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Calcium in PDB 5nfz: Tubulin-Mtc Complex

Protein crystallography data

The structure of Tubulin-Mtc Complex, PDB code: 5nfz was solved by J.J.Field, B.Pera, J.Estevez Gallego, E.Calvo, J.Rodriguez-Salarichs, G.Saez-Calvo, D.Zuwerra, M.Jordi, A.E.Prota, G.Menchon, J.H.Miller, K.-H.Altmann, J.F.Diaz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.78 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.163, 158.787, 180.376, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 21.8

Other elements in 5nfz:

The structure of Tubulin-Mtc Complex also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Tubulin-Mtc Complex (pdb code 5nfz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Tubulin-Mtc Complex, PDB code: 5nfz:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5nfz

Go back to Calcium Binding Sites List in 5nfz
Calcium binding site 1 out of 4 in the Tubulin-Mtc Complex


Mono view


Stereo pair view

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

b:69.1
occ:1.00
O A:GLY44 2.3 80.4 1.0
OD2 A:ASP39 2.3 70.9 1.0
OD1 A:ASP39 2.5 73.2 1.0
O A:THR41 2.5 82.4 1.0
O A:HOH603 2.6 66.1 1.0
OE2 A:GLU55 2.6 61.4 1.0
OG1 A:THR41 2.6 70.5 1.0
OE1 A:GLU55 2.7 71.4 1.0
CG A:ASP39 2.7 71.0 1.0
CD A:GLU55 2.9 66.5 1.0
C A:GLY44 3.4 83.8 1.0
C A:THR41 3.6 81.3 1.0
CB A:THR41 3.6 80.3 1.0
CA A:THR41 4.0 85.6 1.0
CA A:GLY45 4.2 80.4 1.0
N A:GLY45 4.2 84.6 1.0
CB A:ASP39 4.3 71.4 1.0
N A:THR41 4.3 89.7 1.0
O A:HOH661 4.3 61.4 1.0
CZ A:PHE49 4.4 65.6 1.0
N A:GLY44 4.4 82.6 1.0
CG A:GLU55 4.4 65.7 1.0
CA A:GLY44 4.5 85.2 1.0
OD2 A:ASP47 4.5 78.9 1.0
OD1 A:ASN50 4.6 63.6 1.0
CE1 A:PHE49 4.7 69.0 1.0
N A:ILE42 4.7 83.4 1.0
NE2 A:HIS61 4.8 65.2 1.0
ND2 A:ASN50 4.9 61.9 1.0
CG2 A:THR41 4.9 74.3 1.0

Calcium binding site 2 out of 4 in 5nfz

Go back to Calcium Binding Sites List in 5nfz
Calcium binding site 2 out of 4 in the Tubulin-Mtc Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Mtc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:96.9
occ:1.00
O E:HOH204 2.4 70.2 1.0
O A:HOH655 2.9 63.1 1.0
O A:HOH683 3.3 66.8 1.0
OD2 E:ASP44 3.8 0.2 1.0
OG A:SER158 3.9 54.0 1.0
NZ A:LYS166 4.0 46.4 1.0
O A:GLY162 4.0 76.8 1.0
O A:HOH636 4.2 67.0 1.0
O A:HOH664 4.3 70.7 1.0
CB A:SER158 4.5 53.1 1.0
O A:LYS164 4.8 53.2 1.0
O A:HIS197 4.8 53.3 1.0
CA A:SER158 4.9 56.4 1.0
O A:GLU196 4.9 61.8 1.0
CG E:ASP44 5.0 0.4 1.0

Calcium binding site 3 out of 4 in 5nfz

Go back to Calcium Binding Sites List in 5nfz
Calcium binding site 3 out of 4 in the Tubulin-Mtc Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Mtc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:86.4
occ:1.00
O B:HOH642 2.4 59.8 1.0
OE1 B:GLU113 2.5 78.1 1.0
OE2 B:GLU113 3.1 80.8 1.0
CD B:GLU113 3.2 74.1 1.0
CG B:GLU113 4.6 63.6 1.0
OE1 B:GLU110 4.7 52.1 1.0

Calcium binding site 4 out of 4 in 5nfz

Go back to Calcium Binding Sites List in 5nfz
Calcium binding site 4 out of 4 in the Tubulin-Mtc Complex


Mono view


Stereo pair view

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

b:54.0
occ:1.00
OE1 C:GLU55 2.4 44.9 1.0
O C:HOH602 2.4 45.9 1.0
O C:THR41 2.4 58.6 1.0
OD2 C:ASP39 2.4 55.0 1.0
O C:GLY44 2.5 61.6 1.0
OG1 C:THR41 2.5 53.9 1.0
OE2 C:GLU55 2.5 47.7 1.0
OD1 C:ASP39 2.6 59.8 1.0
CD C:GLU55 2.8 46.8 1.0
CG C:ASP39 2.8 54.9 1.0
C C:THR41 3.5 61.8 1.0
C C:GLY44 3.5 68.5 1.0
CB C:THR41 3.6 54.5 1.0
CA C:THR41 3.9 58.3 1.0
N C:THR41 4.2 58.4 1.0
N C:GLY45 4.3 70.0 1.0
CA C:GLY45 4.3 70.4 1.0
OD2 C:ASP47 4.3 65.8 1.0
CG C:GLU55 4.3 43.1 1.0
CB C:ASP39 4.3 57.5 1.0
O C:HOH620 4.4 60.5 1.0
N C:GLY44 4.4 70.2 1.0
CA C:GLY44 4.5 66.5 1.0
OD1 C:ASN50 4.6 47.3 1.0
N C:ILE42 4.6 64.0 1.0
NE2 C:HIS61 4.6 45.6 1.0
CZ C:PHE49 4.7 49.6 1.0
CG2 C:THR41 4.9 48.0 1.0
CE1 C:PHE49 4.9 46.3 1.0
ND2 C:ASN50 5.0 43.4 1.0

Reference:

J.J.Field, B.Pera, J.E.Gallego, E.Calvo, J.Rodriguez-Salarichs, G.Saez-Calvo, D.Zuwerra, M.Jordi, J.M.Andreu, A.E.Prota, G.Menchon, J.H.Miller, K.H.Altmann, J.F.Diaz. Zampanolide Binding to Tubulin Indicates Cross-Talk of Taxane Site with Colchicine and Nucleotide Sites. J. Nat. Prod. V. 81 494 2018.
ISSN: ESSN 1520-6025
PubMed: 29023132
DOI: 10.1021/ACS.JNATPROD.7B00704
Page generated: Mon Jul 15 09:02:11 2024

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