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Magnesium in PDB 7z2n: Tubulin-18-Complex

Protein crystallography data

The structure of Tubulin-18-Complex, PDB code: 7z2n was solved by T.Muehlethaler, A.E.Prota, A.Cavalli, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.82 / 2.17
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.016, 157.703, 180.154, 90, 90, 90
R / Rfree (%) 18.9 / 22.4

Other elements in 7z2n:

The structure of Tubulin-18-Complex also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Tubulin-18-Complex (pdb code 7z2n). 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-18-Complex, PDB code: 7z2n:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 7z2n

Go back to Magnesium Binding Sites List in 7z2n
Magnesium binding site 1 out of 5 in the Tubulin-18-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-18-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:39.2
occ:1.00
O A:HOH636 2.0 37.8 1.0
O1G A:GTP501 2.1 33.0 1.0
O A:HOH673 2.1 39.4 1.0
O A:HOH694 2.1 39.5 1.0
O A:HOH631 2.2 38.5 1.0
O1B A:GTP501 2.2 34.6 1.0
PG A:GTP501 3.3 41.3 1.0
PB A:GTP501 3.3 36.3 1.0
O3B A:GTP501 3.6 45.7 1.0
O3A A:GTP501 3.7 43.5 1.0
OE1 A:GLU71 3.7 57.9 1.0
O2G A:GTP501 3.8 41.5 1.0
NZ B:LYS254 3.9 44.7 1.0
CB A:GLN11 4.1 37.4 1.0
OD1 A:ASP69 4.1 40.1 1.0
OD2 A:ASP98 4.2 46.2 1.0
OD2 A:ASP69 4.2 43.4 1.0
N A:GLN11 4.4 40.4 1.0
CB A:ASP98 4.4 43.9 1.0
OE1 A:GLN11 4.5 49.9 1.0
O3G A:GTP501 4.5 38.9 1.0
O1A A:GTP501 4.6 41.6 1.0
O2B A:GTP501 4.6 42.7 1.0
CG A:ASP69 4.6 47.6 1.0
CG A:ASP98 4.7 48.9 1.0
PA A:GTP501 4.7 41.2 1.0
CA A:GLN11 4.8 42.9 1.0
O B:HOH635 4.8 57.4 1.0
CD A:GLU71 4.9 55.9 1.0

Magnesium binding site 2 out of 5 in 7z2n

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Magnesium binding site 2 out of 5 in the Tubulin-18-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-18-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:37.9
occ:1.00
O B:HOH625 2.0 44.0 1.0
OE1 B:GLN11 2.2 50.2 1.0
O1A B:GDP501 2.3 40.6 1.0
O B:HOH605 2.3 48.1 1.0
O C:HOH676 2.3 52.2 1.0
O B:HOH697 2.4 46.5 1.0
O C:HOH788 3.3 61.7 1.0
CD B:GLN11 3.4 54.7 1.0
PA B:GDP501 3.5 39.6 1.0
OD2 B:ASP179 3.7 53.5 1.0
O3A B:GDP501 3.8 43.9 1.0
OD1 B:ASN101 4.2 47.4 1.0
CB B:GLN11 4.2 42.2 1.0
C5' B:GDP501 4.2 42.7 1.0
CG B:GLN11 4.3 49.3 1.0
O5' B:GDP501 4.3 38.3 1.0
NE2 B:GLN11 4.4 54.5 1.0
OE1 C:GLU254 4.6 58.0 1.0
O1B B:GDP501 4.6 38.2 1.0
O2A B:GDP501 4.7 41.0 1.0
CG B:ASP179 4.8 52.5 1.0
ND2 B:ASN101 4.8 45.1 1.0
C8 B:GDP501 4.8 41.2 1.0
PB B:GDP501 4.9 38.3 1.0
CG B:ASN101 4.9 49.0 1.0

Magnesium binding site 3 out of 5 in 7z2n

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Magnesium binding site 3 out of 5 in the Tubulin-18-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-18-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:35.8
occ:1.00
O1G C:GTP501 2.0 33.6 1.0
O C:HOH658 2.0 33.5 1.0
O C:HOH713 2.1 35.4 1.0
O C:HOH649 2.1 36.0 1.0
O1B C:GTP501 2.1 33.3 1.0
O C:HOH623 2.1 34.6 1.0
PG C:GTP501 3.2 35.4 1.0
PB C:GTP501 3.2 34.5 1.0
O3B C:GTP501 3.6 40.3 1.0
O2G C:GTP501 3.6 39.0 1.0
O3A C:GTP501 3.7 39.4 1.0
NZ D:LYS254 3.8 39.5 1.0
OD1 C:ASP69 4.1 41.7 1.0
OD2 C:ASP98 4.2 45.9 1.0
CB C:GLN11 4.2 33.3 1.0
OE2 C:GLU71 4.2 53.0 1.0
CG C:GLU71 4.2 43.3 1.0
OD2 C:ASP69 4.3 37.6 1.0
N C:GLN11 4.4 31.9 1.0
O3G C:GTP501 4.4 34.5 1.0
CB C:ASP98 4.4 37.0 1.0
O2B C:GTP501 4.5 38.5 1.0
O1A C:GTP501 4.6 36.2 1.0
CG C:ASP69 4.6 40.6 1.0
CD C:GLU71 4.7 44.9 1.0
PA C:GTP501 4.7 36.1 1.0
CG C:ASP98 4.7 41.1 1.0
NE2 C:GLN11 4.8 45.9 1.0
CA C:GLN11 4.9 34.2 1.0
CE D:LYS254 4.9 37.7 1.0

Magnesium binding site 4 out of 5 in 7z2n

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Magnesium binding site 4 out of 5 in the Tubulin-18-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-18-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:77.6
occ:1.00
O D:HOH611 2.3 67.9 1.0
O1A D:GDP501 2.3 76.7 1.0
OE1 D:GLN11 2.3 72.7 1.0
O D:HOH636 2.4 66.8 1.0
O D:HOH608 2.5 75.1 1.0
CD D:GLN11 3.4 76.2 1.0
PA D:GDP501 3.7 62.6 1.0
CB D:GLN11 3.9 67.9 1.0
O1B D:GDP501 4.0 62.0 1.0
CG D:GLN11 4.2 67.8 1.0
O3A D:GDP501 4.3 60.0 1.0
NE2 D:GLN11 4.3 71.1 1.0
O2A D:GDP501 4.4 64.5 1.0
PB D:GDP501 4.7 59.5 1.0
OD1 D:ASN101 4.7 74.4 1.0
O5' D:GDP501 4.8 62.4 1.0
C5' D:GDP501 4.9 65.5 1.0
O3B D:GDP501 5.0 71.2 1.0

Magnesium binding site 5 out of 5 in 7z2n

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Magnesium binding site 5 out of 5 in the Tubulin-18-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-18-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg402

b:85.8
occ:1.00
OE2 F:GLU331 2.3 93.4 1.0
O1B F:ACP401 2.4 102.5 1.0
O3G F:ACP401 2.5 93.1 1.0
OE1 F:GLU331 2.7 91.3 1.0
CD F:GLU331 2.8 89.2 1.0
NZ F:LYS74 3.3 97.0 1.0
OD1 F:ASN333 3.5 87.7 1.0
PB F:ACP401 3.6 100.2 1.0
O2B F:ACP401 3.9 104.6 1.0
PG F:ACP401 4.0 105.7 1.0
ND2 F:ASN333 4.0 87.9 1.0
CG F:ASN333 4.1 84.0 1.0
CG F:GLU331 4.3 75.4 1.0
C3B F:ACP401 4.5 98.4 1.0
CE F:LYS74 4.6 92.3 1.0
O1G F:ACP401 4.7 106.2 1.0
O3A F:ACP401 4.9 94.9 1.0
O2G F:ACP401 5.0 90.2 1.0

Reference:

N.M.De La Roche, T.Muhlethaler, R.M.C.Di Martino, J.A.Ortega, D.Gioia, B.Roy, A.E.Prota, M.O.Steinmetz, A.Cavalli. Novel Fragment-Derived Colchicine-Site Binders As Microtubule-Destabilizing Agents. Eur.J.Med.Chem. V. 241 14614 2022.
ISSN: ISSN 0223-5234
PubMed: 35939994
DOI: 10.1016/J.EJMECH.2022.114614
Page generated: Thu Oct 3 16:14:35 2024

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