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Magnesium in PDB 8bde: Tubulin-Baccatin III Complex

Protein crystallography data

The structure of Tubulin-Baccatin III Complex, PDB code: 8bde was solved by A.E.Prota, D.Lucena-Agell, Y.Ma, J.Estevez-Gallego, S.Li, K.Bargsten, K.H.Altmann, N.Gaillard, S.Kamimura, T.Muehlethaler, F.Gago, M.A.Oliva, M.O.Steinmetz, W.S.Fang, J.F.Diaz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.20 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.1, 157.15, 179.15, 90, 90, 90
R / Rfree (%) 19.2 / 21.8

Other elements in 8bde:

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

Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Tubulin-Baccatin III Complex (pdb code 8bde). 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-Baccatin III Complex, PDB code: 8bde:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 8bde

Go back to Magnesium Binding Sites List in 8bde
Magnesium binding site 1 out of 5 in the Tubulin-Baccatin III Complex


Mono view


Stereo pair view

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

b:36.0
occ:1.00
O A:HOH664 2.0 34.8 1.0
O2G A:GTP501 2.0 30.6 1.0
O A:HOH708 2.1 37.2 1.0
O A:HOH656 2.1 36.7 1.0
O1B A:GTP501 2.1 30.0 1.0
O A:HOH685 2.2 34.8 1.0
PG A:GTP501 3.1 33.5 1.0
PB A:GTP501 3.2 34.1 1.0
O3G A:GTP501 3.6 36.1 1.0
O3B A:GTP501 3.6 40.5 1.0
O3A A:GTP501 3.7 35.2 1.0
NZ B:LYS254 3.7 36.2 1.0
OE2 A:GLU71 4.0 65.5 1.0
OD1 A:ASP69 4.1 41.6 1.0
CB A:GLN11 4.2 34.5 1.0
OD2 A:ASP69 4.3 40.1 1.0
CG A:GLU71 4.3 55.0 1.0
OD2 A:ASP98 4.4 40.1 1.0
CB A:ASP98 4.4 35.5 1.0
N A:GLN11 4.4 39.9 1.0
O1G A:GTP501 4.4 36.7 1.0
O1A A:GTP501 4.5 34.5 1.0
O2B A:GTP501 4.5 35.1 1.0
NE2 A:GLN11 4.5 43.9 1.0
CG A:ASP69 4.6 43.0 1.0
PA A:GTP501 4.7 35.1 1.0
CD A:GLU71 4.7 61.1 1.0
CG A:ASP98 4.7 42.3 1.0
CE B:LYS254 4.8 35.1 1.0
CA A:GLN11 4.9 34.0 1.0

Magnesium binding site 2 out of 5 in 8bde

Go back to Magnesium Binding Sites List in 8bde
Magnesium binding site 2 out of 5 in the Tubulin-Baccatin III Complex


Mono view


Stereo pair view

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

b:29.8
occ:1.00
O1A B:GDP501 2.3 33.5 1.0
OE1 B:GLN11 2.3 40.9 1.0
O B:HOH625 2.3 43.0 1.0
O C:HOH674 2.4 47.6 1.0
O B:HOH693 2.5 42.3 1.0
O B:HOH613 2.5 43.3 1.0
O B:HOH728 2.7 67.6 1.0
CD B:GLN11 3.5 45.0 1.0
PA B:GDP501 3.6 33.5 1.0
OD2 B:ASP179 3.8 41.7 1.0
O3A B:GDP501 3.9 34.8 1.0
CB B:GLN11 4.1 32.8 1.0
CG B:GLN11 4.2 38.9 1.0
OD1 B:ASN101 4.3 38.8 1.0
C5' B:GDP501 4.4 33.8 1.0
O5' B:GDP501 4.4 33.5 1.0
NE2 B:GLN11 4.5 46.5 1.0
OE1 C:GLU254 4.5 46.1 1.0
O1B B:GDP501 4.6 29.4 1.0
O C:HOH656 4.6 49.6 1.0
O2A B:GDP501 4.7 33.3 1.0
C8 B:GDP501 4.8 36.1 1.0
CG B:ASP179 4.9 40.1 1.0
PB B:GDP501 4.9 30.4 1.0
O B:HOH710 4.9 56.1 1.0

Magnesium binding site 3 out of 5 in 8bde

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


Mono view


Stereo pair view

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

b:32.3
occ:1.00
O C:HOH694 2.0 32.3 1.0
O1B C:GTP501 2.0 33.7 1.0
O1G C:GTP501 2.0 32.3 1.0
O C:HOH769 2.1 33.8 1.0
O C:HOH692 2.1 31.3 1.0
O C:HOH684 2.1 31.0 1.0
PB C:GTP501 3.2 31.7 1.0
PG C:GTP501 3.2 33.0 1.0
O3B C:GTP501 3.5 36.6 1.0
O2G C:GTP501 3.6 33.5 1.0
O3A C:GTP501 3.7 33.2 1.0
OE1 C:GLU71 3.9 52.3 1.0
NZ D:LYS254 3.9 33.6 1.0
OD1 C:ASP69 4.0 35.4 1.0
CB C:GLN11 4.2 29.9 1.0
CG C:GLU71 4.2 40.9 1.0
OD2 C:ASP69 4.2 35.2 1.0
OD2 C:ASP98 4.3 39.7 1.0
N C:GLN11 4.4 30.7 1.0
CB C:ASP98 4.4 39.7 1.0
O2B C:GTP501 4.4 32.9 1.0
O3G C:GTP501 4.5 29.8 1.0
CD C:GLU71 4.6 46.5 1.0
CG C:ASP69 4.6 35.4 1.0
O1A C:GTP501 4.6 30.4 1.0
CG C:ASP98 4.7 38.5 1.0
PA C:GTP501 4.8 31.1 1.0
OE1 C:GLN11 4.8 42.0 1.0
CA C:GLN11 4.9 29.9 1.0

Magnesium binding site 4 out of 5 in 8bde

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


Mono view


Stereo pair view

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

b:82.6
occ:1.00
O D:HOH670 2.0 75.6 1.0
OE1 D:GLN11 2.1 85.6 1.0
O1A D:GDP501 2.4 58.4 1.0
O D:HOH688 2.7 64.4 1.0
O D:HOH606 2.8 71.4 1.0
CD D:GLN11 3.4 67.5 1.0
PA D:GDP501 3.7 55.6 1.0
O D:HOH707 3.9 63.1 1.0
O3A D:GDP501 4.0 52.4 1.0
NE2 D:GLN11 4.2 62.2 1.0
OD1 D:ASN101 4.3 75.6 1.0
C5' D:GDP501 4.3 59.3 1.0
CB D:GLN11 4.3 51.7 1.0
CG D:GLN11 4.3 61.2 1.0
O5' D:GDP501 4.5 58.5 1.0
O2A D:GDP501 4.8 54.6 1.0
O1B D:GDP501 4.8 45.5 1.0

Magnesium binding site 5 out of 5 in 8bde

Go back to Magnesium Binding Sites List in 8bde
Magnesium binding site 5 out of 5 in the Tubulin-Baccatin III Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Baccatin III Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg401

b:82.3
occ:1.00
O F:HOH514 2.1 85.5 1.0
OE1 F:GLU331 2.3 105.5 1.0
O2B F:ACP402 2.4 125.7 1.0
OD1 F:ASN333 2.5 97.4 1.0
O1G F:ACP402 2.6 134.7 1.0
CD F:GLU331 3.0 98.4 1.0
OE2 F:GLU331 3.0 104.0 1.0
O3G F:ACP402 3.3 135.0 1.0
PG F:ACP402 3.4 134.8 1.0
PB F:ACP402 3.7 123.9 1.0
CG F:ASN333 3.7 86.9 1.0
NZ F:LYS74 4.1 95.8 1.0
O1B F:ACP402 4.1 123.7 1.0
C3B F:ACP402 4.2 129.8 1.0
ND2 F:ASN333 4.2 83.2 1.0
CG F:GLU331 4.4 82.0 1.0
O2G F:ACP402 4.8 133.2 1.0
CE F:LYS74 4.9 90.9 1.0
CB F:ASN333 4.9 73.3 1.0
O3A F:ACP402 5.0 118.1 1.0

Reference:

A.E.Prota, D.Lucena-Agell, Y.Ma, J.Estevez-Gallego, S.Li, K.Bargsten, F.Josa-Prado, K.H.Altmann, N.Gaillard, S.Kamimura, T.Muhlethaler, F.Gago, M.A.Oliva, M.O.Steinmetz, W.S.Fang, J.F.Diaz. Structural Insight Into the Stabilization of Microtubules By Taxanes. Elife V. 12 2023.
ISSN: ESSN 2050-084X
PubMed: 36876916
DOI: 10.7554/ELIFE.84791
Page generated: Thu Oct 3 19:17:55 2024

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