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Calcium in PDB 6fjm: Tubulin-Disorazole Z Complex

Protein crystallography data

The structure of Tubulin-Disorazole Z Complex, PDB code: 6fjm was solved by G.Menchon, A.E.Prota, D.Lucena Agell, P.Bucher, R.Jansen, H.Irschik, R.Mueller, I.Paterson, J.F.Diaz, K.-H.Altmann, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.97 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.390, 157.630, 179.630, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 21.3

Other elements in 6fjm:

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

Magnesium (Mg) 5 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Tubulin-Disorazole Z Complex (pdb code 6fjm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Tubulin-Disorazole Z Complex, PDB code: 6fjm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 6fjm

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Calcium binding site 1 out of 7 in the Tubulin-Disorazole Z Complex


Mono view


Stereo pair view

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

b:81.9
occ:1.00
 O A:THR41 2.3 91.3 1.0
OD2 A:ASP39 2.3 76.2 1.0
O A:GLY44 2.3 80.5 1.0
OD1 A:ASP39 2.4 83.7 1.0
OE2 A:GLU55 2.6 72.7 1.0
O A:HOH610 2.6 91.5 1.0
OE1 A:GLU55 2.6 85.7 1.0
CG A:ASP39 2.7 84.0 1.0
OG1 A:THR41 2.7 74.6 1.0
CD A:GLU55 2.9 82.7 1.0
C A:THR41 3.4 90.0 1.0
C A:GLY44 3.5 94.3 1.0
CB A:THR41 3.5 80.4 1.0
CA A:THR41 3.9 89.6 1.0
N A:THR41 4.1 85.9 1.0
CB A:ASP39 4.2 82.0 1.0
N A:GLY44 4.2 93.8 1.0
N A:GLY45 4.4 1.0 1.0
CZ A:PHE49 4.4 75.4 1.0
CG A:GLU55 4.4 72.7 1.0
CA A:GLY45 4.4 0.2 1.0
CA A:GLY44 4.5 94.0 1.0
N A:ILE42 4.5 92.1 1.0
NE2 A:HIS61 4.6 77.6 1.0
OD2 A:ASP47 4.6 77.6 1.0
OD1 A:ASN50 4.7 76.5 1.0
CG2 A:THR41 4.9 80.2 1.0
ND2 A:ASN50 4.9 67.0 1.0
CA A:ILE42 4.9 96.4 1.0
CE1 A:PHE49 5.0 71.8 1.0
N A:GLY43 5.0 95.1 1.0
CA A:ASP39 5.0 90.4 1.0
C A:ASP39 5.0 89.8 1.0

Calcium binding site 2 out of 7 in 6fjm

Go back to Calcium Binding Sites List in 6fjm
Calcium binding site 2 out of 7 in the Tubulin-Disorazole Z Complex


Mono view


Stereo pair view

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

b:0.2
occ:1.00
 O B:HOH712 2.3 97.8 1.0
O B:HOH684 4.0 62.8 1.0
OD1 B:ASP120 4.2 68.6 1.0
OD2 B:ASP116 4.3 76.4 1.0
OD2 B:ASP120 4.3 67.1 1.0
CB B:ASP116 4.5 51.8 1.0
O B:HOH668 4.6 81.6 1.0
CG B:ASP116 4.6 60.9 1.0
CG B:ASP120 4.7 62.8 1.0

Calcium binding site 3 out of 7 in 6fjm

Go back to Calcium Binding Sites List in 6fjm
Calcium binding site 3 out of 7 in the Tubulin-Disorazole Z Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Disorazole Z Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca505

b:0.9
occ:1.00
 O B:HOH617 2.3 77.3 1.0
OE1 B:GLU113 2.8 93.9 1.0
OE2 B:GLU113 3.5 92.5 1.0
CD B:GLU113 3.5 85.4 1.0
OE1 B:GLU110 4.7 51.1 1.0

Calcium binding site 4 out of 7 in 6fjm

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Calcium binding site 4 out of 7 in the Tubulin-Disorazole Z Complex


Mono view


Stereo pair view

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

b:58.1
occ:1.00
 O C:GLY44 2.4 66.2 1.0
O C:HOH602 2.4 49.4 1.0
O C:THR41 2.4 65.8 1.0
OE1 C:GLU55 2.4 48.1 1.0
OD2 C:ASP39 2.5 53.3 1.0
OG1 C:THR41 2.5 55.5 1.0
OE2 C:GLU55 2.5 57.0 1.0
OD1 C:ASP39 2.6 58.4 1.0
CD C:GLU55 2.8 58.1 1.0
CG C:ASP39 2.9 57.9 1.0
C C:THR41 3.4 70.4 1.0
CB C:THR41 3.5 65.8 1.0
C C:GLY44 3.5 74.8 1.0
CA C:THR41 3.9 71.1 1.0
N C:THR41 4.2 65.4 1.0
CA C:GLY45 4.2 66.3 1.0
OD2 C:ASP47 4.3 68.0 1.0
N C:GLY45 4.3 71.2 1.0
CG C:GLU55 4.3 52.1 1.0
O C:HOH620 4.4 52.8 1.0
CB C:ASP39 4.4 63.0 1.0
N C:GLY44 4.4 66.2 1.0
CZ C:PHE49 4.5 48.4 1.0
OD1 C:ASN50 4.5 43.8 1.0
CA C:GLY44 4.5 74.7 1.0
N C:ILE42 4.6 70.1 1.0
NE2 C:HIS61 4.7 50.0 1.0
CG2 C:THR41 4.8 58.3 1.0
ND2 C:ASN50 4.9 41.6 1.0
CE1 C:PHE49 4.9 47.6 1.0

Calcium binding site 5 out of 7 in 6fjm

Go back to Calcium Binding Sites List in 6fjm
Calcium binding site 5 out of 7 in the Tubulin-Disorazole Z Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Tubulin-Disorazole Z Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca504

b:99.9
occ:1.00
 NH1 D:ARG308 3.1 91.6 1.0
CZ D:ARG308 3.8 96.8 1.0
NH2 D:ARG308 4.0 0.8 1.0
CG D:ASN339 4.1 61.2 1.0
OD1 D:ASN339 4.1 57.7 1.0
CB D:ASN339 4.2 45.0 1.0
CE2 D:TYR312 4.3 47.3 1.0
CD1 D:PHE296 4.4 60.5 1.0
O D:PHE296 4.5 66.1 1.0
ND2 D:ASN339 4.5 60.2 1.0
CD2 D:TYR342 4.6 49.8 1.0
CB D:PHE296 4.6 50.5 1.0
OH D:TYR312 4.8 64.2 1.0
NE D:ARG308 4.8 93.1 1.0
CG D:PHE296 4.9 57.5 1.0
CG D:ARG308 4.9 63.8 1.0
CB D:TYR342 4.9 47.2 1.0
CG D:TYR342 4.9 51.4 1.0

Calcium binding site 6 out of 7 in 6fjm

Go back to Calcium Binding Sites List in 6fjm
Calcium binding site 6 out of 7 in the Tubulin-Disorazole Z Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Tubulin-Disorazole Z Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca505

b:0.3
occ:1.00
 O D:PRO222 3.7 74.3 1.0
CE2 D:TYR224 3.9 70.9 1.0
CD2 D:TYR224 4.0 69.7 1.0
CZ D:TYR224 4.4 70.8 1.0
O D:VAL177 4.4 74.9 1.0
N D:TYR224 4.4 62.9 1.0
CA D:THR223 4.5 68.8 1.0
C D:THR223 4.6 75.8 1.0
CG D:TYR224 4.6 70.5 1.0
CG1 D:VAL177 4.7 65.1 1.0
C D:PRO222 4.8 76.1 1.0
OH D:TYR224 4.9 78.4 1.0
CE1 D:TYR224 4.9 68.1 1.0
CD1 D:TYR224 5.0 66.9 1.0

Calcium binding site 7 out of 7 in 6fjm

Go back to Calcium Binding Sites List in 6fjm
Calcium binding site 7 out of 7 in the Tubulin-Disorazole Z Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Tubulin-Disorazole Z Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca201

b:0.9
occ:1.00
 O A:HOH678 3.2 79.7 1.0
O A:HOH711 3.3 75.4 1.0
OD2 E:ASP44 3.4 0.7 1.0
O A:HOH685 3.4 55.4 1.0
OG A:SER158 3.7 59.3 1.0
CB A:SER158 4.0 57.3 1.0
NZ A:LYS166 4.1 54.1 1.0
O A:GLY162 4.2 83.4 1.0
CG E:ASP44 4.6 0.7 1.0
CA A:SER158 4.6 63.6 1.0
O A:GLU196 4.6 67.6 1.0
O A:HIS197 5.0 58.9 1.0
CA A:HIS197 5.0 57.5 1.0

Reference:

G.Menchon, A.E.Prota, D.Lucena-Agell, P.Bucher, R.Jansen, H.Irschik, R.Muller, I.Paterson, J.F.Diaz, K.H.Altmann, M.O.Steinmetz. A Fluorescence Anisotropy Assay to Discover and Characterize Ligands Targeting the Maytansine Site of Tubulin. Nat Commun V. 9 2106 2018.
ISSN: ESSN 2041-1723
PubMed: 29844393
DOI: 10.1038/S41467-018-04535-8
Page generated: Tue Jul 16 07:48:13 2024

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