Magnesium in PDB 5xke: Crystal Structure of T2R-Ttl-Demecolcine Complex

Protein crystallography data

The structure of Crystal Structure of T2R-Ttl-Demecolcine Complex, PDB code: 5xke was solved by Y.Wang, J.Yang, T.Wang, L.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.405, 158.023, 182.429, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 26.4

Other elements in 5xke:

The structure of Crystal Structure of T2R-Ttl-Demecolcine Complex also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of T2R-Ttl-Demecolcine Complex (pdb code 5xke). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of T2R-Ttl-Demecolcine Complex, PDB code: 5xke:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5xke

Go back to Magnesium Binding Sites List in 5xke
Magnesium binding site 1 out of 4 in the Crystal Structure of T2R-Ttl-Demecolcine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of T2R-Ttl-Demecolcine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:33.2
occ:1.00
 O A:HOH613 2.0 43.4 1.0
O2G A:GTP501 2.0 36.8 1.0
O A:HOH619 2.2 51.8 1.0
O A:HOH641 2.2 38.2 1.0
O1B A:GTP501 2.2 35.5 1.0
O A:HOH615 2.3 40.0 1.0
PG A:GTP501 3.2 36.7 1.0
PB A:GTP501 3.3 36.2 1.0
O3B A:GTP501 3.6 37.7 1.0
O1G A:GTP501 3.7 37.5 1.0
NZ B:LYS252 3.9 50.5 1.0
O3A A:GTP501 3.9 36.0 1.0
OD1 A:ASP69 4.2 50.0 1.0
CB A:GLN11 4.2 40.5 1.0
OE1 A:GLU71 4.2 62.8 1.0
OD2 A:ASP69 4.4 49.6 1.0
CB A:ASP98 4.5 53.1 1.0
O3G A:GTP501 4.5 36.5 1.0
N A:GLN11 4.5 42.2 1.0
OE1 A:GLN11 4.6 40.5 1.0
O A:HOH639 4.6 43.5 1.0
O1A A:GTP501 4.7 35.3 1.0
O2B A:GTP501 4.7 37.3 1.0
OD2 A:ASP98 4.7 54.7 1.0
CD A:GLU71 4.7 61.7 1.0
CG A:ASP69 4.8 50.6 1.0
CG A:ASP98 4.8 54.5 1.0
PA A:GTP501 4.9 35.0 1.0
OG1 A:THR145 4.9 38.3 1.0
CA A:GLN11 5.0 40.5 1.0
CE B:LYS252 5.0 48.2 1.0
OE2 A:GLU71 5.0 64.6 1.0

Magnesium binding site 2 out of 4 in 5xke

Go back to Magnesium Binding Sites List in 5xke
Magnesium binding site 2 out of 4 in the Crystal Structure of T2R-Ttl-Demecolcine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of T2R-Ttl-Demecolcine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:28.6
occ:1.00
 O B:HOH622 2.0 48.2 1.0
O1A B:GDP501 2.1 31.3 1.0
O C:HOH622 2.2 39.4 1.0
OE1 B:GLN11 2.4 44.4 1.0
O B:HOH617 2.6 40.9 1.0
O B:HOH637 2.6 35.0 1.0
O B:HOH644 3.0 52.8 1.0
CD B:GLN11 3.4 45.3 1.0
PA B:GDP501 3.5 30.4 1.0
O3A B:GDP501 3.9 30.8 1.0
OD2 B:ASP177 4.0 49.6 1.0
CB B:GLN11 4.0 41.4 1.0
CG B:GLN11 4.2 44.1 1.0
C5' B:GDP501 4.4 32.3 1.0
O1B B:GDP501 4.4 31.5 1.0
O5' B:GDP501 4.4 30.8 1.0
OE1 C:GLU254 4.4 51.4 1.0
NE2 B:GLN11 4.4 46.5 1.0
OD1 B:ASN99 4.4 35.3 1.0
O2A B:GDP501 4.6 30.8 1.0
CG B:ASP177 4.8 48.9 1.0
C8 B:GDP501 4.8 36.5 1.0
PB B:GDP501 4.9 31.4 1.0

Magnesium binding site 3 out of 4 in 5xke

Go back to Magnesium Binding Sites List in 5xke
Magnesium binding site 3 out of 4 in the Crystal Structure of T2R-Ttl-Demecolcine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of T2R-Ttl-Demecolcine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:34.9
occ:1.00
 O1G C:GTP501 2.0 33.3 1.0
O1B C:GTP501 2.0 32.2 1.0
O C:HOH612 2.1 26.0 1.0
O C:HOH619 2.1 23.1 1.0
O C:HOH651 2.1 40.2 1.0
O C:HOH636 2.3 30.4 1.0
PG C:GTP501 3.1 33.2 1.0
PB C:GTP501 3.1 32.4 1.0
O3B C:GTP501 3.4 33.0 1.0
O2G C:GTP501 3.6 33.8 1.0
O3A C:GTP501 3.7 33.0 1.0
NZ D:LYS252 3.9 50.7 1.0
OD1 C:ASP69 4.1 39.1 1.0
OD2 C:ASP69 4.3 39.1 1.0
CB C:GLN11 4.3 35.3 1.0
O3G C:GTP501 4.4 32.8 1.0
OE1 C:GLU71 4.4 52.1 1.0
OD2 C:ASP98 4.5 49.4 1.0
CB C:ASP98 4.5 47.5 1.0
N C:GLN11 4.5 33.7 1.0
O2B C:GTP501 4.5 32.6 1.0
O1A C:GTP501 4.6 33.5 1.0
CG C:ASP69 4.6 39.2 1.0
NE2 C:GLN11 4.7 38.9 1.0
PA C:GTP501 4.7 33.1 1.0
OG1 C:THR145 4.8 37.9 1.0
CG C:ASP98 4.8 48.6 1.0
CB C:GLU71 4.8 48.9 1.0
ND2 D:ASN247 5.0 97.9 1.0

Magnesium binding site 4 out of 4 in 5xke

Go back to Magnesium Binding Sites List in 5xke
Magnesium binding site 4 out of 4 in the Crystal Structure of T2R-Ttl-Demecolcine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of T2R-Ttl-Demecolcine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:77.3
occ:1.00
 O1B D:GTP501 2.9 74.3 1.0
O2G D:GTP501 3.0 77.5 1.0
O1G D:GTP501 3.1 77.5 1.0
OE1 D:GLU69 3.5 0.1 1.0
NE2 D:GLN11 3.6 82.1 1.0
PG D:GTP501 3.6 79.6 1.0
CB D:GLN11 3.6 79.1 1.0
PB D:GTP501 4.2 73.4 1.0
OG1 D:THR72 4.3 0.3 1.0
OD2 D:ASP67 4.3 75.0 1.0
CG D:GLN11 4.3 81.0 1.0
CG2 D:THR72 4.3 0.7 1.0
O3B D:GTP501 4.4 76.8 1.0
N D:GLN11 4.4 74.8 1.0
CD D:GLN11 4.4 81.2 1.0
CD D:GLU69 4.4 0.1 1.0
CA D:GLN11 4.5 77.2 1.0
O1A D:GTP501 4.6 73.0 1.0
OD1 D:ASP67 4.6 71.6 1.0
O3A D:GTP501 4.7 72.8 1.0
CB D:GLU69 4.8 0.1 1.0
CG D:ASP67 4.9 73.6 1.0
O3G D:GTP501 4.9 79.2 1.0
CB D:THR72 5.0 0.8 1.0

Reference:

W.Yan, J.Yang. Identification of A Powerful and Reversible Microtubule-Inhibitor with Efficacy Against Multidrug-Resistant Tumors To Be Published.
Page generated: Mon Dec 14 22:09:24 2020

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