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Calcium in PDB 4iij: Crystal Structure of Tubulin-Stathmin-Ttl-Apo Complex

Protein crystallography data

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-Apo Complex, PDB code: 4iij was solved by A.E.Prota, M.M.Magiera, M.Kuijpers, K.Bargsten, D.Frey, M.Wieser, R.Jaussi, C.C.Hoogenraad, R.A.Kammerer, C.Janke, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 62.28 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 103.530, 155.910, 181.020, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 23.5

Other elements in 4iij:

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

Magnesium (Mg) 5 atoms
Chlorine (Cl) 1 atom

Calcium Binding Sites:

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

Calcium binding site 1 out of 3 in 4iij

Go back to Calcium Binding Sites List in 4iij
Calcium binding site 1 out of 3 in the Crystal Structure of Tubulin-Stathmin-Ttl-Apo 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-Apo Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:0.3
occ:1.00
OG1 A:THR41 2.7 0.3 1.0
OD1 A:ASP39 2.8 75.7 1.0
OE2 A:GLU55 2.9 86.7 1.0
HA3 A:GLY45 2.9 0.8 1.0
OE1 A:GLU55 2.9 98.1 1.0
O A:GLY44 2.9 99.7 1.0
OD2 A:ASP39 3.0 83.9 1.0
HZ A:PHE49 3.1 85.6 1.0
CD A:GLU55 3.2 94.2 1.0
CG A:ASP39 3.2 85.1 1.0
O A:THR41 3.3 0.7 1.0
HD22 A:ASN50 3.6 0.7 1.0
OD1 A:ASN50 3.7 89.0 1.0
OD1 A:ASP47 3.7 82.0 1.0
CZ A:PHE49 3.8 71.3 1.0
CA A:GLY45 3.8 86.5 1.0
C A:GLY44 3.8 94.0 1.0
CB A:THR41 3.9 0.7 1.0
HB A:THR41 3.9 0.3 1.0
HE1 A:PHE49 4.0 88.9 1.0
HE2 A:HIS61 4.1 0.4 1.0
H A:THR41 4.2 0.3 1.0
N A:GLY45 4.2 83.6 1.0
CE1 A:PHE49 4.2 74.1 1.0
ND2 A:ASN50 4.3 83.9 1.0
C A:THR41 4.3 0.4 1.0
HA2 A:GLY45 4.3 0.8 1.0
HB2 A:ASP47 4.4 83.7 1.0
CG A:ASN50 4.4 76.1 1.0
H A:GLY44 4.5 0.1 1.0
CA A:THR41 4.5 0.1 1.0
H A:ASP47 4.6 90.8 1.0
CB A:ASP39 4.6 80.4 1.0
C A:GLY45 4.6 91.7 1.0
CG A:GLU55 4.6 95.3 1.0
HB2 A:ASP39 4.7 96.5 1.0
CG A:ASP47 4.7 79.7 1.0
N A:THR41 4.7 0.8 1.0
CE2 A:PHE49 4.8 75.5 1.0
HG2 A:GLU55 4.8 0.4 1.0
NE2 A:HIS61 4.8 92.0 1.0
HE2 A:PHE49 4.9 90.6 1.0
HG3 A:GLU55 4.9 0.4 1.0
H A:GLY45 5.0 0.3 1.0
HG23 A:THR41 5.0 98.5 1.0

Calcium binding site 2 out of 3 in 4iij

Go back to Calcium Binding Sites List in 4iij
Calcium binding site 2 out of 3 in the Crystal Structure of Tubulin-Stathmin-Ttl-Apo 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-Apo Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:87.8
occ:1.00
OE1 B:GLU113 2.8 71.3 1.0
CD B:GLU113 3.6 72.8 1.0
OE2 B:GLU113 3.6 74.3 1.0
OE1 B:GLU110 4.3 53.6 1.0

Calcium binding site 3 out of 3 in 4iij

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

b:68.3
occ:1.00
OD2 C:ASP39 2.6 59.0 1.0
O C:THR41 2.6 66.3 1.0
OE2 C:GLU55 2.7 64.9 1.0
OG1 C:THR41 2.7 65.4 1.0
OE1 C:GLU55 2.7 54.2 1.0
OD1 C:ASP39 2.8 67.3 1.0
O C:GLY44 2.9 87.8 1.0
HG1 C:THR41 3.0 78.5 1.0
CD C:GLU55 3.0 56.2 1.0
CG C:ASP39 3.1 64.7 1.0
C C:GLY44 3.4 80.8 1.0
HA3 C:GLY45 3.5 93.8 1.0
C C:THR41 3.6 73.1 1.0
H C:GLY44 3.7 0.7 1.0
CB C:THR41 3.7 74.4 1.0
HB C:THR41 3.8 89.2 1.0
HZ C:PHE49 3.8 68.8 1.0
HE2 C:HIS61 3.9 69.0 1.0
N C:GLY45 4.0 71.9 1.0
H C:THR41 4.0 80.3 1.0
OD1 C:ASP47 4.0 70.2 1.0
HA2 C:GLY44 4.0 96.8 1.0
CA C:THR41 4.1 73.5 1.0
CA C:GLY44 4.1 80.7 1.0
CA C:GLY45 4.2 78.2 1.0
N C:GLY44 4.2 88.1 1.0
O C:HOH626 4.3 52.0 1.0
HD22 C:ASN50 4.3 76.2 1.0
N C:THR41 4.4 66.9 1.0
OD1 C:ASN50 4.4 55.0 1.0
CG C:GLU55 4.5 56.4 1.0
CB C:ASP39 4.6 68.4 1.0
CZ C:PHE49 4.6 57.3 1.0
H C:GLY45 4.6 86.3 1.0
NE2 C:HIS61 4.7 57.5 1.0
N C:ILE42 4.7 77.5 1.0
HA C:ILE42 4.7 77.5 1.0
HE1 C:PHE49 4.8 66.9 1.0
HA2 C:GLY45 4.8 93.8 1.0
HG3 C:GLU55 4.9 67.6 1.0
HB3 C:ASP39 4.9 82.0 1.0
HB2 C:ASP39 5.0 82.0 1.0
HG2 C:GLU55 5.0 67.6 1.0
HA C:THR41 5.0 88.2 1.0

Reference:

A.E.Prota, M.M.Magiera, M.Kuijpers, K.Bargsten, D.Frey, M.Wieser, R.Jaussi, C.C.Hoogenraad, R.A.Kammerer, C.Janke, M.O.Steinmetz. Structural Basis of Tubulin Tyrosination By Tubulin Tyrosine Ligase. J.Cell Biol. V. 200 259 2013.
ISSN: ISSN 0021-9525
PubMed: 23358242
DOI: 10.1083/JCB.201211017
Page generated: Tue Jul 8 22:55:45 2025

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