 52.9 1.0
CB A:SER158 4.6 52.7 1.0
CG E:ASP44 4.7 0.8 1.0
C A:GLU196 4.7 62.8 1.0
N A:HIS197 4.9 58.9 1.0

Reference:

C.A.Leverett, S.C.Sukuru, B.C.Vetelino, S.Musto, K.Parris, J.Pandit, F.Loganzo, A.H.Varghese, G.Bai, B.Liu, D.Liu, S.Hudson, V.R.Doppalapudi, J.Stock, C.J.O'donnell, C.Subramanyam. Design, Synthesis, and Cytotoxic Evaluation of Novel Tubulysin Analogues As Adc Payloads. Acs Med Chem Lett V. 7 999 2016.
ISSN: ISSN 1948-5875
PubMed: 27882198
DOI: 10.1021/ACSMEDCHEMLETT.6B00274
Page generated: Mon Jul 15 07:05:58 2024

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