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Magnesium in PDB 5lp6: Crystal Structure of Tubulin-Stathmin-Ttl-Thiocolchicine Complex

Protein crystallography data

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-Thiocolchicine Complex, PDB code: 5lp6 was solved by J.Marangon, M.Christodoulou, F.Casagrande, G.Tiana, L.Dalla Via, A.Aliverti, D.Passarella, G.Cappelletti, S.Ricagno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.85 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 103.619, 155.285, 180.445, 90.00, 90.00, 90.00
R / Rfree (%) 27.3 / 30.5

Other elements in 5lp6:

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

Calcium (Ca) 1 atom
Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Tubulin-Stathmin-Ttl-Thiocolchicine Complex (pdb code 5lp6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Tubulin-Stathmin-Ttl-Thiocolchicine Complex, PDB code: 5lp6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5lp6

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Magnesium binding site 1 out of 8 in the Crystal Structure of Tubulin-Stathmin-Ttl-Thiocolchicine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Tubulin-Stathmin-Ttl-Thiocolchicine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:68.2
occ:1.00
 O1B A:GTP501 2.4 83.4 1.0
O2G A:GTP501 2.5 84.5 1.0
O1G A:GTP501 3.1 84.0 1.0
PG A:GTP501 3.3 84.8 1.0
OE1 A:GLU71 3.5 77.5 1.0
PB A:GTP501 3.6 84.0 1.0
ND2 B:ASN249 3.7 89.7 1.0
OD1 A:ASP69 3.8 74.2 1.0
CG A:GLU71 3.9 77.2 1.0
O3B A:GTP501 3.9 85.2 1.0
OD2 A:ASP69 4.0 74.5 1.0
NZ B:LYS254 4.1 74.6 1.0
O3A A:GTP501 4.1 84.4 1.0
CD A:GLU71 4.2 77.5 1.0
CB A:GLN11 4.2 69.5 1.0
CG A:ASP69 4.4 74.3 1.0
OE1 A:GLN11 4.4 69.9 1.0
N A:GLN11 4.5 69.3 1.0
CB A:ASP98 4.6 74.0 1.0
O1A A:GTP501 4.7 84.5 1.0
O3G A:GTP501 4.7 83.2 1.0
CG A:ASP98 4.8 74.1 1.0
CA A:GLN11 4.9 69.2 1.0
PA A:GTP501 5.0 84.4 1.0
O2B A:GTP501 5.0 84.3 1.0

Magnesium binding site 2 out of 8 in 5lp6

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Magnesium binding site 2 out of 8 in the Crystal Structure of Tubulin-Stathmin-Ttl-Thiocolchicine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Tubulin-Stathmin-Ttl-Thiocolchicine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:95.3
occ:1.00
 O A:GLY44 2.3 82.6 1.0
OG1 A:THR41 2.4 81.8 1.0
OE2 A:GLU55 2.5 75.9 1.0
OD1 A:ASP39 2.7 80.0 1.0
O A:THR41 3.3 82.0 1.0
CG A:ASP39 3.4 80.2 1.0
C A:GLY44 3.4 82.7 1.0
OD1 A:ASN50 3.5 75.4 1.0
OD2 A:ASP39 3.5 80.0 1.0
CD A:GLU55 3.5 75.6 1.0
OD1 A:ASP47 3.5 81.7 1.0
CB A:THR41 3.6 81.8 1.0
OE1 A:GLU55 3.6 75.6 1.0
CA A:GLY45 3.7 83.1 1.0
CZ A:PHE49 4.0 77.9 1.0
N A:GLY45 4.0 82.9 1.0
CG A:ASP47 4.1 81.4 1.0
C A:THR41 4.2 82.1 1.0
ND2 A:ASN50 4.3 75.3 1.0
CG A:ASN50 4.3 75.2 1.0
C A:GLY45 4.3 83.1 1.0
CA A:THR41 4.4 81.8 1.0
N A:ASP46 4.5 82.9 1.0
OD2 A:ASP47 4.6 81.5 1.0
CE1 A:PHE49 4.6 77.9 1.0
CA A:GLY44 4.7 82.6 1.0
CE2 A:PHE49 4.7 78.0 1.0
CG2 A:THR41 4.7 81.8 1.0
N A:THR41 4.7 81.6 1.0
CB A:ASP39 4.7 80.2 1.0
CG A:GLU55 4.8 75.1 1.0
N A:GLY44 4.9 82.5 1.0
CB A:ASP47 4.9 81.2 1.0
O A:GLY45 4.9 83.2 1.0
N A:ASP47 5.0 81.6 1.0

Magnesium binding site 3 out of 8 in 5lp6

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Magnesium binding site 3 out of 8 in the Crystal Structure of Tubulin-Stathmin-Ttl-Thiocolchicine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Tubulin-Stathmin-Ttl-Thiocolchicine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg505

b:79.2
occ:1.00
 NZ A:LYS166 3.7 77.5 1.0
OD1 A:ASP199 3.9 76.4 1.0
O A:HIS197 4.3 77.5 1.0
O A:GLU196 4.4 78.4 1.0
O A:GLY162 4.5 78.4 1.0
OD2 A:ASP199 4.5 76.5 1.0
CG A:ASP199 4.6 76.3 1.0
C A:HIS197 4.8 77.3 1.0
CA A:HIS197 4.8 77.7 1.0
OG A:SER158 4.9 73.9 1.0
O A:LYS164 4.9 77.8 1.0
CE A:LYS166 5.0 77.2 1.0

Magnesium binding site 4 out of 8 in 5lp6

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Magnesium binding site 4 out of 8 in the Crystal Structure of Tubulin-Stathmin-Ttl-Thiocolchicine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Tubulin-Stathmin-Ttl-Thiocolchicine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg506

b:84.3
occ:1.00
 OE2 A:GLU411 3.0 73.9 1.0
OE1 A:GLU411 3.4 74.3 1.0
CD A:GLU411 3.5 74.2 1.0
O1S B:MES503 3.6 99.1 1.0
NH1 A:ARG105 4.0 69.4 1.0
O A:GLY410 4.3 74.6 1.0
CD E:ARG61 4.5 76.3 1.0
CB B:ASP163 4.7 73.7 1.0
CG A:GLU411 4.8 74.0 1.0
CG2 A:THR109 4.8 74.0 1.0

Magnesium binding site 5 out of 8 in 5lp6

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Magnesium binding site 5 out of 8 in the Crystal Structure of Tubulin-Stathmin-Ttl-Thiocolchicine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Tubulin-Stathmin-Ttl-Thiocolchicine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:88.0
occ:1.00
 O1A B:GDP501 2.6 78.5 1.0
NE2 B:GLN11 3.3 71.5 1.0
OD1 B:ASN101 3.3 70.3 1.0
OD2 B:ASP179 3.5 82.8 1.0
PA B:GDP501 3.9 79.0 1.0
ND2 B:ASN101 3.9 70.5 1.0
CG B:ASN101 4.0 70.3 1.0
O3A B:GDP501 4.0 79.1 1.0
OE1 C:GLU254 4.0 80.7 1.0
C5' B:GDP501 4.1 77.9 1.0
OE2 C:GLU254 4.4 80.5 1.0
O5' B:GDP501 4.4 77.7 1.0
CD C:GLU254 4.5 80.2 1.0
CG B:ASP179 4.5 82.7 1.0
CD B:GLN11 4.6 71.3 1.0
CB B:ASP179 4.8 82.0 1.0

Magnesium binding site 6 out of 8 in 5lp6

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Magnesium binding site 6 out of 8 in the Crystal Structure of Tubulin-Stathmin-Ttl-Thiocolchicine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Tubulin-Stathmin-Ttl-Thiocolchicine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg505

b:71.5
occ:1.00
 OE2 B:GLU113 2.9 87.0 1.0
OE1 B:GLU113 3.3 86.8 1.0
CD B:GLU113 3.4 86.4 1.0
OE1 B:GLU110 4.4 76.8 1.0
CG B:GLU113 4.9 85.2 1.0

Magnesium binding site 7 out of 8 in 5lp6

Go back to Magnesium Binding Sites List in 5lp6
Magnesium binding site 7 out of 8 in the Crystal Structure of Tubulin-Stathmin-Ttl-Thiocolchicine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Tubulin-Stathmin-Ttl-Thiocolchicine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg506

b:87.6
occ:1.00
 O B:HOH613 2.2 68.5 1.0
OD2 B:ASP116 3.3 78.9 1.0
CG B:ASP116 4.1 78.3 1.0
CB B:ASP116 4.1 78.1 1.0
OD1 B:ASP120 4.5 75.0 1.0
OD2 B:ASP120 4.5 75.5 1.0
CG B:ASP120 5.0 75.0 1.0

Magnesium binding site 8 out of 8 in 5lp6

Go back to Magnesium Binding Sites List in 5lp6
Magnesium binding site 8 out of 8 in the Crystal Structure of Tubulin-Stathmin-Ttl-Thiocolchicine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Tubulin-Stathmin-Ttl-Thiocolchicine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:56.0
occ:1.00
 O1B C:GTP501 2.3 79.1 1.0
O1G C:GTP501 2.5 78.5 1.0
PG C:GTP501 3.5 77.7 1.0
PB C:GTP501 3.6 78.6 1.0
O2G C:GTP501 3.6 78.1 1.0
OE1 C:GLU71 3.7 73.1 1.0
CB C:GLN11 3.8 72.9 1.0
O3B C:GTP501 3.9 78.7 1.0
OD1 C:ASP69 4.0 70.8 1.0
O3A C:GTP501 4.0 80.0 1.0
OD2 C:ASP69 4.1 71.1 1.0
CG C:GLU71 4.1 72.8 1.0
NZ D:LYS254 4.2 71.3 1.0
OE1 C:GLN11 4.2 73.0 1.0
N C:GLN11 4.2 72.5 1.0
CD C:GLU71 4.4 72.9 1.0
CG C:ASP69 4.5 71.0 1.0
OD2 C:ASP98 4.6 74.2 1.0
O1A C:GTP501 4.6 80.3 1.0
CA C:GLN11 4.7 72.7 1.0
O3G C:GTP501 4.9 77.0 1.0
O2B C:GTP501 4.9 79.5 1.0
CD C:GLN11 4.9 72.8 1.0
CG C:GLN11 4.9 72.8 1.0
CB C:ASP98 4.9 74.3 1.0
PA C:GTP501 4.9 79.9 1.0

Reference:

J.Marangon, M.S.Christodoulou, F.V.Casagrande, G.Tiana, L.Dalla Via, A.Aliverti, D.Passarella, G.Cappelletti, S.Ricagno. Tools For the Rational Design of Bivalent Microtubule-Targeting Drugs. Biochem. Biophys. Res. V. 479 48 2016COMMUN..
ISSN: ESSN 1090-2104
PubMed: 27613098
DOI: 10.1016/J.BBRC.2016.09.022
Page generated: Sun Sep 29 20:21:28 2024

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