Atomistry » Calcium » PDB 5lia-5m27 » 5lxs
Atomistry »
  Calcium »
    PDB 5lia-5m27 »
      5lxs »

Calcium in PDB 5lxs: Tubulin-Ks-1-199-32 Complex

Protein crystallography data

The structure of Tubulin-Ks-1-199-32 Complex, PDB code: 5lxs 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) 72.23 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.580, 157.800, 179.440, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 22.7

Other elements in 5lxs:

The structure of Tubulin-Ks-1-199-32 Complex also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Tubulin-Ks-1-199-32 Complex (pdb code 5lxs). 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-Ks-1-199-32 Complex, PDB code: 5lxs:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5lxs

Go back to Calcium Binding Sites List in 5lxs
Calcium binding site 1 out of 4 in the Tubulin-Ks-1-199-32 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Ks-1-199-32 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:59.2
occ:1.00
O A:THR41 2.4 72.4 1.0
OD2 A:ASP39 2.5 57.9 1.0
OD1 A:ASP39 2.5 65.5 1.0
OE1 A:GLU55 2.6 62.8 1.0
O A:GLY44 2.6 71.8 1.0
OE2 A:GLU55 2.6 55.0 1.0
OG1 A:THR41 2.7 62.8 1.0
O A:HOH631 2.8 62.4 1.0
CG A:ASP39 2.8 64.7 1.0
CD A:GLU55 2.9 60.1 1.0
CB A:THR41 3.4 61.0 1.0
C A:THR41 3.4 73.5 1.0
C A:GLY44 3.5 70.2 1.0
CA A:THR41 3.8 68.1 1.0
N A:THR41 4.1 70.3 1.0
N A:GLY45 4.3 64.6 1.0
N A:GLY44 4.3 73.9 1.0
CA A:GLY45 4.3 64.3 1.0
CB A:ASP39 4.4 64.6 1.0
CA A:GLY44 4.4 78.4 1.0
CG A:GLU55 4.4 60.6 1.0
O A:HOH672 4.5 58.1 1.0
N A:ILE42 4.6 81.7 1.0
OD1 A:ASN50 4.6 50.5 1.0
CZ A:PHE49 4.6 52.9 1.0
CG2 A:THR41 4.8 60.8 1.0
NE2 A:HIS61 4.8 53.9 1.0
CE1 A:PHE49 5.0 54.5 1.0
OD2 A:ASP47 5.0 73.4 1.0

Calcium binding site 2 out of 4 in 5lxs

Go back to Calcium Binding Sites List in 5lxs
Calcium binding site 2 out of 4 in the Tubulin-Ks-1-199-32 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Ks-1-199-32 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:85.0
occ:1.00
O B:HOH705 2.4 54.0 1.0
OE1 B:GLU113 2.7 85.2 1.0
CD B:GLU113 3.5 78.4 1.0
OE2 B:GLU113 3.6 89.1 1.0
OE1 B:GLU110 4.1 45.2 1.0
OG B:SER97 4.5 86.8 1.0
CG B:GLU113 4.9 55.7 1.0

Calcium binding site 3 out of 4 in 5lxs

Go back to Calcium Binding Sites List in 5lxs
Calcium binding site 3 out of 4 in the Tubulin-Ks-1-199-32 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Ks-1-199-32 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:52.9
occ:1.00
O C:GLY44 2.4 55.1 1.0
OD2 C:ASP39 2.4 48.8 1.0
OG1 C:THR41 2.5 54.5 1.0
OE2 C:GLU55 2.5 41.4 1.0
O C:HOH605 2.5 51.9 1.0
OE1 C:GLU55 2.5 47.8 1.0
O C:THR41 2.6 53.2 1.0
OD1 C:ASP39 2.6 56.0 1.0
CD C:GLU55 2.9 47.9 1.0
CG C:ASP39 2.9 54.2 1.0
C C:GLY44 3.6 62.2 1.0
C C:THR41 3.6 60.9 1.0
CB C:THR41 3.6 59.4 1.0
CA C:THR41 4.0 61.8 1.0
CA C:GLY45 4.3 64.9 1.0
N C:THR41 4.3 59.0 1.0
OD1 C:ASN50 4.3 37.8 1.0
N C:GLY45 4.3 62.7 1.0
OD2 C:ASP47 4.4 71.4 1.0
CG C:GLU55 4.4 40.6 1.0
CB C:ASP39 4.4 57.1 1.0
CZ C:PHE49 4.5 49.1 1.0
N C:GLY44 4.6 72.2 1.0
CA C:GLY44 4.6 69.1 1.0
NE2 C:HIS61 4.7 37.9 1.0
O C:HOH683 4.7 49.3 1.0
N C:ILE42 4.8 63.7 1.0
ND2 C:ASN50 4.8 37.0 1.0
CG2 C:THR41 4.9 50.7 1.0
CE1 C:PHE49 4.9 47.6 1.0

Calcium binding site 4 out of 4 in 5lxs

Go back to Calcium Binding Sites List in 5lxs
Calcium binding site 4 out of 4 in the Tubulin-Ks-1-199-32 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Ks-1-199-32 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca201

b:82.2
occ:1.00
O A:HOH683 3.5 45.4 1.0
OD2 E:ASP44 3.5 90.0 1.0
OG A:SER158 4.1 48.8 1.0
O A:GLU196 4.4 45.2 1.0
NZ A:LYS166 4.4 36.4 1.0
CB A:SER158 4.5 40.8 1.0
O A:GLY162 4.6 54.7 1.0
CG E:ASP44 4.6 89.6 1.0
O A:HOH622 4.8 52.2 1.0
OD1 A:ASP199 4.9 45.0 1.0
CA A:HIS197 4.9 37.7 1.0
O A:HIS197 4.9 48.1 1.0

Reference:

A.E.Prota, K.Bargsten, M.Redondo-Horcajo, A.B.Smith, C.H.Yang, H.M.Mcdaid, I.Paterson, S.B.Horwitz, J.Fernando Diaz, M.O.Steinmetz. Structural Basis of Microtubule Stabilization By Discodermolide. Chembiochem V. 18 905 2017.
ISSN: ESSN 1439-7633
PubMed: 28207984
DOI: 10.1002/CBIC.201600696
Page generated: Mon Jul 15 07:50:24 2024

Last articles

Mg in 4Y52
Mg in 4Y30
Mg in 4Y2V
Mg in 4Y2X
Mg in 4Y2Y
Mg in 4Y2U
Mg in 4Y2T
Mg in 4Y2Q
Mg in 4Y2R
Mg in 4Y2S
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy