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Magnesium in PDB 4tuy: Tubulin-Rhizoxin Complex

Protein crystallography data

The structure of Tubulin-Rhizoxin Complex, PDB code: 4tuy was solved by A.E.Prota, K.Bargsten, J.F.Diaz, M.Marsh, C.Cuevas, M.Liniger, C.Neuhaus, J.M.Andreu, 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) 62.70 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.310, 156.920, 181.120, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 21.7

Other elements in 4tuy:

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

Calcium (Ca) 2 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 5 in 4tuy

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Magnesium binding site 1 out of 5 in the Tubulin-Rhizoxin Complex


Mono view


Stereo pair view

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

b:29.2
occ:1.00
O2G A:GTP501 2.0 22.8 1.0
O A:HOH844 2.0 28.1 1.0
O A:HOH620 2.1 25.0 1.0
O A:HOH624 2.1 32.5 1.0
O1B A:GTP501 2.1 25.6 1.0
O A:HOH623 2.2 33.0 1.0
PG A:GTP501 3.2 28.7 1.0
PB A:GTP501 3.3 24.9 1.0
O3B A:GTP501 3.6 37.4 1.0
O1G A:GTP501 3.7 33.3 1.0
OE1 A:GLU71 3.8 55.5 1.0
NZ B:LYS254 3.9 33.4 1.0
O3A A:GTP501 3.9 35.9 1.0
OD1 A:ASP69 4.1 35.1 1.0
CB A:GLN11 4.2 27.7 1.0
CB A:ASP98 4.3 31.2 1.0
OD2 A:ASP69 4.4 39.2 1.0
OD2 A:ASP98 4.4 37.8 1.0
O A:HOH784 4.4 53.0 1.0
N A:GLN11 4.4 33.2 1.0
O3G A:GTP501 4.5 26.3 1.0
O1A A:GTP501 4.5 32.1 1.0
O2B A:GTP501 4.6 31.4 1.0
OE1 A:GLN11 4.7 40.9 1.0
CG A:ASP69 4.7 36.7 1.0
CG A:ASP98 4.8 34.1 1.0
PA A:GTP501 4.8 29.2 1.0
CE B:LYS254 4.9 32.7 1.0
CA A:GLN11 4.9 30.9 1.0
CB A:GLU71 4.9 55.6 1.0
CD A:GLU71 4.9 61.8 1.0

Magnesium binding site 2 out of 5 in 4tuy

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Magnesium binding site 2 out of 5 in the Tubulin-Rhizoxin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Rhizoxin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:21.0
occ:1.00
O B:HOH620 2.1 32.0 1.0
OE1 B:GLN11 2.1 36.3 1.0
O1A B:GDP501 2.2 30.1 1.0
O C:HOH693 2.4 40.3 1.0
O B:HOH630 2.6 34.0 1.0
O B:HOH698 2.6 62.8 1.0
O B:HOH624 2.7 30.8 1.0
CD B:GLN11 3.3 37.1 1.0
PA B:GDP501 3.6 27.1 1.0
O3A B:GDP501 4.0 32.2 1.0
CB B:GLN11 4.1 26.8 1.0
OD2 B:ASP179 4.1 36.3 1.0
CG B:GLN11 4.2 32.6 1.0
NE2 B:GLN11 4.3 36.7 1.0
C5' B:GDP501 4.3 34.2 1.0
O B:HOH757 4.3 56.2 1.0
OD1 B:ASN101 4.4 34.5 1.0
O5' B:GDP501 4.4 29.2 1.0
O C:HOH821 4.4 46.1 1.0
O1B B:GDP501 4.5 23.9 1.0
OE1 C:GLU254 4.6 39.4 1.0
O B:HOH758 4.6 58.1 1.0
O2A B:GDP501 4.7 25.1 1.0
C8 B:GDP501 4.9 31.5 1.0
PB B:GDP501 5.0 27.6 1.0
CG B:ASP179 5.0 37.8 1.0

Magnesium binding site 3 out of 5 in 4tuy

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Magnesium binding site 3 out of 5 in the Tubulin-Rhizoxin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Rhizoxin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:25.7
occ:1.00
O1G C:GTP501 2.0 20.5 1.0
O C:HOH652 2.0 28.2 1.0
O1B C:GTP501 2.0 23.6 1.0
O C:HOH977 2.1 24.9 1.0
O C:HOH658 2.1 31.5 1.0
O C:HOH659 2.2 24.7 1.0
PG C:GTP501 3.2 26.9 1.0
PB C:GTP501 3.2 23.8 1.0
O3B C:GTP501 3.6 34.5 1.0
O2G C:GTP501 3.7 26.9 1.0
O3A C:GTP501 3.9 32.3 1.0
NZ D:LYS254 4.0 37.4 1.0
OE1 C:GLU71 4.0 46.8 1.0
OD1 C:ASP69 4.0 33.9 1.0
CG C:GLU71 4.1 38.1 1.0
OD2 C:ASP69 4.2 25.7 1.0
CB C:GLN11 4.2 22.1 1.0
N C:GLN11 4.4 21.8 1.0
CB C:ASP98 4.4 32.9 1.0
O3G C:GTP501 4.5 24.1 1.0
OD2 C:ASP98 4.5 39.1 1.0
CG C:ASP69 4.5 26.2 1.0
O1A C:GTP501 4.5 27.0 1.0
O2B C:GTP501 4.5 25.2 1.0
O C:HOH813 4.6 48.5 1.0
CD C:GLU71 4.6 43.5 1.0
OE1 C:GLN11 4.8 41.3 1.0
PA C:GTP501 4.8 29.5 1.0
CG C:ASP98 4.9 36.5 1.0
CA C:GLN11 4.9 27.3 1.0

Magnesium binding site 4 out of 5 in 4tuy

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Magnesium binding site 4 out of 5 in the Tubulin-Rhizoxin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Rhizoxin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:46.0
occ:1.00
O D:HOH770 2.1 43.7 1.0
OE1 D:GLN11 2.1 63.9 1.0
O1A D:GDP501 2.2 60.5 1.0
O D:HOH764 2.3 43.2 1.0
O D:HOH763 2.5 53.4 1.0
CD D:GLN11 3.3 74.1 1.0
PA D:GDP501 3.7 54.5 1.0
CB D:GLN11 4.2 58.2 1.0
NE2 D:GLN11 4.3 64.9 1.0
CG D:GLN11 4.3 69.3 1.0
C5' D:GDP501 4.3 54.5 1.0
O3A D:GDP501 4.3 46.2 1.0
O5' D:GDP501 4.5 60.6 1.0
O1B D:GDP501 4.5 37.9 1.0
O D:HOH689 4.7 49.2 1.0
O2A D:GDP501 4.7 58.0 1.0
C8 D:GDP501 4.9 42.4 1.0
OD1 D:ASN101 4.9 67.0 1.0

Magnesium binding site 5 out of 5 in 4tuy

Go back to Magnesium Binding Sites List in 4tuy
Magnesium binding site 5 out of 5 in the Tubulin-Rhizoxin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Rhizoxin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg402

b:61.1
occ:1.00
O2B F:ACP401 2.2 0.0 1.0
OE2 F:GLU331 2.5 84.3 1.0
O1G F:ACP401 2.7 0.8 1.0
OE1 F:GLU331 2.7 72.2 1.0
CD F:GLU331 3.0 74.2 1.0
OD1 F:ASN333 3.1 89.1 1.0
PB F:ACP401 3.5 88.0 1.0
O1B F:ACP401 3.8 92.6 1.0
PG F:ACP401 3.8 0.6 1.0
CG F:ASN333 4.1 78.3 1.0
O3G F:ACP401 4.1 0.9 1.0
NZ F:LYS74 4.2 66.3 1.0
C3B F:ACP401 4.4 90.0 1.0
CG F:GLU331 4.5 61.2 1.0
CE F:LYS74 4.5 72.6 1.0
ND2 F:ASN333 4.5 79.0 1.0
O3A F:ACP401 4.8 68.3 1.0
O1A F:ACP401 4.8 78.9 1.0

Reference:

A.E.Prota, K.Bargsten, J.F.Diaz, M.Marsh, C.Cuevas, M.Liniger, C.Neuhaus, J.M.Andreu, K.H.Altmann, M.O.Steinmetz. A New Tubulin-Binding Site and Pharmacophore For Microtubule-Destabilizing Anticancer Drugs. Proc.Natl.Acad.Sci.Usa V. 111 13817 2014.
ISSN: ESSN 1091-6490
PubMed: 25114240
DOI: 10.1073/PNAS.1408124111
Page generated: Tue Aug 20 04:16:45 2024

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