Atomistry » Magnesium » PDB 7yyw-7z4l » 7z2p
Atomistry »
  Magnesium »
    PDB 7yyw-7z4l »
      7z2p »

Magnesium in PDB 7z2p: Tubulin-Nocodazole Complex

Protein crystallography data

The structure of Tubulin-Nocodazole Complex, PDB code: 7z2p was solved by A.E.Prota, T.Muehlethaler, A.Cavalli, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.37 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.732, 158.09, 179.553, 90, 90, 90
R / Rfree (%) 17.8 / 20.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Tubulin-Nocodazole Complex (pdb code 7z2p). 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-Nocodazole Complex, PDB code: 7z2p:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 7z2p

Go back to Magnesium Binding Sites List in 7z2p
Magnesium binding site 1 out of 5 in the Tubulin-Nocodazole Complex


Mono view


Stereo pair view

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

b:27.0
occ:1.00
O A:HOH619 2.1 25.1 1.0
O1G A:GTP501 2.1 23.1 1.0
O1B A:GTP501 2.1 24.5 1.0
O A:HOH689 2.1 25.9 1.0
O A:HOH670 2.1 28.1 1.0
O A:HOH658 2.2 29.7 1.0
PG A:GTP501 3.2 28.3 1.0
PB A:GTP501 3.3 26.1 1.0
O3B A:GTP501 3.6 34.4 1.0
O2G A:GTP501 3.8 29.3 1.0
O3A A:GTP501 3.8 31.4 1.0
OE2 A:GLU71 4.0 44.3 1.0
NZ B:LYS254 4.0 34.8 1.0
OD1 A:ASP69 4.0 32.6 1.0
CB A:GLN11 4.1 26.1 1.0
OD2 A:ASP69 4.2 31.7 1.0
OD2 A:ASP98 4.2 40.7 1.0
N A:GLN11 4.3 28.7 1.0
CG A:GLU71 4.4 41.1 1.0
O1A A:GTP501 4.4 27.8 1.0
CB A:ASP98 4.5 33.1 1.0
O3G A:GTP501 4.5 27.2 1.0
O2B A:GTP501 4.6 30.3 1.0
OE1 A:GLN11 4.6 40.5 1.0
CG A:ASP69 4.6 35.8 1.0
CD A:GLU71 4.7 43.1 1.0
PA A:GTP501 4.7 29.4 1.0
CG A:ASP98 4.7 40.1 1.0
CA A:GLN11 4.8 27.4 1.0
O B:HOH614 4.8 52.9 1.0

Magnesium binding site 2 out of 5 in 7z2p

Go back to Magnesium Binding Sites List in 7z2p
Magnesium binding site 2 out of 5 in the Tubulin-Nocodazole Complex


Mono view


Stereo pair view

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

b:18.4
occ:1.00
OE1 B:GLN11 2.2 31.9 1.0
O B:HOH646 2.2 30.6 1.0
O1A B:GDP501 2.3 26.8 1.0
O C:HOH704 2.3 36.4 1.0
O B:HOH613 2.4 33.5 1.0
O B:HOH677 2.5 28.3 1.0
O B:HOH748 2.7 54.1 1.0
CD B:GLN11 3.4 39.1 1.0
PA B:GDP501 3.6 26.2 1.0
O3A B:GDP501 3.8 29.4 1.0
OD2 B:ASP179 3.9 34.7 1.0
CB B:GLN11 4.1 28.1 1.0
CG B:GLN11 4.2 34.7 1.0
O C:HOH651 4.3 41.7 1.0
NE2 B:GLN11 4.4 37.8 1.0
C5' B:GDP501 4.4 29.9 1.0
OE1 C:GLU254 4.4 40.8 1.0
OD1 B:ASN101 4.5 33.0 1.0
O5' B:GDP501 4.5 29.5 1.0
O B:HOH747 4.5 53.3 1.0
O1B B:GDP501 4.6 24.1 1.0
O2A B:GDP501 4.7 28.1 1.0
C8 B:GDP501 4.8 30.2 1.0
PB B:GDP501 4.8 25.7 1.0
O B:HOH716 4.9 42.4 1.0
CG B:ASP179 4.9 38.8 1.0

Magnesium binding site 3 out of 5 in 7z2p

Go back to Magnesium Binding Sites List in 7z2p
Magnesium binding site 3 out of 5 in the Tubulin-Nocodazole Complex


Mono view


Stereo pair view

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

b:26.0
occ:1.00
O1G C:GTP501 2.0 24.1 1.0
O C:HOH701 2.0 27.6 1.0
O C:HOH642 2.1 25.6 1.0
O1B C:GTP501 2.1 21.8 1.0
O C:HOH752 2.1 24.9 1.0
O C:HOH682 2.1 28.9 1.0
PG C:GTP501 3.1 26.4 1.0
PB C:GTP501 3.2 25.2 1.0
O3B C:GTP501 3.5 30.1 1.0
O2G C:GTP501 3.6 28.4 1.0
O3A C:GTP501 3.7 27.8 1.0
NZ D:LYS254 3.8 31.9 1.0
OE2 C:GLU71 4.0 46.8 1.0
OD1 C:ASP69 4.1 28.7 1.0
CB C:GLN11 4.2 22.6 1.0
OD2 C:ASP69 4.2 28.1 1.0
OD2 C:ASP98 4.2 40.1 1.0
CG C:GLU71 4.3 33.0 1.0
N C:GLN11 4.4 22.3 1.0
O3G C:GTP501 4.4 24.3 1.0
CB C:ASP98 4.5 32.9 1.0
O2B C:GTP501 4.5 26.6 1.0
O1A C:GTP501 4.6 27.1 1.0
CG C:ASP69 4.6 32.7 1.0
CD C:GLU71 4.7 42.6 1.0
CE D:LYS254 4.7 28.4 1.0
CG C:ASP98 4.7 36.9 1.0
PA C:GTP501 4.7 24.6 1.0
OE1 C:GLN11 4.8 37.0 1.0
O D:HOH601 4.9 66.4 1.0
CA C:GLN11 4.9 23.6 1.0
O D:HOH645 4.9 42.4 1.0

Magnesium binding site 4 out of 5 in 7z2p

Go back to Magnesium Binding Sites List in 7z2p
Magnesium binding site 4 out of 5 in the Tubulin-Nocodazole Complex


Mono view


Stereo pair view

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

b:52.5
occ:1.00
O D:HOH619 1.9 52.2 1.0
OE1 D:GLN11 2.2 53.6 1.0
O D:HOH674 2.4 55.1 1.0
O1A D:GDP501 2.5 46.8 1.0
O D:HOH654 2.6 51.6 1.0
CD D:GLN11 3.4 60.0 1.0
PA D:GDP501 3.8 47.6 1.0
O3A D:GDP501 4.0 44.9 1.0
CB D:GLN11 4.2 52.4 1.0
NE2 D:GLN11 4.3 61.2 1.0
CG D:GLN11 4.3 52.3 1.0
C5' D:GDP501 4.4 49.5 1.0
OD1 D:ASN101 4.5 59.6 1.0
O5' D:GDP501 4.6 48.8 1.0
O1B D:GDP501 4.7 40.4 1.0
O2A D:GDP501 4.8 48.7 1.0
C8 D:GDP501 4.9 45.3 1.0

Magnesium binding site 5 out of 5 in 7z2p

Go back to Magnesium Binding Sites List in 7z2p
Magnesium binding site 5 out of 5 in the Tubulin-Nocodazole Complex


Mono view


Stereo pair view

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

b:57.5
occ:1.00
OE2 F:GLU331 2.0 83.7 1.0
O3G F:ACP401 2.1 71.4 1.0
O2B F:ACP401 2.5 82.7 1.0
CD F:GLU331 2.8 71.9 1.0
OE1 F:GLU331 2.8 77.8 1.0
ND2 F:ASN333 3.2 77.8 1.0
PG F:ACP401 3.5 96.0 1.0
PB F:ACP401 3.7 74.8 1.0
NZ F:LYS74 3.7 83.1 1.0
C3B F:ACP401 3.9 79.5 1.0
O1B F:ACP401 4.1 90.1 1.0
CG F:ASN333 4.2 74.6 1.0
CG F:GLU331 4.2 62.6 1.0
O1G F:ACP401 4.4 93.0 1.0
O2G F:ACP401 4.5 82.3 1.0
CE F:LYS74 4.8 76.6 1.0
CB F:ASN333 4.9 55.3 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 16:14:56 2024

Last articles

Mg in 8CIP
Mg in 8CGU
Mg in 8CHU
Mg in 8CGZ
Mg in 8CGR
Mg in 8CGJ
Mg in 8CAH
Mg in 8CGI
Mg in 8CEP
Mg in 8CF8
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy