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Magnesium in PDB 6fjm: Tubulin-Disorazole Z Complex

Protein crystallography data

The structure of Tubulin-Disorazole Z Complex, PDB code: 6fjm was solved by G.Menchon, A.E.Prota, D.Lucena Agell, P.Bucher, R.Jansen, H.Irschik, R.Mueller, I.Paterson, J.F.Diaz, 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) 55.97 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.390, 157.630, 179.630, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 21.3

Other elements in 6fjm:

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

Calcium (Ca) 7 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Tubulin-Disorazole Z Complex (pdb code 6fjm). 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-Disorazole Z Complex, PDB code: 6fjm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6fjm

Go back to Magnesium Binding Sites List in 6fjm
Magnesium binding site 1 out of 5 in the Tubulin-Disorazole Z Complex


Mono view


Stereo pair view

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

b:38.9
occ:1.00
O2G A:GTP501 2.1 36.5 1.0
O A:HOH614 2.1 38.8 1.0
O A:HOH658 2.1 34.4 1.0
O1B A:GTP501 2.2 36.1 1.0
O A:HOH645 2.2 35.2 1.0
O A:HOH644 2.3 44.2 1.0
PG A:GTP501 3.2 38.4 1.0
PB A:GTP501 3.3 39.6 1.0
O3B A:GTP501 3.6 52.5 1.0
NZ B:LYS254 3.7 52.7 1.0
O3A A:GTP501 3.7 44.9 1.0
O1G A:GTP501 3.8 37.5 1.0
OE2 A:GLU71 4.0 66.9 1.0
OD1 A:ASP69 4.1 52.3 1.0
CB A:GLN11 4.1 37.0 1.0
OD2 A:ASP69 4.3 48.8 1.0
N A:GLN11 4.3 42.7 1.0
CG A:GLU71 4.4 66.0 1.0
OD2 A:ASP98 4.4 54.1 1.0
O1A A:GTP501 4.4 37.6 1.0
CB A:ASP98 4.5 44.4 1.0
O3G A:GTP501 4.5 35.5 1.0
O2B A:GTP501 4.6 42.6 1.0
PA A:GTP501 4.6 39.3 1.0
CG A:ASP69 4.6 56.9 1.0
CD A:GLU71 4.7 65.2 1.0
NE2 A:GLN11 4.7 50.9 1.0
CG A:ASP98 4.8 50.3 1.0
CE B:LYS254 4.8 43.3 1.0
CA A:GLN11 4.8 44.3 1.0

Magnesium binding site 2 out of 5 in 6fjm

Go back to Magnesium Binding Sites List in 6fjm
Magnesium binding site 2 out of 5 in the Tubulin-Disorazole Z Complex


Mono view


Stereo pair view

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

b:33.7
occ:1.00
OE1 B:GLN11 2.1 51.4 1.0
O B:HOH619 2.1 46.7 1.0
O C:HOH693 2.2 55.8 1.0
O1A B:GDP501 2.3 39.1 1.0
O B:HOH667 2.4 43.6 1.0
O B:HOH610 2.6 42.4 1.0
CD B:GLN11 3.3 47.6 1.0
O B:HOH740 3.4 65.3 1.0
PA B:GDP501 3.5 37.5 1.0
O3A B:GDP501 3.7 45.2 1.0
OD2 B:ASP179 3.9 48.5 1.0
CB B:GLN11 4.0 35.9 1.0
CG B:GLN11 4.1 38.6 1.0
NE2 B:GLN11 4.3 48.9 1.0
C5' B:GDP501 4.3 40.8 1.0
O5' B:GDP501 4.3 42.0 1.0
ND2 B:ASN101 4.4 40.1 1.0
O C:HOH683 4.4 63.2 1.0
OE1 C:GLU254 4.5 50.5 1.0
O1B B:GDP501 4.6 33.1 1.0
O2A B:GDP501 4.7 37.1 1.0
PB B:GDP501 4.8 36.3 1.0
C8 B:GDP501 4.8 38.9 1.0
CG B:ASP179 4.9 48.0 1.0
OD1 B:ASN101 4.9 44.7 1.0

Magnesium binding site 3 out of 5 in 6fjm

Go back to Magnesium Binding Sites List in 6fjm
Magnesium binding site 3 out of 5 in the Tubulin-Disorazole Z Complex


Mono view


Stereo pair view

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

b:34.0
occ:1.00
O1G C:GTP501 2.0 33.0 1.0
O C:HOH661 2.0 33.7 1.0
O C:HOH737 2.1 32.3 1.0
O C:HOH630 2.1 39.4 1.0
O1B C:GTP501 2.1 31.3 1.0
O C:HOH653 2.2 35.2 1.0
PG C:GTP501 3.1 39.0 1.0
PB C:GTP501 3.1 31.8 1.0
O3B C:GTP501 3.5 42.4 1.0
O2G C:GTP501 3.5 40.3 1.0
O3A C:GTP501 3.7 42.5 1.0
NZ D:LYS254 3.9 45.0 1.0
OD1 C:ASP69 4.1 49.2 1.0
OE2 C:GLU71 4.1 56.3 1.0
OD2 C:ASP98 4.3 48.4 1.0
CB C:GLN11 4.3 29.0 1.0
CG C:GLU71 4.3 53.4 1.0
OD2 C:ASP69 4.3 38.0 1.0
CB C:ASP98 4.4 42.5 1.0
O3G C:GTP501 4.4 31.6 1.0
N C:GLN11 4.4 31.6 1.0
O2B C:GTP501 4.4 36.7 1.0
O1A C:GTP501 4.6 37.6 1.0
CG C:ASP69 4.6 42.1 1.0
CG C:ASP98 4.7 42.7 1.0
CD C:GLU71 4.7 56.7 1.0
PA C:GTP501 4.7 34.4 1.0
O C:HOH811 4.8 87.2 1.0
NE2 C:GLN11 4.9 46.4 1.0
CA C:GLN11 5.0 36.6 1.0
CE D:LYS254 5.0 42.3 1.0

Magnesium binding site 4 out of 5 in 6fjm

Go back to Magnesium Binding Sites List in 6fjm
Magnesium binding site 4 out of 5 in the Tubulin-Disorazole Z Complex


Mono view


Stereo pair view

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

b:51.3
occ:1.00
OE1 D:GLN11 1.9 81.0 1.0
O D:HOH618 2.0 51.8 1.0
O D:HOH707 2.3 60.4 1.0
O1A D:GDP501 2.3 65.9 1.0
O D:HOH663 2.9 66.4 1.0
CD D:GLN11 3.1 74.3 1.0
PA D:GDP501 3.8 60.3 1.0
CG D:GLN11 4.0 69.4 1.0
CB D:GLN11 4.0 69.2 1.0
NE2 D:GLN11 4.0 64.9 1.0
O3A D:GDP501 4.3 55.4 1.0
C5' D:GDP501 4.5 60.7 1.0
C8 D:GDP501 4.6 56.6 1.0
O2A D:GDP501 4.6 62.5 1.0
O5' D:GDP501 4.7 64.6 1.0
O1B D:GDP501 4.8 50.5 1.0
OD1 D:ASN101 5.0 77.9 1.0

Magnesium binding site 5 out of 5 in 6fjm

Go back to Magnesium Binding Sites List in 6fjm
Magnesium binding site 5 out of 5 in the Tubulin-Disorazole Z Complex


Mono view


Stereo pair view

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

b:0.1
occ:1.00
OE2 F:GLU331 2.6 0.8 1.0
O1G F:ACP401 2.7 1.0 1.0
O1B F:ACP401 2.7 0.0 1.0
OD1 F:ASN333 2.7 0.3 1.0
OE1 F:GLU331 2.9 0.1 1.0
CD F:GLU331 3.1 98.3 1.0
NZ F:LYS74 3.3 98.8 1.0
CG F:ASN333 3.8 89.9 1.0
PB F:ACP401 3.9 0.1 1.0
PG F:ACP401 3.9 0.8 1.0
O F:HOH513 4.2 81.9 1.0
ND2 F:ASN333 4.2 92.4 1.0
C3B F:ACP401 4.2 0.8 1.0
O2B F:ACP401 4.3 0.6 1.0
CE F:LYS74 4.5 92.6 1.0
CG F:GLU331 4.7 80.2 1.0
O3G F:ACP401 4.7 0.1 1.0
O F:HOH523 4.8 85.3 1.0

Reference:

G.Menchon, A.E.Prota, D.Lucena-Agell, P.Bucher, R.Jansen, H.Irschik, R.Muller, I.Paterson, J.F.Diaz, K.H.Altmann, M.O.Steinmetz. A Fluorescence Anisotropy Assay to Discover and Characterize Ligands Targeting the Maytansine Site of Tubulin. Nat Commun V. 9 2106 2018.
ISSN: ESSN 2041-1723
PubMed: 29844393
DOI: 10.1038/S41467-018-04535-8
Page generated: Tue Oct 1 00:31:22 2024

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